Poly(dimethylsiloxane) microchip-based immunoassay with multiple reaction zones: Toward on-chip multiplex detection platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao, Guocheng; Wang, Jun; Li, Zhaohui

2011-09-20

In this work, a poly(dimethylsiloxane) (PDMS) microchip-based immuno-sensing platform with integrated pneumatic micro valves is described. The microchip was fabricated with multiple layer soft lithography technology. By controlling the activation status of corresponding valves, reagent flows in the microchannel network can be well manipulated so that immuno-reactions only take place at designated reaction zones (DRZs). Four DRZs are included in the prototype microchip. Since these DRZs are all isolated from each other by micro valves, cross contamination is prevented. Using the inner surface of the all-PDMS microchannel as immunoassay substrate, on-chip sandwich format solid phase immunoassay was performed to demonstratemore » the feasibility of this immuno-sensing platform. Mouse IgG and fluorescein isothiocyanate (FITC) were used as the model analyte and the signal reporter respectively. Only 10 ul sample is needed for the assay and low detection limit of 5 ng/ml (≈33 pM) was achieved though low-cost polyclonal antibodies were used in our experiment for feasibility study only. The encouraging results from mouse IgG immunoassay proved the feasibility of our microchip design. With slight modification of the assay protocol, the same chip design can be used for multi-target detection and can provide a simple, cost-effective and integrated microchip solution for multiplex immunoassay applications.« less

Application of Advanced Multi-Core Processor Technologies to Oceanographic Research

DTIC Science & Technology

2013-09-30

STM32 NXP LPC series No Proprietary Microchip PIC32/DSPIC No > 500 mW; < 5 W ARM Cortex TI OMAP TI Sitara Broadcom BCM2835 Varies FPGA...1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Application of Advanced Multi-Core Processor Technologies...state-of-the-art information processing architectures. OBJECTIVES Next-generation processor architectures (multi-core, multi-threaded) hold the

Multi-block sulfonated poly(phenylene) copolymer proton exchange membranes

DOEpatents

Fujimoto, Cy H [Albuquerque, NM; Hibbs, Michael [Albuquerque, NM; Ambrosini, Andrea [Albuquerque, NM

2012-02-07

Improved multi-block sulfonated poly(phenylene) copolymer compositions, methods of making the same, and their use as proton exchange membranes (PEM) in hydrogen fuel cells, direct methanol fuel cells, in electrode casting solutions and electrodes. The multi-block architecture has defined, controllable hydrophobic and hydrophilic segments. These improved membranes have better ion transport (proton conductivity) and water swelling properties.

Highly-efficient multi-watt Yb:CaLnAlO4 microchip lasers

NASA Astrophysics Data System (ADS)

Loiko, Pavel; Serres, Josep Maria; Mateos, Xavier; Xu, Xiaodong; Xu, Jun; Yumashev, Konstantin; Griebner, Uwe; Petrov, Valentin; Aguiló, Magdalena; Díaz, Francesc; Major, Arkady

2017-02-01

Tetragonal rare-earth calcium aluminates, CaLnAlO4 where Ln = Gd or Y (CALGO and CALYO, respectively), are attractive laser crystal hosts due to their locally disordered structure and high thermal conductivity. In the present work, we report on highly-efficient power-scalable microchip lasers based on 8 at.% Yb:CALGO and 3 at.% Yb:CALYO crystals grown by the Czochralski method. Pumped by an InGaAs laser diode at 978 nm, the 6 mm-long Yb:CALGO microchip laser generated 7.79 W at 1057-1065 nm with a slope efficiency of η = 84% (with respect to the absorbed pump power) and an optical-to-optical efficiency of ηopt = 49%. The 3 mm-long Yb:CALYO microchip laser generated 5.06 W at 1048-1056 nm corresponding to η = 91% and ηopt = 32%. Both lasers produced linearly polarized output (σ- polarization) with an almost circular beam profile and beam quality factors M2 x,y <1.1. The output performance of the developed lasers was modeled yielding a loss coefficient as low as 0.004-0.007 cm-1. The results indicate that the Yb3+- doped calcium aluminates are very promising candidates for high-peak-power passively Q-switched microchip lasers.

Passive Q-switching of microchip lasers based on Ho:YAG ceramics.

PubMed

Lan, R; Loiko, P; Mateos, X; Wang, Y; Li, J; Pan, Y; Choi, S Y; Kim, M H; Rotermund, F; Yasukevich, A; Yumashev, K; Griebner, U; Petrov, V

2016-06-20

A Ho:YAG ceramic microchip laser pumped by a Tm fiber laser at 1910 nm is passively Q-switched by single- and multi-layer graphene, single-walled carbon nanotubes (SWCNTs), and Cr²⁺:ZnSe saturable absorbers (SAs). Employing SWCNTs, this laser generated an average power of 810 mW at 2090 nm with a slope efficiency of 68% and continuous wave to Q-switching conversion efficiency of 70%. The shortest pulse duration was 85 ns at a repetition rate of 165 kHz, and the pulse energy reached 4.9 μJ. The laser performance and pulse stability were superior compared to graphene SAs even for a different number of graphene layers (n=1 to 4). A model for the description of the Ho:YAG laser Q-switched by carbon nanostructures is presented. This modeling allowed us to estimate the saturation intensity for multi-layered graphene and SWCNT SAs to be 1.2±0.2 and 7±1  MW/cm², respectively. When using Cr²⁺:ZnSe, the Ho:YAG microchip laser generated 11 ns/25 μJ pulses at a repetition rate of 14.8 kHz.

Quantitative aspects of microchip isotachophoresis for high precision determination of main components in pharmaceuticals.

PubMed

Hradski, Jasna; Chorváthová, Mária Drusková; Bodor, Róbert; Sabo, Martin; Matejčík, Štefan; Masár, Marián

2016-12-01

Although microchip electrophoresis (MCE) is intended to provide reliable quantitative data, so far there is only limited attention paid to these important aspects. This study gives a general overview of key aspects to be followed to reach high-precise determination using isotachophoresis (ITP) on the microchip with conductivity detection. From the application point of view, the procedure for the determination of acetate, a main component in the pharmaceutical preparation buserelin acetate, was developed. Our results document that run-to-run fluctuations in the sample injection volume limit the reproducibility of quantitation based on the external calibration. The use of a suitable internal standard (succinate in this study) improved the repeatability of the precision of acetate determination from six to eight times. The robustness of the procedure was studied in terms of impact of fluctuations in various experimental parameters (driving current, concentration of the leading ions, pH of the leading electrolyte and buffer impurities) on the precision of the ITP determination. The use of computer simulation programs provided means to assess the ITP experiments using well-defined theoretical models. A long-term validity of the calibration curves on two microchips and two MCE equipments was verified. This favors ITP over other microchip electrophoresis techniques, when chip-to-chip or equipment-to-equipment transfer of the analytical method is required. The recovery values in the range of 98-101 % indicate very accurate determination of acetate in buserelin acetate, which is used in the treatment of hormone-dependent tumors. This study showed that microchip ITP is suitable for reliable determination of main components in pharmaceutical preparations.

Passive micromixer for luminol-peroxide chemiluminescence detection.

PubMed

Lok, Khoi Seng; Kwok, Yien Chian; Nguyen, Nam-Trung

2011-06-21

This paper reports a microchip with an integrated passive micromixer based on chaotic advection. The micromixer with staggered herringbone structures was used for luminol-peroxide chemiluminescence detection. The micromixer was examined to assess its suitability for chemiluminescence reaction. The relationship between the flow rate and the location of maximum chemiluminescence intensity was investigated. The light intensity was detected using an optical fiber attached along the mixing channel and a photon detector. A linear correlation between chemiluminescence intensity and the concentration of cobalt(ii) ions or hydrogen peroxide was observed. This microchip has a potential application in environmental monitoring for industries involved in heavy metals and in medical diagnostics.

The impact of neurotechnology on rehabilitation.

PubMed

Berger, Theodore W; Gerhardt, Greg; Liker, Mark A; Soussou, Walid

2008-01-01

This paper present results of a multi-disciplinary project that is developing a microchip-based neural prosthesis for the hippocampus, a region of the brain responsible for the formation of long-term memories. Damage to the hippocampus is frequently associated with epilepsy, stroke, and dementia (Alzheimer's disease) and is considered to underlie the memory deficits related to these neurological conditions. The essential goals of the multi-laboratory effort include: (1) experimental study of neuron and neural network function--how does the hippocampus encode information? (2) formulation of biologically realistic models of neural system dynamics--can that encoding process be described mathematically to realize a predictive model of how the hippocampus responds to any event? (3) microchip implementation of neural system models--can the mathematical model be realized as a set of electronic circuits to achieve parallel processing, rapid computational speed, and miniaturization? and (4) creation of hybrid neuron-silicon interfaces-can structural and functional connections between electronic devices and neural tissue be achieved for long-term, bi-directional communication with the brain? By integrating solutions to these component problems, we are realizing a microchip-based model of hippocampal nonlinear dynamics that can perform the same function as part of the hippocampus. Through bi-directional communication with other neural tissue that normally provides the inputs and outputs to/from a damaged hippocampal area, the biomimetic model could serve as a neural prosthesis. A proof-of-concept will be presented in which the CA3 region of the hippocampal slice is surgically removed and is replaced by a microchip model of CA3 nonlinear dynamics--the "hybrid" hippocampal circuit displays normal physiological properties. How the work in brain slices is being extended to behaving animals also will be described.

A Quantum Non-Demolition Parity measurement in a mixed-species trapped-ion quantum processor

NASA Astrophysics Data System (ADS)

Marinelli, Matteo; Negnevitsky, Vlad; Lo, Hsiang-Yu; Flühmann, Christa; Mehta, Karan; Home, Jonathan

2017-04-01

Quantum non-demolition measurements of multi-qubit systems are an important tool in quantum information processing, in particular for syndrome extraction in quantum error correction. We have recently demonstrated a protocol for quantum non-demolition measurement of the parity of two beryllium ions by detection of a co-trapped calcium ion. The measurement requires a sequence of quantum gates between the three ions, using mixed-species gates between beryllium hyperfine qubits and a calcium optical qubit. Our work takes place in a multi-zone segmented trap setup in which we have demonstrated high fidelity control of both species and multi-well ion shuttling. The advantage of using two species of ion is that we can individually manipulate and read out the state of each ion species without disturbing the internal state of the other. The methods demonstrated here can be used for quantum error correcting codes as well as quantum metrology and are key ingredients for realizing a hybrid universal quantum computer based on trapped ions. Mixed-species control may also enable the investigation of new avenues in quantum simulation and quantum state control. left the group and working in a company now.

Multi-watt passively Q-switched Yb:YAB/Cr:YAG microchip lasers

NASA Astrophysics Data System (ADS)

Serres, Josep Maria; Loiko, Pavel; Mateos, Xavier; Liu, Junhai; Zhang, Huaijing; Yumashev, Konstantin; Griebner, Uwe; Petrov, Valentin; Aguiló, Magdalena; Díaz, Francesc

2017-02-01

A trigonal 5.6 at.% Yb:YAl3(BO3)4 (Yb:YAB) crystal is employed in continuous-wave (CW) and passively Q-switched microchip lasers pumped by a diode at 978 nm. Using a 3 mm-thick, c-cut Yb:YAB crystal, which has a higher pump absorption efficiency, efficient CW microchip laser operation is demonstrated. This laser generated a maximum output power of 7.18 W at 1041-1044 nm with a slope efficiency η of 67% (with respect to the absorbed pump power) and an almost diffraction-limited beam, M2 x,y < 1.1. Inserting a Cr:YAG saturable absorber, stable passive Q-switching of the Yb:YAB microchip laser was obtained. The maximum average output power from the Yb:YAB/Cr:YAG laser reached 2.82 W at 1042 nm with η = 53% and a conversion efficiency with respect to the CW mode of 65% (when using a 0.7 mm-thick Cr:YAG). The latter corresponded to a pulse duration and energy of 7.1 ns / 47 μJ at a pulse repetition rate (PRR) of 60 kHz. Using a 1.3 mm-thick Cr:YAG, 2.02 W were achieved at 1041 nm corresponding to η = 38%. The pulse characteristics were 4.9 ns / 83 μJ at PRR = 24.3 kHz and the maximum peak power reached 17 kW. Yb:YAB crystals are very promising for compact sub-ns power-scalable microchip lasers.

Intelligent microchip networks: an agent-on-chip synthesis framework for the design of smart and robust sensor networks

NASA Astrophysics Data System (ADS)

Bosse, Stefan

2013-05-01

Sensorial materials consisting of high-density, miniaturized, and embedded sensor networks require new robust and reliable data processing and communication approaches. Structural health monitoring is one major field of application for sensorial materials. Each sensor node provides some kind of sensor, electronics, data processing, and communication with a strong focus on microchip-level implementation to meet the goals of miniaturization and low-power energy environments, a prerequisite for autonomous behaviour and operation. Reliability requires robustness of the entire system in the presence of node, link, data processing, and communication failures. Interaction between nodes is required to manage and distribute information. One common interaction model is the mobile agent. An agent approach provides stronger autonomy than a traditional object or remote-procedure-call based approach. Agents can decide for themselves, which actions are performed, and they are capable of flexible behaviour, reacting on the environment and other agents, providing some degree of robustness. Traditionally multi-agent systems are abstract programming models which are implemented in software and executed on program controlled computer architectures. This approach does not well scale to micro-chip level and requires full equipped computers and communication structures, and the hardware architecture does not consider and reflect the requirements for agent processing and interaction. We propose and demonstrate a novel design paradigm for reliable distributed data processing systems and a synthesis methodology and framework for multi-agent systems implementable entirely on microchip-level with resource and power constrained digital logic supporting Agent-On-Chip architectures (AoC). The agent behaviour and mobility is fully integrated on the micro-chip using pipelined communicating processes implemented with finite-state machines and register-transfer logic. The agent behaviour, interaction (communication), and mobility features are modelled and specified on a machine-independent abstract programming level using a state-based agent behaviour language (APL). With this APL a high-level agent compiler is able to synthesize a hardware model (RTL, VHDL), a software model (C, ML), or a simulation model (XML) suitable to simulate a multi-agent system using the SeSAm simulator framework. Agent communication is provided by a simple tuple-space database implemented on node level providing fault tolerant access of global data. A novel synthesis development kit (SynDK) based on a graph-structured database approach is introduced to support the rapid development of compilers and synthesis tools, used for example for the design and implementation of the APL compiler.

Extending the upper temperature range of gas chromatography with all-silicon microchip columns using a heater/clamp assembly.

PubMed

Ghosh, Abhijit; Johnson, Jacob E; Nuss, Johnathan G; Stark, Brittany A; Hawkins, Aaron R; Tolley, Luke T; Iverson, Brian D; Tolley, H Dennis; Lee, Milton L

2017-09-29

Miniaturization of gas chromatography (GC) instrumentation is of interest because it addresses current and future issues relating to compactness, portability and field application. While incremental advancements continue to be reported in GC with columns fabricated in microchips (referred to in this paper as "microchip columns"), the current performance is far from acceptable. This lower performance compared to conventional GC is due to factors such as pooling of the stationary phase in corners of non-cylindrical channels, adsorption of sensitive compounds on incompletely deactivated surfaces, shorter column lengths and less than optimum interfacing to injector and detector. In this work, a GC system utilizing microchip columns was developed that solves the latter challenge, i.e., microchip interfacing to injector and detector. A microchip compression clamp was constructed to heat the microchip (i.e., primary heater), and seal the injector and detector fused silica interface tubing to the inlet and outlet ports of the microchip channels with minimum extra-column dead volume. This clamp allowed occasional operation up to 375°C and routine operation up to 300°C. The compression clamp was constructed of a low expansion alloy, Kovar™, to minimize leaking due to thermal expansion mismatch at the interface during repeated thermal cycling, and it was tested over several months for more than one hundred injections without forming leaks. A 5.9m long microcolumn with rectangular cross section of 158μm×80μm, which approximately matches a 100μm i.d. cylindrical fused silica column, was fabricated in a silicon wafer using deep reactive ion etching (DRIE) and high temperature fusion bonding; finally, the channel was coated statically with a 1% vinyl, 5% phenyl, 94% methylpolysiloxane stationary phase. High temperature separations of C10-C40 n-alkanes and a commercial diesel sample were demonstrated using the system under both temperature programmed GC (TPGC) and thermal gradient GC (TGGC) conditions. TGGC analysis of a complex essential oil sample was also demonstrated. Addition of a secondary heater and polyimide insulation proved to be helpful in achieving the desired elution temperature without having to raise the primary heater temperature above 300°C for high boiling point compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

Multi-Watt Average Power Nanosecond Microchip Laser and Power Scalability Estimates

NASA Technical Reports Server (NTRS)

Konoplev, Oleg A.; Vasilyev, Alexey A.; Seas, Antonios A.; Yu, Anthony W.; Li, Steven X.; Shaw, George B.; Stephen, Mark A.; Krainak, Michael A.

2011-01-01

We demonstrated up to 2 W average power, CW-pumped, passively- Q-switched, 1.5 ns monolithic MCL with single-longitudinal mode-operation. We discuss laser design issues to bring the average power to 5-1 OW and beyond.

A hydrophobic ionic liquid compartmentalized sampling/labeling and its separation techniques in polydimethylsiloxane microchip capillary electrophoresis.

PubMed

Quan, Hong Hua; Li, Ming; Huang, Yan; Hahn, Jong Hoon

2017-01-01

This paper demonstrates a novel compartmentalized sampling/labeling method and its separation techniques using a hydrophobic ionic liquid (IL)-1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)-imidate (BmimNTf 2 )-as the immiscible phase, which is capable of minimizing signal losses during microchip capillary electrophoresis (MCE). The MCE device consists of a silica tube connected to a straight polydimethylsiloxane (PDMS) separation channel. Poly(diallyldimethylammonium chloride) (PDDAC) was coated on the inner surface of channel to ease the introduction of IL plugs and enhance the IL wetting on the PDMS surface for sample releasing. Electroosmotic flow (EOF)-based sample compartmentalization was carried out through a sequenced injection into sampling tubes with the following order: leading IL plug/sample segment/terminal IL plug. The movement of the sample segment was easily controlled by applying an electrical voltage across both ends of the chip without a sample volume change. This approach effectively prevented analyte diffusion before injection into MCE channels. When the sample segment was manipulated to the PDDAC-modified PDMS channel, the sample plug then was released from isolation under EOF while IL plugs adsorbed onto channel surfaces owing to strong adhesion. A mixture of flavin adenine nucleotides (FAD) and flavin mononucleotides (FMN) was successfully separated on a 2.5 cm long separation channel, for which the theoretical numbers of plates were 15 000 and 17 000, respectively. The obtained peak intensity was increased 6.3-fold over the corresponding value from conventional electrokinetic injection with the same sampling time. Furthermore, based on the compartmented sample segment serving as an interim reactor, an on-chip fluorescence labeling is demonstrated. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Multi-Scale Correlative Tomography of a Li-Ion Battery Composite Cathode

PubMed Central

Moroni, Riko; Börner, Markus; Zielke, Lukas; Schroeder, Melanie; Nowak, Sascha; Winter, Martin; Manke, Ingo; Zengerle, Roland; Thiele, Simon

2016-01-01

Focused ion beam/scanning electron microscopy tomography (FIB/SEMt) and synchrotron X-ray tomography (Xt) are used to investigate the same lithium manganese oxide composite cathode at the same specific spot. This correlative approach allows the investigation of three central issues in the tomographic analysis of composite battery electrodes: (i) Validation of state-of-the-art binary active material (AM) segmentation: Although threshold segmentation by standard algorithms leads to very good segmentation results, limited Xt resolution results in an AM underestimation of 6 vol% and severe overestimation of AM connectivity. (ii) Carbon binder domain (CBD) segmentation in Xt data: While threshold segmentation cannot be applied for this purpose, a suitable classification method is introduced. Based on correlative tomography, it allows for reliable ternary segmentation of Xt data into the pore space, CBD, and AM. (iii) Pore space analysis in the micrometer regime: This segmentation technique is applied to an Xt reconstruction with several hundred microns edge length, thus validating the segmentation of pores within the micrometer regime for the first time. The analyzed cathode volume exhibits a bimodal pore size distribution in the ranges between 0–1 μm and 1–12 μm. These ranges can be attributed to different pore formation mechanisms. PMID:27456201

Characterization and performance of injection molded poly(methylmethacrylate) microchips for capillary electrophoresis

PubMed Central

Nikcevic, Irena; Lee, Se Hwan; Piruska, Aigars; Ahn, Chong H.; Ridgway, Thomas H.; Limbach, Patrick A.; Wehmeyer, K. R.; Heineman, William R.; Seliskar, Carl J.

2009-01-01

Injection molded poly(methylmethacrylate) (IM-PMMA), chips were evaluated as potential candidates for capillary electrophoresis disposable chip applications. Mass production and usage of plastic microchips depends on chip-to-chip reproducibility and on analysis accuracy. Several important properties of IM-PMMA chips were considered: fabrication quality evaluated by environmental scanning electron microscope imaging, surface quality measurements, selected thermal/electrical properties as indicated by measurement of the current versus applied voltage (I–V) characteristic, and the influence of channel surface treatments. Electroosmotic flow was also evaluated for untreated and O2 reactive ion etching (RIE) treated surface microchips. The performance characteristics of single lane plastic microchip capillary electrophoresis (MCE) separations were evaluated using a mixture of two dyes - fluorescein (FL) and fluorescein isothiocyanate (FITC). To overcome non-wettability of the native IM-PMMA surface, a modifier, polyethylene oxide was added to the buffer as a dynamic coating. Chip performance reproducibility was studied for chips with and without surface modification via the process of RIE with O2 and by varying the hole position for the reservoir in the cover plate or on the pattern side of the chip. Additionally, the importance of reconditioning steps to achieve optimal performance reproducibility was also examined. It was found that more reproducible quantitative results were obtained when normalized values of migration time, peak area and peak height of FL and FITC were used instead of actual measured parameters PMID:17477932

Enhanced performance of Cr,Yb:YAG microchip laser by bonding Yb:YAG crystal.

PubMed

Cheng, Ying; Dong, Jun; Ren, Yingying

2012-10-22

Highly efficient, laser-diode pumped Yb:YAG/Cr,Yb:YAG self-Q-switched microchip lasers by bonding Yb:YAG crystal have been demonstrated for the first time to our best knowledge. The effect of transmission of output coupler (T(oc)) on the enhanced performance of Yb:YAG/Cr,Yb:YAG microchip lasers has been investigated and found that the best laser performance was achieved with T(oc) = 50%. Slope efficiency of over 38% was achieved. Average output power of 0.8 W was obtained at absorbed pump power of 2.5 W; corresponding optical-to-optical efficiency of 32% was obtained. Laser pulses with pulse width of 1.68 ns, pulse energy of 12.4 μJ, and peak power of 7.4 kW were obtained. The lasers oscillated in multi-longitudinal modes. The wide separation of longitudinal modes was attributed to the mode selection by combined etalon effect of Cr,Yb:YAG, Yb:YAG thin plates and output coupler. Stable periodical pulse trains at different pump power levels have been observed owing to the longitudinal modes coupling and competition.

A simple and highly sensitive spectroscopic fluorescence-detection system for multi-channel plastic-microchip electrophoresis based on side-entry laser-beam zigzag irradiation.

PubMed

Anazawa, Takashi; Uchiho, Yuichi; Yokoi, Takahide; Chalkidis, George; Yamazaki, Motohiro

2017-06-27

A five-color fluorescence-detection system for eight-channel plastic-microchip electrophoresis was developed. In the eight channels (with effective electrophoretic lengths of 10 cm), single-stranded DNA fragments were separated (with single-base resolution up to 300 bases within 10 min), and seventeen-loci STR genotyping for forensic human identification was successfully demonstrated. In the system, a side-entry laser beam is passed through the eight channels (eight A channels), with alternately arrayed seven sacrificial channels (seven B channels), by a technique called "side-entry laser-beam zigzag irradiation." Laser-induced fluorescence from the eight A channels and Raman-scattered light from the seven B channels are then simultaneously, uniformly, and spectroscopically detected, in the direction perpendicular to the channel array plane, through a transmission grating and a CCD camera. The system is therefore simple and highly sensitive. Because the microchip is fabricated by plastic-injection molding, it is inexpensive and disposable and thus suitable for actual use in various fields.

Microchip amplifier for in vitro, in vivo, and automated whole cell patch-clamp recording

PubMed Central

Kolb, Ilya; Kodandaramaiah, Suhasa B.; Chubykin, Alexander A.; Yang, Aimei; Bear, Mark F.; Boyden, Edward S.; Forest, Craig R.

2014-01-01

Patch clamping is a gold-standard electrophysiology technique that has the temporal resolution and signal-to-noise ratio capable of reporting single ion channel currents, as well as electrical activity of excitable single cells. Despite its usefulness and decades of development, the amplifiers required for patch clamping are expensive and bulky. This has limited the scalability and throughput of patch clamping for single-ion channel and single-cell analyses. In this work, we have developed a custom patch-clamp amplifier microchip that can be fabricated using standard commercial silicon processes capable of performing both voltage- and current-clamp measurements. A key innovation is the use of nonlinear feedback elements in the voltage-clamp amplifier circuit to convert measured currents into logarithmically encoded voltages, thereby eliminating the need for large high-valued resistors, a factor that has limited previous attempts at integration. Benchtop characterization of the chip shows low levels of current noise [1.1 pA root mean square (rms) over 5 kHz] during voltage-clamp measurements and low levels of voltage noise (8.2 μV rms over 10 kHz) during current-clamp measurements. We demonstrate the ability of the chip to perform both current- and voltage-clamp measurement in vitro in HEK293FT cells and cultured neurons. We also demonstrate its ability to perform in vivo recordings as part of a robotic patch-clamping system. The performance of the patch-clamp amplifier microchip compares favorably with much larger commercial instrumentation, enabling benchtop commoditization, miniaturization, and scalable patch-clamp instrumentation. PMID:25429119

Integrating Internal Standards into Disposable Capillary Electrophoresis Devices To Improve Quantification

PubMed Central

2017-01-01

To improve point-of-care quantification using microchip capillary electrophoresis (MCE), the chip-to-chip variabilities inherent in disposable, single-use devices must be addressed. This work proposes to integrate an internal standard (ISTD) into the microchip by adding it to the background electrolyte (BGE) instead of the sample—thus eliminating the need for additional sample manipulation, microchip redesigns, and/or system expansions required for traditional ISTD usage. Cs and Li ions were added as integrated ISTDs to the BGE, and their effects on the reproducibility of Na quantification were explored. Results were then compared to the conclusions of our previous publication which used Cs and Li as traditional ISTDs. The in-house fabricated microchips, electrophoretic protocols, and solution matrixes were kept constant, allowing the proposed method to be reliably compared to the traditional method. Using the integrated ISTDs, both Cs and Li improved the Na peak area reproducibility approximately 2-fold, to final RSD values of 2.2–4.7% (n = 900). In contrast (to previous work), Cs as a traditional ISTD resulted in final RSDs of 2.5–8.8%, while the traditional Li ISTD performed poorly with RSDs of 6.3–14.2%. These findings suggest integrated ISTDs are a viable method to improve the precision of disposable MCE devices—giving matched or superior results to the traditional method in this study while neither increasing system cost nor complexity. PMID:28192985

Laser micromachined isoelectric focusing devices on polymer substrate for electrospray mass spectrometry

NASA Astrophysics Data System (ADS)

Lin, Yuehe; Wen, Jenny; Fan, Xiang; Matson, Dean W.; Smith, Richard D.

1999-08-01

A microfabricated device for isoelectric focusing (IEF) incorporating an optimized electrospray ionization (ESI) tip was constructed on polycarbonate plates using a laser micromachining technique. The separation channels on an IEF chip were 16 cm long, 50 micrometers wide and 30 micrometers deep. Electrical potentials used for IEF focusing and electrospray were applied through platinum electrodes placed in the buffer reservoirs, and which were isolated from the separation channel by molecular porous membranes. On-line ESI produced directly from a sharp `tip' on the microchip was evaluated. The results indicate that this design can produce a stable electrospray that is further improved and made more flexible with the assistance of sheath gas and sheath liquid. Error analysis of the spectral data shows that the standard deviation in signal intensity for an analyte peak was less than approximately 5% over 3 hours. The production of stable electrosprays directly from microchip IEF devices represents a step towards easily- fabricated microanalytical devices. IEF separations of protein mixtures were demonstrated for uncoated polycarbonate microchips. On-line IEF/ESI-MS was demonstrated using the microfabricated chip with an ion-trap ESI mass spectrometer for characterization of protein mixtures.

Measurement of blood coagulation with considering RBC aggregation through a microchip-based light transmission aggregometer.

PubMed

Lim, Hyunjung; Nam, Jeonghun; Xue, Shubin; Shin, Sehyun

2011-01-01

Even though blood coagulation can be tested by various methods and techniques, the effect of RBC aggregation on blood coagulation is not fully understood. The present study monitored clot formation in a microchip-based light transmission aggregometer. Citrated blood samples with and without the addition of calcium ion solution were initially disaggregated by rotating a stirrer in the microchip. After abrupt stop of the rotating stirrer, the transmitted light intensity over time was recorded. The syllectogram (light intensity vs. time graph) manifested a rapid increase that is associated with RBC aggregation followed by a decrease that is associated with blood coagulation. The time to reach the peak point was used as a new index of coagulation time (CT) and ranged from 200 to 500 seconds in the present measurements. The CT was inversely proportional to the concentration of fibrinogen, which enhances RBC aggregation. In addition, the CT was inversely proportional to the hematocrit, which is similar to the case of the prothrombin time (PT), as measured by a commercial coagulometer. Thus, we carefully concluded that RBC aggregation should be considered in tests of blood coagulation.

Integration of serpentine channels for microchip electrophoresis with a palladium decoupler and electrochemical detection

PubMed Central

Bowen, Amanda L; Martin, R. Scott

2010-01-01

While it has been shown that microchip electrophoresis with electrochemical detection can be used to separate and detect electroactive species, there is a need to increase the separation performance of these devices so that complex mixtures can be routinely analyzed. Previous work in microchip electrophoresis has demonstrated that increasing the separation channel length leads to an increase in resolution between closely eluting analytes. This paper details the use of lengthened serpentine microchannels for microchip electrophoresis and electrochemical detection where a palladium decoupler is used to ground the separation voltage so that the working electrodes remain in the fluidic network. In this work, palladium electrodepositions were used to increase the decoupler surface area and more efficiently dissipate hydrogen produced at the decoupler. Dopamine and norepinephrine, which only differ in structure by a hydroxyl group, were used as model analytes. It was found that increasing the separation channel length led to improvements in both resolution and the number of theoretical plates for these analytes. The use of a bi-layer valving device, where PDMS-based valves are utilized for the injection process, along with serpentine microchannels and amperometric detection resulted in a multi-analyte separation and an average of 28,700 theoretical plates. It was also shown that the increased channel length is beneficial when separating and detecting analytes from a high ionic strength matrix. This was demonstrated by monitoring the stimulated release of neuro-transmitters from a confluent layer of PC 12 cells. PMID:19739137

Multi-longitudinal-mode micro-laser model

NASA Astrophysics Data System (ADS)

Staliunas, Kestutis

2017-10-01

We derive a convenient model for broad aperture micro-lasers, such as microchip lasers, broad area semiconductor lasers, or VCSELs, taking into account several longitudinal mode families. We provide linear stability analysis, and show characteristic spatio-temporal dynamics in such multi-longitudinal mode laser models. Moreover, we derive the coupled mode model in the presence of intracavity refraction index modulation (intracavity photonic crystal). Contribution to the Topical Issue "Theory and Applications of the Lugiato-Lefever Equation", edited by Yanne K. Chembo, Damia Gomila, Mustapha Tlidi, Curtis R. Menyuk.

In-depth study of in-trap high-resolution mass separation by transversal ion ejection from a multi-reflection time-of-flight device.

PubMed

Fischer, Paul; Knauer, Stefan; Marx, Gerrit; Schweikhard, Lutz

2018-01-01

The recently introduced method of ion separation by transversal ejection of unwanted species in electrostatic ion-beam traps and multi-reflection time-of-flight devices has been further studied in detail. As this separation is performed during the ion storage itself, there is no need for additional external devices such as ion gates or traps for either pre- or postselection of the ions of interest. The ejection of unwanted contaminant ions is performed by appropriate pulses of the potentials of deflector electrodes. These segmented ring electrodes are located off-center in the trap, i.e., between one of the two ion mirrors and the central drift tube, which also serves as a potential lift for capturing incoming ions and axially ejecting ions of interest after their selection. The various parameters affecting the selection effectivity and resolving power are illustrated with tin-cluster measurements, where isotopologue ion species provide mass differences down to a single atomic mass unit at ion masses of several hundred. Symmetric deflection voltages of only 10 V were found sufficient for the transversal ejection of ion species with as few as three deflection pulses. The duty cycle, i.e., the pulse duration with respect to the period of ion revolution, has been varied, resulting in resolving powers of up to several tens of thousands for this selection technique.

In-depth study of in-trap high-resolution mass separation by transversal ion ejection from a multi-reflection time-of-flight device

NASA Astrophysics Data System (ADS)

Fischer, Paul; Knauer, Stefan; Marx, Gerrit; Schweikhard, Lutz

2018-01-01

The recently introduced method of ion separation by transversal ejection of unwanted species in electrostatic ion-beam traps and multi-reflection time-of-flight devices has been further studied in detail. As this separation is performed during the ion storage itself, there is no need for additional external devices such as ion gates or traps for either pre- or postselection of the ions of interest. The ejection of unwanted contaminant ions is performed by appropriate pulses of the potentials of deflector electrodes. These segmented ring electrodes are located off-center in the trap, i.e., between one of the two ion mirrors and the central drift tube, which also serves as a potential lift for capturing incoming ions and axially ejecting ions of interest after their selection. The various parameters affecting the selection effectivity and resolving power are illustrated with tin-cluster measurements, where isotopologue ion species provide mass differences down to a single atomic mass unit at ion masses of several hundred. Symmetric deflection voltages of only 10 V were found sufficient for the transversal ejection of ion species with as few as three deflection pulses. The duty cycle, i.e., the pulse duration with respect to the period of ion revolution, has been varied, resulting in resolving powers of up to several tens of thousands for this selection technique.

Problems Associated with the Microchip Data of Stray Dogs and Cats Entering RSPCA Queensland Shelters

PubMed Central

Lancaster, Emily; Rand, Jacquie; Collecott, Sheila; Paterson, Mandy

2015-01-01

Simple Summary Microchip identification has become an important tool to reunite stray dogs and cats with their owners, and is now compulsory in most states of Australia. Improvement of the microchipping system in Australia is limited by a lack of published Australian data documenting the problems experienced by shelter staff when using microchip data to contact the owner of a stray animal. In this study we determine the character and frequency of inaccurate microchip data to identify weaknesses in the current microchipping system. This information could be used to develop strategies that increase the accuracy of microchip data that will increase the reclaiming of stray animals. Abstract A lack of published information documenting problems with the microchip data for the reclaiming of stray animals entering Australian shelters limits improvement of the current microchipping system. A retrospective study analysing admission data for stray, adult dogs (n = 7258) and cats (n = 6950) entering the Royal Society for the Prevention of Cruelty to Animals (RSPCA) Queensland between January 2012 and December 2013 was undertaken to determine the character and frequency of microchip data problems and their impact on outcome for the animal. Only 28% of dogs and 9% of cats were microchipped, and a substantial proportion (37%) had problems with their data, including being registered to a previous owner or organisation (47%), all phone numbers incorrect/disconnected (29%), and the microchip not registered (14%). A higher proportion of owners could be contacted when the microchip had no problems, compared to those with problems (dogs, 93% vs. 70%; cats, 75% vs. 41%). The proportion of animals reclaimed declined significantly between microchipped animals with no data problems, microchipped animals with data problems and non-microchipped animals—87%, 69%, and 37%, respectively, for dogs and 61%, 33%, and 5%, respectively, for cats. Strategies are needed to increase the accuracy of microchip data to facilitate the reclaiming of stray dogs and cats. PMID:26479238

Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries

PubMed Central

2015-01-01

A hybrid microchip/capillary electrophoresis (CE) system was developed to allow unbiased and lossless sample loading and high-throughput repeated injections. This new hybrid CE system consists of a poly(dimethylsiloxane) (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel, and a fused-silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channel and the fused-silica capillary separation column. Analytes are rapidly separated in the fused-silica capillary, and following separation, high-sensitivity MS detection is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high-throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates, and CE separation voltages. PMID:24865952

Pneumatic Microvalve-Based Hydrodynamic Sample Injection for High-Throughput, Quantitative Zone Electrophoresis in Capillaries

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelly, Ryan T.; Wang, Chenchen; Rausch, Sarah J.

2014-07-01

A hybrid microchip/capillary CE system was developed to allow unbiased and lossless sample loading and high throughput repeated injections. This new hybrid CE system consists of a polydimethylsiloxane (PDMS) microchip sample injector featuring a pneumatic microvalve that separates a sample introduction channel from a short sample loading channel and a fused silica capillary separation column that connects seamlessly to the sample loading channel. The sample introduction channel is pressurized such that when the pneumatic microvalve opens briefly, a variable-volume sample plug is introduced into the loading channel. A high voltage for CE separation is continuously applied across the loading channelmore » and the fused silica capillary separation column. Analytes are rapidly separated in the fused silica capillary with high resolution. High sensitivity MS detection after CE separation is accomplished via a sheathless CE/ESI-MS interface. The performance evaluation of the complete CE/ESI-MS platform demonstrated that reproducible sample injection with well controlled sample plug volumes could be achieved by using the PDMS microchip injector. The absence of band broadening from microchip to capillary indicated a minimum dead volume at the junction. The capabilities of the new CE/ESI-MS platform in performing high throughput and quantitative sample analyses were demonstrated by the repeated sample injection without interrupting an ongoing separation and a good linear dependence of the total analyte ion abundance on the sample plug volume using a mixture of peptide standards. The separation efficiency of the new platform was also evaluated systematically at different sample injection times, flow rates and CE separation voltages.« less

Rapid analysis of perchlorate in drinking water at parts per billion levels using microchip electrophoresis.

PubMed

Gertsch, Jana C; Noblitt, Scott D; Cropek, Donald M; Henry, Charles S

2010-05-01

A microchip capillary electrophoresis (MCE) system has been developed for the determination of perchlorate in drinking water. The United States Environmental Protection Agency (USEPA) recently proposed a health advisory limit for perchlorate in drinking water of 15 parts per billion (ppb), a level requiring large, sophisticated instrumentation, such as ion chromatography coupled with mass spectrometry (IC-MS), for detection. An inexpensive, portable system is desired for routine online monitoring applications of perchlorate in drinking water. Here, we present an MCE method using contact conductivity detection for perchlorate determination. The method has several advantages, including reduced analysis times relative to IC, inherent portability, high selectivity, and minimal sample pretreatment. Resolution of perchlorate from more abundant ions was achieved using zwitterionic, sulfobetaine surfactants, N-hexadecyl-N,N-dimethyl-3-ammonio-1-propane sulfonate (HDAPS) and N-tetradecyl-N,N-dimethyl-3-ammonio-1-propane sulfonate (TDAPS). The system performance and the optimization of the separation chemistry, including the use of these surfactants to resolve perchlorate from other anions, are discussed in this work. The system is capable of detection limits of 3.4 +/- 1.8 ppb (n = 6) in standards and 5.6 +/- 1.7 ppb (n = 6) in drinking water.

Preconcentration and Separation of Mixed-Species Samples Near a Nano-Junction in a Convergent Microchannel

PubMed Central

Chiu, Ping-Hsien; Weng, Chen-Hsun; Yang, Ruey-Jen

2015-01-01

A fluidic microchip incorporating a convergent microchannel and a Nafion-nanoporous membrane is proposed for the preconcentration and separation of multi-species samples on a single platform. In the device, sample preconcentration is achieved by means of the ion concentration polarization effect induced at the micro/nano interface under the application of an external electric field, while species separation is achieved by exploiting the different electrophoretic mobilities of the sample components. The experimental results show that the device is capable of detecting C-reactive protein (CRP) with an initial concentration as low as 9.50 × 10−6 mg/L given a sufficient preconcentration time and driving voltage. In addition, it is shown that a mixed-species sample consisting of three negatively-charged components (bovine serum albumin (BSA), tetramethylrhodamine(TAMRA) isothiocyanate-Dextran and fluorescent polymer beads) can be separated and preconcentrated within 20 min given a driving voltage of 100 V across 1 cm microchannel in length. In general, the present results confirm the feasibility of the device for the immunoassay or detection of various multi-species samples under low concentration in the biochemical and biomedical fields. The novel device can therefore improve the detection limit of traditional medical facilities. PMID:26690167

Lab on a Chip Packing of Submicron Particles for High Performance EOF Pumping

DTIC Science & Technology

2010-08-26

and wet etching techniques, using a soda lime glass substrate coated with chromium and photoresist (Nanofilm, Westlake Village, CA). A weir structure...observed previously for these soda lime glass microchips [8]. Images of the three segments of different sized particles con- tainedwithin the packed... Silica beads High pressure Lab on a chip a b s t r a c t The packing of submicrometer sized silica beads inside a microchannel was enabled by a novel

Nonlinear multi-photon laser wave-mixing optical detection in microarrays and microchips for ultrasensitive detection and separation of biomarkers for cancer and neurodegenerative diseases

NASA Astrophysics Data System (ADS)

Iwabuchi, Manna; Hetu, Marcel; Maxwell, Eric; Pradel, Jean S.; Ramos, Sashary; Tong, William G.

2015-09-01

Multi-photon degenerate four-wave mixing is demonstrated as an ultrasensitive absorption-based optical method for detection, separation and identification of biomarker proteins in the development of early diagnostic methods for HIV- 1, cancer and neurodegenerative diseases using compact, portable microarrays and capillary- or microchip-based chemical separation systems that offer high chemical specificity levels. The wave-mixing signal has a quadratic dependence on concentration, and hence, it allows more reliable monitoring of smaller changes in analyte properties. Our wave-mixing detection sensitivity is comparable or better than those of current methods including enzyme-linked immunoassay for clinical diagnostic and screening. Detection sensitivity is excellent since the wave-mixing signal is a coherent laser-like beam that can be collected with virtually 100% collection efficiency with high S/N. Our analysis time is short (1-15 minutes) for molecular weight-based protein separation as compared to that of a conventional separation technique, e.g., sodium dodecyl sulfate-polyacrylamide gel electrophoresis. When ultrasensitive wavemixing detection is paired with high-resolution capillary- or microchip-based separation systems, biomarkers can be separated and identified at the zepto- and yocto-mole levels for a wide range of analytes. Specific analytes can be captured in a microchannel through the use of antibody-antigen interactions that provide better chemical specificity as compared to size-based separation alone. The technique can also be combined with immune-precipitation and a multichannel capillary array for high-throughput analysis of more complex protein samples. Wave mixing allows the use of chromophores and absorption-modifying tags, in addition to conventional fluorophores, for online detection of immunecomplexes related to cancer.

Sub-micron surface plasmon resonance sensor systems

NASA Technical Reports Server (NTRS)

Glazier, James A. (Inventor); Amarie, Dragos (Inventor)

2012-01-01

A sensor for detecting the presence of a target analyte, ligand or molecule in a test fluid, comprising a light transmissive substrate on which an array of surface plasmon resonant (SPR) elements is mounted is described. A multi-channel sensor for detecting the presence of several targets with a single microchip sensor is described. A multi-channel sensor including collections of SPR elements which are commonly functionalized to one of several targets is also described. The detectors sense changes in the resonant response of the SPR elements indicative of binding with the targets.

Sub-micron surface plasmon resonance sensor systems

NASA Technical Reports Server (NTRS)

Glazier, James A. (Inventor); Dragnea, Bogdan (Inventor); Amarie, Dragos (Inventor)

2010-01-01

A sensor for detecting the presence of a target analyte, ligand or molecule in a test fluid, comprising a light transmissive substrate on which an array of surface plasmon resonant (SPR) elements is mounted is described. A multi-channel sensor for detecting the presence of several targets with a single microchip sensor is described. A multi-channel sensor including collections of SPR elements which are commonly functionalized to one of several targets is also described. The detectors sense changes in the resonant response of the SPR elements indicative of binding with the targets.

Sub-micron surface plasmon resonance sensor systems

NASA Technical Reports Server (NTRS)

Amarie, Dragos (Inventor); Glazier, James A. (Inventor); Dragnea, Bogdan (Inventor)

2010-01-01

A sensor for detecting the presence of a target analyte, ligand or molecule in a test fluid, comprising a light transmissive substrate on which an array of surface plasmon resonant (SPR) elements is mounted is described. A multi-channel sensor for detecting the presence of several targets with a single micro-chip sensor is described. A multi-channel sensor including collections of SPR elements which are commonly functionalized to one of several targets is also described. The detectors sense changes in the resonant response of the SPR elements indicative of binding with the targets.

Sub-micron surface plasmon resonance sensor systems

NASA Technical Reports Server (NTRS)

Glazier, James A. (Inventor); Amarie, Dragos (Inventor)

2011-01-01

A sensor for detecting the presence of a target analyte, ligand or molecule in a test fluid, comprising a light transmissive substrate on which an array of surface plasmon resonant (SPR) elements is mounted is described. A multi-channel sensor for detecting the presence of several targets with a single micro-chip sensor is described. A multi-channel sensor including collections of SPR elements which are commonly functionalized to one of several targets is also described. The detectors sense changes in the resonant response of the SPR elements indicative of binding with the targets.

Hand-held analyser based on microchip electrophoresis with contactless conductivity detection for measurement of chemical warfare agent degradation products

NASA Astrophysics Data System (ADS)

Duran, Karolina-Petkovic; Zhu, Yonggang; Chen, Chuanpin; Swallow, Anthony; Stewart, Robert; Hoobin, Pam; Leech, Patrick; Ovenden, Simon

2008-12-01

This paper reports on the development of a hand-held device for on-site detection of organophosphonate nerve agent degradation products. This field-deployable analyzer relies on efficient microchip electrophoresis separation of alkyl methylphosphonic acids and their sensitive contactless conductivity detection. Miniaturized, low-powered design is coupled with promising analytical performance for separating the breakdown products of chemical warfare agents such as Soman, Sarin and VX . The detector has a detection limit of about 10 μg/mL and has a good linear response in the range 10-300 μg/mL concentration range. Applicability to environmental samples is demonstrated .The new hand-held analyzer offers great promise for converting conventional ion chromatography or capillary electrophoresis sophisticated systems into a portable forensic laboratory for faster, simpler and more reliable on-site screening.

Electrochemical Oscillations of Nickel Electrodissolution in an Epoxy-Based Microchip Flow Cell

PubMed Central

Cioffi, Alexander G.; Martin, R. Scott; Kiss, István Z.

2011-01-01

We investigate the nonlinear dynamics of transpassive electrodissolution of nickel in sulfuric acid in an epoxy-based microchip flow cell. We observed bistability, smooth, relaxation, and period-2 waveform current oscillations with external resistance attached to the electrode in the microfabricated electrochemical cell with 0.05 mm diameter Ni wire under potentiostatic control. Experiments with 1mm × 0.1 mm Ni electrode show spontaneous oscillations without attached external resistance; similar surface area electrode in macrocell does not exhibit spontaneous oscillations. Combined experimental and numerical studies show that spontaneous oscillation with the on-chip fabricated electrochemical cell occurs because of the unusually large ohmic potential drop due to the constrained current in the narrow flow channel. This large IR potential drop is expected to have an important role in destabilizing negative differential resistance electrochemical (e.g., metal dissolution and electrocatalytic) systems in on-chip integrated microfludic flow cells. The proposed experimental setup can be extendend to multi-electrode configurations; the epoxy-based substrate procedure thus holds promise in electroanalytical applications that require collector-generator multi-electrodes wires with various electrode sizes, compositions, and spacings as well as controlled flow conditions. PMID:21822407

Electrochemical Oscillations of Nickel Electrodissolution in an Epoxy-Based Microchip Flow Cell.

PubMed

Cioffi, Alexander G; Martin, R Scott; Kiss, István Z

2011-08-01

We investigate the nonlinear dynamics of transpassive electrodissolution of nickel in sulfuric acid in an epoxy-based microchip flow cell. We observed bistability, smooth, relaxation, and period-2 waveform current oscillations with external resistance attached to the electrode in the microfabricated electrochemical cell with 0.05 mm diameter Ni wire under potentiostatic control. Experiments with 1mm × 0.1 mm Ni electrode show spontaneous oscillations without attached external resistance; similar surface area electrode in macrocell does not exhibit spontaneous oscillations. Combined experimental and numerical studies show that spontaneous oscillation with the on-chip fabricated electrochemical cell occurs because of the unusually large ohmic potential drop due to the constrained current in the narrow flow channel. This large IR potential drop is expected to have an important role in destabilizing negative differential resistance electrochemical (e.g., metal dissolution and electrocatalytic) systems in on-chip integrated microfludic flow cells. The proposed experimental setup can be extendend to multi-electrode configurations; the epoxy-based substrate procedure thus holds promise in electroanalytical applications that require collector-generator multi-electrodes wires with various electrode sizes, compositions, and spacings as well as controlled flow conditions.

Double-helix micro-channels on microfluidic chips for enhanced continuous on-chip derivatization followed by electrophoretic separation.

PubMed

Peng, Xianglu; Zhao, Lei; Guo, Jinxiu; Yang, Shenghong; Ding, Hui; Wang, Xiayan; Pu, Qiaosheng

2015-10-15

Micro-channels that contain a special inner structure are critical for efficient mixing and chemical reactions. In this paper, we described the facile fabrication of an integrated microchip with double-helix type micro-channels to improve mixing efficiency and to facilitate multi-step derivatization reactions prior to electrophoretic separation. With a prepared microchip, reagents, samples and reaction products could be driven through micro-channels by siphon, and no other pumping device was necessary. To test its performance, reductive amination of aldehydes with 8-aminonaphthalene-1,3,6-trisulfonate acid disodium (ANTS) was attempted via microchip electrophoresis with laser induced fluorescence (LIF). The effect of the geometry of the reaction micro-channel on the reaction's efficiency was evaluated. Under the selected conditions, successful derivatization of five aldehydes was realized for highly reproducible analysis. The relative standard deviations of the peak areas for 30 consecutive injections were in the range of 0.28-1.61%. The method was applied for the determination of aldehydes in real samples with standard addition recoveries of 87.8-102.8%. Good tolerance of organic solvents was achieved, and the proposed method can potentially be employed for rapid screening of excessively added aldehyde food flavoring. Copyright © 2015 Elsevier B.V. All rights reserved.

Computing the complex : Dusty plasmas in the presence of magnetic fields and UV radiation

NASA Astrophysics Data System (ADS)

Land, V.

2007-12-01

About 90% of the visible universe is plasma. Interstellar clouds, stellar cores and atmospheres, the Solar wind, the Earth's ionosphere, polar lights, and lightning are all plasma; ionized gases, consisting of electrons, ions, and neutrals. Not only many industries, like the microchip and solar cell industry, but also future fusion power stations, rely heavily on the use of plasma. More and more, home appliances include plasma technologies, like compact fluorescent light sources, and plasma screens. Dust particles, which can disrupt plasma processes, enter these plasmas, through chemical reactions in the plasma, or through interactions between plasma and walls. For instance, during microchip fabrication, dust particles can destroy the tiny, nanometre-sized structures on the surface of these chips. On the other hand, dust particles orbiting Young Stellar Objects coagulate and form the seeds of planets. In order to understand fundamental processes, such as planet formation, or to optimize industrial plasma processes, a thorough description of dusty plasma is necessary. Dust particles immersed in plasma collect ions and electrons from the plasma and charge up electrically. Therefore, the presence of dust changes plasma, while at the same time many forces start acting on the dust. Therefore, the dust and plasma become coupled, making dusty plasma a very complex medium to describe, in which many length and time scales play a role, from the Debye length to the length of the electrodes, and from the inverse plasma frequencies to the dust transport times. Using a self-consistent fluid model, we simulate these multi-scale dusty plasmas in radio frequency discharges under micro-gravity. We show that moderate non-linear scattering of ions by the dust particles is the most important aspect in the calculation of the ion drag force. This force is also responsible for the formation of a dust-free 'void' in dusty plasma under micro-gravity, caused by ions moving from the centre of the void towards the outside of the discharge. The void thus requires electron-impact ionizations inside the void. The electrons gain the energy for these ionizations inside the dust cloud surrounding the void, however. We show that a growing electron temperature gradient is responsible for the transport of electron energy from the surrounding dust cloud into the void. An axial magnetic field in the discharge magnetizes the electrons. This changes the ambipolar flux of ions through the bulk of the discharge. The ion drag force changes, resulting in a differently shaped void and faster void formation. Experiments in a direct current discharge, show a response of both dust and plasma in the E?B direction, when a magnetic field is applied. The dust response consists of two phases: an initial fast phase, and a later, slow phase. Using a Particle-In-Cell plus Monte Carlo model, we show that the dust charge can be reduced by adding a flux of ultraviolet radiation. A source of ultraviolet light can thus serve as a tool to manipulate dusty plasmas, but might also be important for the coagulation of dust particles around young stars and planet formation in general.

Analysis of carbonaceous biomarkers with the Mars Organic Analyzer microchip capillary electrophoresis system: aldehydes and ketones.

PubMed

Stockton, Amanda M; Tjin, Caroline Chandra; Huang, Grace L; Benhabib, Merwan; Chiesl, Thomas N; Mathies, Richard A

2010-11-01

A microchip CE method is developed for the analysis of two oxidized forms of carbon, aldehydes and ketones, with the Mars Organic Analyzer (MOA). Fluorescent derivitization is achieved in ∼ 15 min by hydrazone formation with Cascade Blue hydrazide in 30 mM borate pH 5-6. The microchip CE separation and analysis method is optimized via separation in 30 mM borate buffer, pH 9.5, at 20°C. A carbonyl standard consisting of ten aldehydes and ketones found in extraterrestrial matter is successfully separated; the resulting LOD depends on the reactivity of the compound and range from 70 pM for formaldehyde to 2 μM for benzophenone. To explore the utility of this method for analyzing complex samples, analyses of several fermented beverages are conducted, identifying ten aldehydes and ketones ranging from 30 nM to 5 mM. A Martian regolith simulant sample, consisting of a basalt matrix spiked with soluble ions and acetone, is designed and analyzed, but acetone is found to have a limited detectable lifetime under simulant Martian conditions. This work establishes the capability of the MOA for studying aldehydes and ketones, a critical class of oxidized organic molecules of interest in planetary and in terrestrial environmental and health studies. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Application of Microchip for Biomarker Analysis

NASA Astrophysics Data System (ADS)

Kataoka, Masatoshi; Yatsushiro, Shouki; Yamamura, Shouhei; Abe, Hiroko

Microchip technologies have received considerable attention, due to their competitive advantages, especially in regards to reduced sample and reagent consumption, analysis time, and easy operation. This approach has been successfully used to analyze DNA, amino acids, proteins, and carbohydrates. In the present study, we showed the potential of microchip technologies for the biomarker analysis, blood carbohydrate analysis on microchip electrophoresis, quantitative analysis of protein with antigen-antibody reaction on microchip, and the detection of malaria-infected erythrocyte with a cell microarray chip.

Microchip Module for Blood Sample Preparation and Nucleic Acid Amplification Reactions

PubMed Central

Yuen, Po Ki; Kricka, Larry J.; Fortina, Paolo; Panaro, Nicholas J.; Sakazume, Taku; Wilding, Peter

2001-01-01

A computer numerical control-machined plexiglas-based microchip module was designed and constructed for the integration of blood sample preparation and nucleic acid amplification reactions. The microchip module is comprised of a custom-made heater-cooler for thermal cycling, a series of 254 μm × 254 μm microchannels for transporting human whole blood and reagents in and out of an 8–9 μL dual-purpose (cell isolation and PCR) glass-silicon microchip. White blood cells were first isolated from a small volume of human whole blood (<3 μL) in an integrated cell isolation–PCR microchip containing a series of 3.5-μm feature-sized “weir-type” filters, formed by an etched silicon dam spanning the flow chamber. A genomic target, a region in the human coagulation Factor V gene (226-bp), was subsequently directly amplified by microchip-based PCR on DNA released from white blood cells isolated on the filter section of the microchip mounted onto the microchip module. The microchip module provides a convenient means to simplify nucleic acid analyses by integrating two key steps in genetic testing procedures, cell isolation and PCR and promises to be adaptable for additional types of integrated assays. PMID:11230164

Functionality of veterinary identification microchips following low- (0.5 tesla) and high-field (3 tesla) magnetic resonance imaging.

PubMed

Piesnack, Susann; Frame, Mairi E; Oechtering, Gerhard; Ludewig, Eberhard

2013-01-01

The ability to read patient identification microchips relies on the use of radiofrequency pulses. Since radiofrequency pulses also form an integral part of the magnetic resonance imaging (MRI) process, the possibility of loss of microchip function during MRI scanning is of concern. Previous clinical trials have shown microchip function to be unaffected by MR imaging using a field strength of 1 Tesla and 1.5. As veterinary MRI scanners range widely in field strength, this study was devised to determine whether exposure to lower or higher field strengths than 1 Tesla would affect the function of different types of microchip. In a phantom study, a total of 300 International Standards Organisation (ISO)-approved microchips (100 each of three different types: ISO FDX-B 1.4 × 9 mm, ISO FDX-B 2.12 × 12 mm, ISO HDX 3.8 × 23 mm) were tested in a low field (0.5) and a high field scanner (3.0 Tesla). A total of 50 microchips of each type were tested in each scanner. The phantom was composed of a fluid-filled freezer pack onto which a plastic pillow and a cardboard strip with affixed microchips were positioned. Following an MRI scan protocol simulating a head study, all of the microchips were accurately readable. Neither 0.5 nor 3 Tesla imaging affected microchip function in this study. © 2013 Veterinary Radiology & Ultrasound.

Sensitive detection of influenza viruses with Europium nanoparticles on an epoxy silica sol-gel functionalized polycarbonate-polydimethylsiloxane hybrid microchip.

PubMed

Liu, Jikun; Zhao, Jiangqin; Petrochenko, Peter; Zheng, Jiwen; Hewlett, Indira

2016-12-15

In an effort to develop new tools for diagnosing influenza in resource-limited settings, we fabricated a polycarbonate (PC)-polydimethylsiloxane (PDMS) hybrid microchip using a simple epoxy silica sol-gel coating/bonding method and employed it in sensitive detection of influenza virus with Europium nanoparticles (EuNPs). The incorporation of sol-gel material in device fabrication provided functionalized channel surfaces ready for covalent immobilization of primary antibodies and a strong bonding between PDMS substrates and PC supports without increasing background fluorescence. In microchip EuNP immunoassay (µENIA) of inactivated influenza viruses, replacing native PDMS microchips with hybrid microchips allowed the achievement of a 6-fold increase in signal-to-background ratio, a 12-fold and a 6-fold decreases in limit-of-detection (LOD) in influenza A and B tests respectively. Using influenza A samples with known titers, the LOD of influenza µENIA on hybrid microchips was determined to be ~10(4) TCID50 titer/mL and 10(3)-10(4) EID50 titer/mL. A comparison test indicated that the sensitivity of influenza µENIA enhanced using the hybrid microchips even surpassed that of a commercial laboratory influenza ELISA test. In addition to the sensitivity improvement, assay variation was clearly reduced when hybrid microchips instead of native PDMS microchips were used in the µENIA tests. Finally, infectious reference viruses and nasopharyngeal swab patient specimens were successfully tested using μENIA on hybrid microchip platforms, demonstrating the potential of this unique microchip nanoparticle assay in clinical diagnosis of influenza. Meanwhile, the tests showed the necessity of using nucleic acid confirmatory tests to clarify ambiguous test results obtained from prototype or developed point-of-care testing devices for influenza diagnosis. Published by Elsevier B.V.

Customized oligonucleotide microchips that convert multiple genetic information to simple patterns, are portable and reusable

DOEpatents

Mirzabekov, Andrei; Guschin, Dmitry Y.; Chik, Valentine; Drobyshev, Aleksei; Fotin, Alexander; Yershov, Gennadiy; Lysov, Yuri

2002-01-01

This invention relates to using customized oligonucleotide microchips as biosensors for the detection and identification of nucleic acids specific for different genes, organisms and/or individuals in the environment, in food and in biological samples. The microchips are designed to convert multiple bits of genetic information into simpler patterns of signals that are interpreted as a unit. Because of an improved method of hybridizing oligonucleotides from samples to microchips, microchips are reusable and transportable. For field study, portable laser or bar code scanners are suitable.

Segmented ion thruster

NASA Technical Reports Server (NTRS)

Brophy, John R. (Inventor)

1993-01-01

Apparatus and methods for large-area, high-power ion engines comprise dividing a single engine into a combination of smaller discharge chambers (or segments) configured to operate as a single large-area engine. This segmented ion thruster (SIT) approach enables the development of 100-kW class argon ion engines for operation at a specific impulse of 10,000 s. A combination of six 30-cm diameter ion chambers operating as a single engine can process over 100 kW. Such a segmented ion engine can be operated from a single power processor unit.

Microchip and wedge ion funnels and planar ion beam analyzers using same

DOEpatents

Shvartsburg, Alexandre A; Anderson, Gordon A; Smith, Richard D

2012-10-30

Electrodynamic ion funnels confine, guide, or focus ions in gases using the Dehmelt potential of oscillatory electric field. New funnel designs operating at or close to atmospheric gas pressure are described. Effective ion focusing at such pressures is enabled by fields of extreme amplitude and frequency, allowed in microscopic gaps that have much higher electrical breakdown thresholds in any gas than the macroscopic gaps of present funnels. The new microscopic-gap funnels are useful for interfacing atmospheric-pressure ionization sources to mass spectrometry (MS) and ion mobility separation (IMS) stages including differential IMS or FAIMS, as well as IMS and MS stages in various configurations. In particular, "wedge" funnels comprising two planar surfaces positioned at an angle and wedge funnel traps derived therefrom can compress ion beams in one dimension, producing narrow belt-shaped beams and laterally elongated cuboid packets. This beam profile reduces the ion density and thus space-charge effects, mitigating the adverse impact thereof on the resolving power, measurement accuracy, and dynamic range of MS and IMS analyzers, while a greater overlap with coplanar light or particle beams can benefit spectroscopic methods.

Physiological and behavioural responses of young horses to hot iron branding and microchip implantation.

PubMed

Erber, R; Wulf, M; Becker-Birck, M; Kaps, S; Aurich, J E; Möstl, E; Aurich, C

2012-02-01

Branding is the traditional and well-established method used to mark horses, but recently microchip transponders for implantation have become available. In this study, behaviour, physiological stress variables and skin temperature in foals were determined in response to hot-iron branding (n=7) and microchip implantation (n=7). Salivary cortisol concentrations increased in response to branding (1.8 ± 0.2 ng/mL) and microchip implantation (1.4 ± 0.1ng/mL), but cortisol release over time did not differ. In response to both manipulations there was a transient increase in heart rate (P<0.001) and heart rate variability (P<0.01). Branding and microchip implantation induced a comparable aversive behaviour (branding, score 3.86 ± 0.85; microchip, score 4.00 ± 0.82). Both techniques thus caused similar physiological and behavioural changes indicative of stress. Acutely, implantation of a microchip was as stressful as branding in foals. Branding caused a necrotising skin burn lasting at least 7 days. Moreover branding, but not microchip implantation (P<0.001), was accompanied by a generalized increase in skin temperature which was comparable to low degree post-burn hypermetabolism in humans. Copyright © 2011 Elsevier Ltd. All rights reserved.

A method for UV-bonding in the fabrication of glass electrophoretic microchips.

PubMed

Huang, Z; Sanders, J C; Dunsmor, C; Ahmadzadeh, H; Landers, J P

2001-10-01

This paper presents an approach for the development of methodologies amenable to simple and inexpensive microchip fabrication, potentially applicable to dissimilar materials bonding and chip integration. The method involves a UV-curable glue that can be used for glass microchip fabrication bonding at room temperature. This involves nothing more than fabrication of glue "guide channels" into the microchip architecture that upon exposure to the appropriate UV light source, bonds the etched plate and cover plate together. The microchip performance was verified by capillary zone electrophoresis (CZE) of small fluorescent molecules with no microchannel surface modification carried out, as well as with a DNA fragment separation following surface modification. The performance of these UV-bonded electrophoretic microchips indicates that this method may provide an alternative to high temperature bonding.

Biological cell controllable patch-clamp microchip

NASA Astrophysics Data System (ADS)

Penmetsa, Siva; Nagrajan, Krithika; Gong, Zhongcheng; Mills, David; Que, Long

2010-12-01

A patch-clamp (PC) microchip with cell sorting and positioning functions is reported, which can avoid drawbacks of random cell selection or positioning for a PC microchip. The cell sorting and positioning are enabled by air bubble (AB) actuators. AB actuators are pneumatic actuators, in which air pressure is generated by microheaters within sealed microchambers. The sorting, positioning, and capturing of 3T3 cells by this type of microchip have been demonstrated. Using human breast cancer cells MDA-MB-231 as the model, experiments have been demonstrated by this microchip as a label-free technical platform for real-time monitoring of the cell viability.

Creating Sub-50 nm Nanofluidic Junctions in PDMS Microchip via Self-Assembly Process of Colloidal Silica Beads for Electrokinetic Concentration of Biomolecules

PubMed Central

Syed, A.; Mangano, L.; Mao, P.; Han, J.

2014-01-01

In this work we describe a novel and simple self-assembly of colloidal silica beads to create nanofluidic junction between two microchannels. The nanoporous membrane was used to induce ion concentration polarization inside the microchannel and this electrokinetic preconcentration system allowed rapid concentration of DNA samples by ∼1700 times and protein samples by ∼100 times within 5 minutes. PMID:25254651

Multi-atlas learner fusion: An efficient segmentation approach for large-scale data.

PubMed

Asman, Andrew J; Huo, Yuankai; Plassard, Andrew J; Landman, Bennett A

2015-12-01

We propose multi-atlas learner fusion (MLF), a framework for rapidly and accurately replicating the highly accurate, yet computationally expensive, multi-atlas segmentation framework based on fusing local learners. In the largest whole-brain multi-atlas study yet reported, multi-atlas segmentations are estimated for a training set of 3464 MR brain images. Using these multi-atlas estimates we (1) estimate a low-dimensional representation for selecting locally appropriate example images, and (2) build AdaBoost learners that map a weak initial segmentation to the multi-atlas segmentation result. Thus, to segment a new target image we project the image into the low-dimensional space, construct a weak initial segmentation, and fuse the trained, locally selected, learners. The MLF framework cuts the runtime on a modern computer from 36 h down to 3-8 min - a 270× speedup - by completely bypassing the need for deformable atlas-target registrations. Additionally, we (1) describe a technique for optimizing the weak initial segmentation and the AdaBoost learning parameters, (2) quantify the ability to replicate the multi-atlas result with mean accuracies approaching the multi-atlas intra-subject reproducibility on a testing set of 380 images, (3) demonstrate significant increases in the reproducibility of intra-subject segmentations when compared to a state-of-the-art multi-atlas framework on a separate reproducibility dataset, (4) show that under the MLF framework the large-scale data model significantly improve the segmentation over the small-scale model under the MLF framework, and (5) indicate that the MLF framework has comparable performance as state-of-the-art multi-atlas segmentation algorithms without using non-local information. Copyright © 2015 Elsevier B.V. All rights reserved.

Chaotic dynamics and synchronization in microchip solid-state lasers with optoelectronic feedback.

PubMed

Uchida, Atsushi; Mizumura, Keisuke; Yoshimori, Shigeru

2006-12-01

We experimentally observe the dynamics of a two-mode Nd:YVO4 microchip solid-state laser with optoelectronic feedback. The total laser output is detected and fed back to the injection current of the laser diode for pumping. Chaotic oscillations are observed in the microchip laser with optoelectronic self-feedback. We also observe the dynamics of two microchip lasers coupled mutually with optoelectronic link. The output of one laser is detected by a photodiode and the electronic signal converted from the laser output is sent to the pumping of the other laser. Chaotic fluctuation of the laser output is observed when the relaxation oscillation frequency is close to each other between the two microchip lasers. Synchronization of periodic wave form is also obtained when the microchip lasers have a single-longitudinal mode.

Effects of radiation from a radiofrequency identification (RFID) microchip on human cancer cells.

PubMed

Lai, Henry C; Chan, Ho Wing; Singh, Narendra P

2016-01-01

Radiofrequency identification (RFID) microchips are used to remotely identify objects, e.g. an animal in which a chip is implanted. A passive RFID microchip absorbs energy from an external source and emits a radiofrequency identification signal which is then decoded by a detector. In the present study, we investigated the effect of the radiofrequency energy emitted by a RFID microchip on human cancer cells. Molt-4 leukemia, BT474 breast cancer, and HepG2 hepatic cancer cells were exposed in vitro to RFID microchip-emitted radiofrequency field for 1 h. Cells were counted before and after exposure. Effects of pretreatment with the spin-trap compound N-tert-butyl-alpha-phenylnitrone or the iron-chelator deferoxamine were also investigated. Results We found that the energy effectively killed/retarded the growth of the three different types of cancer cells, and the effect was blocked by the spin-trap compound or the iron-chelator, whereas an inactive microchip and energy from the external source had no significant effect on the cells. Conclusions Data of the present study suggest that radiofrequency field from the microchip affects cancer cells via the Fenton Reaction. Implantation of RFID microchips in tumors may provide a new method for cancer treatment.

Design and Simulation of Material-Integrated Distributed Sensor Processing with a Code-Based Agent Platform and Mobile Multi-Agent Systems

PubMed Central

Bosse, Stefan

2015-01-01

Multi-agent systems (MAS) can be used for decentralized and self-organizing data processing in a distributed system, like a resource-constrained sensor network, enabling distributed information extraction, for example, based on pattern recognition and self-organization, by decomposing complex tasks in simpler cooperative agents. Reliable MAS-based data processing approaches can aid the material-integration of structural-monitoring applications, with agent processing platforms scaled to the microchip level. The agent behavior, based on a dynamic activity-transition graph (ATG) model, is implemented with program code storing the control and the data state of an agent, which is novel. The program code can be modified by the agent itself using code morphing techniques and is capable of migrating in the network between nodes. The program code is a self-contained unit (a container) and embeds the agent data, the initialization instructions and the ATG behavior implementation. The microchip agent processing platform used for the execution of the agent code is a standalone multi-core stack machine with a zero-operand instruction format, leading to a small-sized agent program code, low system complexity and high system performance. The agent processing is token-queue-based, similar to Petri-nets. The agent platform can be implemented in software, too, offering compatibility at the operational and code level, supporting agent processing in strong heterogeneous networks. In this work, the agent platform embedded in a large-scale distributed sensor network is simulated at the architectural level by using agent-based simulation techniques. PMID:25690550

Design and simulation of material-integrated distributed sensor processing with a code-based agent platform and mobile multi-agent systems.

PubMed

Bosse, Stefan

2015-02-16

Multi-agent systems (MAS) can be used for decentralized and self-organizing data processing in a distributed system, like a resource-constrained sensor network, enabling distributed information extraction, for example, based on pattern recognition and self-organization, by decomposing complex tasks in simpler cooperative agents. Reliable MAS-based data processing approaches can aid the material-integration of structural-monitoring applications, with agent processing platforms scaled to the microchip level. The agent behavior, based on a dynamic activity-transition graph (ATG) model, is implemented with program code storing the control and the data state of an agent, which is novel. The program code can be modified by the agent itself using code morphing techniques and is capable of migrating in the network between nodes. The program code is a self-contained unit (a container) and embeds the agent data, the initialization instructions and the ATG behavior implementation. The microchip agent processing platform used for the execution of the agent code is a standalone multi-core stack machine with a zero-operand instruction format, leading to a small-sized agent program code, low system complexity and high system performance. The agent processing is token-queue-based, similar to Petri-nets. The agent platform can be implemented in software, too, offering compatibility at the operational and code level, supporting agent processing in strong heterogeneous networks. In this work, the agent platform embedded in a large-scale distributed sensor network is simulated at the architectural level by using agent-based simulation techniques.

Monitoring Cellular Events in Living Mast Cells Stimulated with an Extremely Small Amount of Fluid on a Microchip

NASA Astrophysics Data System (ADS)

Munaka, Tatsuya; Abe, Hirohisa; Kanai, Masaki; Sakamoto, Takashi; Nakanishi, Hiroaki; Yamaoka, Tetsuji; Shoji, Shuichi; Murakami, Akira

2006-07-01

We successfully developed a measurement system for real-time analysis of cellular function using a newly designed microchip. This microchip was equipped with a micro cell incubation chamber (240 nl) and was stimulated by a very small amount of stimuli (as small as 24 nl). Using the microchip system, cultivation of mast cells was successfully carried out. Monitoring of the cellular events after stimulation with an extremely small amount of fluid on a microchip was performed. This system could be applicable for various types of cellular analysis including real-time monitoring of cellular response by stimulation.

Comparison of Digital Rectal and Microchip Transponder Thermometry in Ferrets (Mustela putorius furo)

PubMed Central

Maxwell, Branden M; Brunell, Marla K; Olsen, Cara H; Bentzel, David E

2016-01-01

Body temperature is a common physiologic parameter measured in both clinical and research settings, with rectal thermometry being implied as the ‘gold standard.’ However, rectal thermometry usually requires physical or chemical restraint, potentially causing falsely elevated readings due to animal stress. A less stressful method may eliminate this confounding variable. The current study compared 2 types of digital rectal thermometers—a calibrated digital thermometer and a common digital thermometer—with an implantable subcutaneous transponder microchip. Microchips were implanted subcutaneously between the shoulder blades of 16 ferrets (8 male, 8 female), and temperatures were measured twice from the microchip reader and once from each of the rectal thermometers. Results demonstrated the microchip temperature readings had very good to good correlation and agreement to those from both of the rectal thermometers. This study indicates that implantable temperature-sensing microchips are a reliable alternative to rectal thermometry for monitoring body temperature in ferrets. PMID:27177569

A Passively Q-Switched, CW-Pumped Fe:ZnSe Laser

DTIC Science & Technology

2014-03-01

passively Q-switched microchip lasers using semiconductor saturable absorbers,” J. Opt. Soc. Amer. B, Opt. Phys., vol. 16, no. 3, pp. 376–388, Mar. 1999...204 IEEE JOURNAL OF QUANTUM ELECTRONICS, VOL. 50, NO. 3, MARCH 2014 A Passively Q-Switched, CW-Pumped Fe:ZnSe Laser Jonathan W. Evans, Patrick A...Berry, and Kenneth L. Schepler Abstract— We report the demonstration of high-average-power passively Q-switched laser oscillation from Fe2+ ions in zinc

Automatic Structural Parcellation of Mouse Brain MRI Using Multi-Atlas Label Fusion

PubMed Central

Ma, Da; Cardoso, Manuel J.; Modat, Marc; Powell, Nick; Wells, Jack; Holmes, Holly; Wiseman, Frances; Tybulewicz, Victor; Fisher, Elizabeth; Lythgoe, Mark F.; Ourselin, Sébastien

2014-01-01

Multi-atlas segmentation propagation has evolved quickly in recent years, becoming a state-of-the-art methodology for automatic parcellation of structural images. However, few studies have applied these methods to preclinical research. In this study, we present a fully automatic framework for mouse brain MRI structural parcellation using multi-atlas segmentation propagation. The framework adopts the similarity and truth estimation for propagated segmentations (STEPS) algorithm, which utilises a locally normalised cross correlation similarity metric for atlas selection and an extended simultaneous truth and performance level estimation (STAPLE) framework for multi-label fusion. The segmentation accuracy of the multi-atlas framework was evaluated using publicly available mouse brain atlas databases with pre-segmented manually labelled anatomical structures as the gold standard, and optimised parameters were obtained for the STEPS algorithm in the label fusion to achieve the best segmentation accuracy. We showed that our multi-atlas framework resulted in significantly higher segmentation accuracy compared to single-atlas based segmentation, as well as to the original STAPLE framework. PMID:24475148

Local Structure and Ion Transport in Glassy Poly(ethylene oxide styrene) Copolymers

NASA Astrophysics Data System (ADS)

Yang, Han-Chang; Mays, Jimmy; Sokolov, Alexei P.; Winey, Karen I.

2014-03-01

Polymer electrolytes have attracted attention for a wide variety of applications in energy production such as lithium-ion batteries and fuel cells. The concept of free volume provides important information about ion mobility and chain dynamics in the polymer matrix. Researchers have recently demonstrated that ion transport in glassy polymer can be improved by designing a system with high free volume. We have studied the effect of temperature and humidity on the intermolecular correlations of poly(ethylene oxide styrene-block-styrene) (PEOSt- b-St) block copolymer and poly(ethylene oxide styrene) (PEOSt) homopolymer using in situ multi-angle x-ray scattering across a wide range of scattering angles (q = 0.007-1.5 Å-1) . An increase in backbone-to-backbone distance is observed, indicating an increase in free volume between different polymer main chains. Structural characterization of the polymer segments will be discussed together with conductivity and dielectric results to better understand the ion transport mechanism in the local environment of the polymer system. Department of Chemistry, University of Tennessee.

Monitoring environmental pollutants by microchip capillary electrophoresis with electrochemical detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Gang; Lin, Yuehe; Wang, Joseph

2006-01-15

This is a review article. During the past decade, significant progress in the development of miniaturized microfluidic systems has Occurred due to the numerous advantages of microchip analysis. This review focuses on recent advances and the key strategies in microchip capillary electrophoresis (CE) with electrochemical detection (ECD) for separating and detecting a variety of environmental pollutants. The subjects covered include the fabrication of microfluidic chips, ECD, typical applications of microchip CE with ECD in environmental analysis, and future prospects. It is expected that microchip CE-ECD will become a powerful tool in the environmental field and will lead to the creationmore » of truly portable devices.« less

Second Microchip Gets Ready for Launch

NASA Image and Video Library

2018-01-24

Second dime-size microchip carrying 1.6 million names gets processed for installation onto the InSight lander. Technicians at Lockheed Martin Space in Littleton, Colorado installed a microchip with 1.6 million names submitted by the public to ride along with NASA's InSight mission to Mars. The chip was installed on Jan. 23, 2018. This joins another microchip that was previously installed that included 800,000 names for a grand total of 2.4 million names going to Mars as early as May 5, 2018. The microchip including names from the NASA InSight mission's "Send Your Name to Mars" campaign was affixed to the spacecraft with a special glue. https://photojournal.jpl.nasa.gov/catalog/PIA22237

Combining multi-atlas segmentation with brain surface estimation

NASA Astrophysics Data System (ADS)

Huo, Yuankai; Carass, Aaron; Resnick, Susan M.; Pham, Dzung L.; Prince, Jerry L.; Landman, Bennett A.

2016-03-01

Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitation in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

Combining Multi-atlas Segmentation with Brain Surface Estimation.

PubMed

Huo, Yuankai; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

2016-02-27

Whole brain segmentation (with comprehensive cortical and subcortical labels) and cortical surface reconstruction are two essential techniques for investigating the human brain. The two tasks are typically conducted independently, however, which leads to spatial inconsistencies and hinders further integrated cortical analyses. To obtain self-consistent whole brain segmentations and surfaces, FreeSurfer segregates the subcortical and cortical segmentations before and after the cortical surface reconstruction. However, this "segmentation to surface to parcellation" strategy has shown limitations in various situations. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. To our knowledge, this is the first work that achieves the reliability of state-of-the-art multi-atlas segmentation and labeling methods together with accurate and consistent cortical surface reconstruction. Compared with previous methods, MaCRUISE has three features: (1) MaCRUISE obtains 132 cortical/subcortical labels simultaneously from a single multi-atlas segmentation before reconstructing volume consistent surfaces; (2) Fuzzy tissue memberships are combined with multi-atlas segmentations to address partial volume effects; (3) MaCRUISE reconstructs topologically consistent cortical surfaces by using the sulci locations from multi-atlas segmentation. Two data sets, one consisting of five subjects with expertly traced landmarks and the other consisting of 100 volumes from elderly subjects are used for validation. Compared with CRUISE, MaCRUISE achieves self-consistent whole brain segmentation and cortical reconstruction without compromising on surface accuracy. MaCRUISE is comparably accurate to FreeSurfer while achieving greater robustness across an elderly population.

Recent Advances in Mycotoxin Determination for Food Monitoring via Microchip

PubMed Central

Man, Yan; Liang, Gang; Li, An; Pan, Ligang

2017-01-01

Mycotoxins are one of the main factors impacting food safety. Mycotoxin contamination has threatened the health of humans and animals. Conventional methods for the detection of mycotoxins are gas chromatography (GC) or liquid chromatography (LC) coupled with mass spectrometry (MS), or enzyme-linked immunosorbent assay (ELISA). However, all these methods are time-consuming, require large-scale instruments and skilled technicians, and consume large amounts of hazardous regents and solvents. Interestingly, a microchip requires less sample consumption and short analysis time, and can realize the integration, miniaturization, and high-throughput detection of the samples. Hence, the application of a microchip for the detection of mycotoxins can make up for the deficiency of the conventional detection methods. This review focuses on the application of a microchip to detect mycotoxins in foods. The toxicities of mycotoxins and the materials of the microchip are firstly summarized in turn. Then the application of a microchip that integrates various kinds of detection methods (optical, electrochemical, photo-electrochemical, and label-free detection) to detect mycotoxins is reviewed in detail. Finally, challenges and future research directions in the development of a microchip to detect mycotoxins are previewed. PMID:29036884

In vitro evaluation of a passive radio frequency identification microchip implanted in human molars subjected to compression forces, for forensic purposes of human identification

PubMed Central

Moreno, Freddy; Vallejo, Diego; Garzón, Herney; Moreno, Sandra

2013-01-01

Objective: To evaluate the in vitro behavior of a passive Radio Frequency Identification (RFID) microchip implanted in human molars subjected to compression forces to determine its technical and clinical viability. Materials and Methods: In vitro experimental study to evaluate the physical behavior of a passive RFID microchip (VeriChip™) implanted in human molars through resin restoration (Filtek P90™ Silorane 3M-ESPE®) to determine the clinical and technical possibilities of the implant and the viability to withstand compression forces exerted by the stomatognathic system during mastication. Results: Through the ANOVA test, it was found that the teeth on which a microchip was implanted show great resistance to compressive forces. It was also evident that teeth with microchips implanted in Class V cavities are more resistant than those implanted in Class I cavities. Conclusions: Although microchip dimensions are big, requiring a sufficiently large cavity, from the biomechanical point of view it is plausible to implant a microchip in a Class V cavity employing restoration material based on resin for forensic purposes of human identification. PMID:24255554

Microchip Capillary Electrophoresis with Electrochemical Detection for Monitoring Environmental Pollutants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Gang; Lin, Yuehe; Wang, Joseph

2006-01-15

This invited paper reviews recent advances and the key strategies in microchip capillary electrophoresis (CE) with electrochemical detection (ECD) for separating and detecting a variety of environmental pollutants. The subjects covered include the fabrication of microfluidic chips, sample pretreatments, ECD, typical applications of microchip CE with ECD in environmental analysis, and future prospects. It is expected that microchip CE-ECD will become a powerful tool in the environmental field and will lead to the creation of truly portable devices.

Megawatt level UV output from [110] Cr⁴⁺:YAG passively Q-switched microchip laser.

PubMed

Bhandari, Rakesh; Taira, Takunori

2011-11-07

Recent development of megawatt peak power, giant pulse microchip lasers has opened new opportunities for efficient wavelength conversion, provided the output of the microchip laser is linearly polarized. We obtain > 2 MW peak power, 260 ps, 100 Hz pulses at 266 nm by fourth harmonic conversion of a linearly polarized Nd:YAG microchip laser that is passively Q-switched with [110] cut Cr⁴⁺:YAG. The SHG and FHG conversion efficiencies are 85% and 51%, respectively.

Pr:YAlO(3) microchip laser.

PubMed

Fibrich, Martin; Jelínková, Helena; Sulc, Jan; Nejezchleb, Karel; Skoda, Václav

2010-08-01

A cw Pr:YAlO(3) microchip-laser operation in the near-IR spectral region is reported. A microchip resonator was formed by dielectric mirrors directly deposited on the Pr:YAlO(3) crystal surfaces. For active medium pumping, a GaN laser diode providing up to 1W of output power at approximately 448 nm was used. 139mW of laser radiation at 747nm wavelength has been extracted from the microchip-laser system. Slope efficiency related to the incident pumping power was approximately 25%.

Fibrosarcoma adjacent to the site of microchip implantation in a cat.

PubMed

Daly, Meighan K; Saba, Corey F; Crochik, Sonia S; Howerth, Elizabeth W; Kosarek, Carrie E; Cornell, Karen K; Roberts, Royce E; Northrup, Nicole C

2008-04-01

A 14-year-old spayed female domestic shorthair cat presented with an interscapular mass. A computed tomography scan, biopsy, and histological examination revealed a fibrosarcoma adjacent to a pet identification microchip. Because the cat was previously vaccinated at this site, it is not possible to establish definitive causation of the fibrosarcoma, but this is the first report of a tumor in the vicinity of a microchip in a cat. Microchip-associated tumors have been reported in rodents and dogs. Veterinarians should be aware that because inflammation may predispose felines to tumor formation, separation and observation of vaccination and implantation sites are indicated. Adherence to American Association of Feline Practitioners (AAFP) vaccination guidelines and monitoring of microchip implantation sites are recommended.

Wavelength locking of CW and Q-switched Er(3+) microchip lasers to acetylene absorption lines using pump-power modulation.

PubMed

Brunel, Marc; Vallet, Marc

2007-02-19

We show that modulating the diode-pump power of a microchip solid-state laser enables to lock its wavelength to a reference molecular line. The method is applied to two different types of Er,Yb:glass monolithic microchip lasers operating at 1.53 microm. First, wavelength locking of a continuous-wave dual-polarization microchip laser to acetylene absorption lines is demonstrated, without using any additional modulator, internal or external. We then show that, remarkably, this simple method is also suitable for stabilizing a passively Q-switched microchip laser. A pulsed wavelength stability of 10(-8) over 1 hour is readily observed. Applications to lidars and to microwave photonics are discussed.

Laser diode side-pumped Nd:YVO4 microchip laser with film-etched microcavity mirrors.

PubMed

Li, Jiyang; Niu, Yanxiong; Chen, Sanbin; Tan, Yidong

2017-10-01

Microchip lasers are applied as the light sources on various occasions with the end-pumping scheme. However, the vibration, the temperature drift, or the mechanical deformation of the pumping light in laser diodes in the end-pumping scheme will lead to instability in the microchip laser output, which causes errors and malfunctioning in the optic systems. In this paper, the side-pumping scheme is applied for improving the disturbance-resisting ability of the microchip laser. The transverse mode and the frequency purity of the laser output are tested. To ensure unicity in the frequency of the laser output, numerical simulations based on Fresnel-Kirchhoff diffraction theory are conducted on the parameters of the microchip laser cavity. Film-etching technique is applied to restrain the area of the film and form the microcavity mirrors. The laser output with microcavity mirrors is ensured to be in single frequency and with good beam quality, which is significant in the applications of microchip lasers as the light sources in optical systems.

DNA analysis using an integrated microchip for multiplex PCR amplification and electrophoresis for reference samples.

PubMed

Le Roux, Delphine; Root, Brian E; Reedy, Carmen R; Hickey, Jeffrey A; Scott, Orion N; Bienvenue, Joan M; Landers, James P; Chassagne, Luc; de Mazancourt, Philippe

2014-08-19

A system that automatically performs the PCR amplification and microchip electrophoretic (ME) separation for rapid forensic short tandem repeat (STR) forensic profiling in a single disposable plastic chip is demonstrated. The microchip subassays were optimized to deliver results comparable to conventional benchtop methods. The microchip process was accomplished in sub-90 min compared with >2.5 h for the conventional approach. An infrared laser with a noncontact temperature sensing system was optimized for a 45 min PCR compared with the conventional 90 min amplification time. The separation conditions were optimized using LPA-co-dihexylacrylamide block copolymers specifically designed for microchip separations to achieve accurate DNA size calling in an effective length of 7 cm in a plastic microchip. This effective separation length is less than half of other reports for integrated STR analysis and allows a compact, inexpensive microchip design. This separation quality was maintained when integrated with microchip PCR. Thirty samples were analyzed conventionally and then compared with data generated by the microfluidic chip system. The microfluidic system allele calling was 100% concordant with the conventional process. This study also investigated allelic ladder consistency over time. The PCR-ME genetic profiles were analyzed using binning palettes generated from two sets of allelic ladders run three and six months apart. Using these binning palettes, no allele calling errors were detected in the 30 samples demonstrating that a microfluidic platform can be highly consistent over long periods of time.

Microchip Lasers

DTIC Science & Technology

2016-10-31

microchip laser : (top) schematic and (bottom) photograph of working device mounted on 12.7-mm- dia. post. switch 17 (355-nm UV ), 1.5 µJ of fourth......USA E-mail: zayhowski@ll.mit.edu Abstract Microchip lasers are a rich family of solid-state lasers defined by their small size, robust integration

Apparatus for Precise Indium-Bump Bonding of Microchips

NASA Technical Reports Server (NTRS)

Wild, Larry; Mulder, Jerry; Alvarado, Nicholas

2005-01-01

An improved apparatus has been designed and built for use in precise positioning and pressing of a microchip onto a substrate (which could, optionally, be another microchip) for the purpose of indium-bump bonding. The apparatus (see figure) includes the following: A stereomicroscope, A stage for precise positioning of the microchip in rotation angle (theta) about the nominally vertical pressing axis and in translation along two nominally horizontal coordinate axes (x and y), and An actuator system that causes a bonding tip to press the microchip against the substrate with a precisely controlled force. In operation, the microscope and the stage are used to position the microchip under the bonding tip and to align the indium bumps on the chip and the substrate, then the actuator system is used to apply a prescribed bonding force for a prescribed time. The improved apparatus supplants a partly similar prior apparatus that operated with less precision and repeatability, producing inconsistent and unreliable bonds. Results of the use of the prior apparatus included broken microchips, uneven bonds, and bonds characterized, variously, by overcompression or undercompression. In that apparatus, the bonding force was generated and controlled by use of a micrometer head positioned over the center of a spring-loaded scale, and the force was applied to the microchip via the scale, which was equipped for digital readout of the force. The inconsistency of results was attributed to the following causes: It was not possible to control the bonding force with sufficient precision or repeatability. Particularly troublesome was the inability to control the force at levels less than the weight of 150 g. Excessive compliance in the spring-loaded scale, combined with deviations from parallelarity of the substrate and bonding-tip surfaces, gave rise to nonuniformity in the pressure applied to the microchip, thereby generating excessive stresses and deformations in the microchip. In the improved apparatus, the bonding tip and the components that hold the substrate and the microchip are more rigid and precise than in the prior apparatus, so as to ensure less deviation from parallelarity of the bonding-tip and substrate surfaces, thereby ensuring more nearly uniform distribution of bonding force over the area of the microchip. The bonding force is now applied through, and measured by, a load cell that makes it possible to exert finer control over the force. The force can be set at any value between 0 and the weight of 800 g in increments of 0.2 g.

Fully automatic multi-atlas segmentation of CTA for partial volume correction in cardiac SPECT/CT

NASA Astrophysics Data System (ADS)

Liu, Qingyi; Mohy-ud-Din, Hassan; Boutagy, Nabil E.; Jiang, Mingyan; Ren, Silin; Stendahl, John C.; Sinusas, Albert J.; Liu, Chi

2017-05-01

Anatomical-based partial volume correction (PVC) has been shown to improve image quality and quantitative accuracy in cardiac SPECT/CT. However, this method requires manual segmentation of various organs from contrast-enhanced computed tomography angiography (CTA) data. In order to achieve fully automatic CTA segmentation for clinical translation, we investigated the most common multi-atlas segmentation methods. We also modified the multi-atlas segmentation method by introducing a novel label fusion algorithm for multiple organ segmentation to eliminate overlap and gap voxels. To evaluate our proposed automatic segmentation, eight canine 99mTc-labeled red blood cell SPECT/CT datasets that incorporated PVC were analyzed, using the leave-one-out approach. The Dice similarity coefficient of each organ was computed. Compared to the conventional label fusion method, our proposed label fusion method effectively eliminated gaps and overlaps and improved the CTA segmentation accuracy. The anatomical-based PVC of cardiac SPECT images with automatic multi-atlas segmentation provided consistent image quality and quantitative estimation of intramyocardial blood volume, as compared to those derived using manual segmentation. In conclusion, our proposed automatic multi-atlas segmentation method of CTAs is feasible, practical, and facilitates anatomical-based PVC of cardiac SPECT/CT images.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Xing; Ibrahim, Yehia M.; Chen, Tsung-Chi

We report the first evaluation of a platform coupling a high speed field asymmetric ion mobility spectrometry microchip (µFAIMS) with drift tube ion mobility and mass spectrometry (IMS-MS). The µFAIMS/IMS-MS platform was used to analyze biological samples and simultaneously acquire multidimensional information of detected features from the measured FAIMS compensation fields and IMS drift times, while also obtaining accurate ion masses. These separations thereby increase the overall separation power, resulting increased information content, and provide more complete characterization of more complex samples. The separation conditions were optimized for sensitivity and resolving power by the selection of gas compositions and pressuresmore » in the FAIMS and IMS separation stages. The resulting performance provided three dimensional separations, benefitting both broad complex mixture studies and targeted analyses by e.g. improving isomeric separations and allowing detection of species obscured by “chemical noise” and other interfering peaks.« less

Production of Microchips from Polystyrene Plates

ERIC Educational Resources Information Center

Pace, Sarah Lindsey

2009-01-01

Currently manufactured microchips are expensive to make, require specialized equipment, and leave a large environmental footprint. To counter this, an alternative procedure that is cheaper and leaves a smaller environmental footprint should be made. The goal of this research project is to develop a process that creates microchips from polystyrene…

Comparison of body temperature readings between an implantable microchip and a cloacal probe in lorikeets (Trichoglossus haematodus sp.).

PubMed

Hoskinson, Christine; McCain, Stephanie; Allender, Matthew C

2014-01-01

Body temperature readings can be a useful diagnostic tool for identifying the presence of subclinical disease. Traditionally, rectal or cloacal thermometry has been used to obtain body temperatures. The use of implantable microchips to obtain these temperatures has been studied in a variety of animals, but not yet in avian species. Initially, timepoint one (T₁), nine lorikeets were anesthetized via facemask induction with 5% isoflurane and maintained at 2-3% for microchip placement and body temperature data collection. Body temperature was measured at 0 and 2 min post-anesthetic induction both cloacally, using a Cardell veterinary monitor and also via implantable microchip, utilizing a universal scanner. On two more occasions, timepoints two and three (T₂, T₃), the same nine lorikeets were manually restrained to obtain body temperature readings both cloacally and via microchip, again at minutes 0 and 2. There was no statistical difference between body temperatures, for both methods, at T₁. Microchip temperatures were statistically different than cloacal temperatures at T₂ and T₃. Body temperatures at T₁, were statistically different from those obtained at T₂ and T₃ for both methods. Additional studies are warranted to verify the accuracy of microchip core body temperature readings in avian species. © 2014 Wiley Periodicals, Inc.

Superpixel-based segmentation of muscle fibers in multi-channel microscopy.

PubMed

Nguyen, Binh P; Heemskerk, Hans; So, Peter T C; Tucker-Kellogg, Lisa

2016-12-05

Confetti fluorescence and other multi-color genetic labelling strategies are useful for observing stem cell regeneration and for other problems of cell lineage tracing. One difficulty of such strategies is segmenting the cell boundaries, which is a very different problem from segmenting color images from the real world. This paper addresses the difficulties and presents a superpixel-based framework for segmentation of regenerated muscle fibers in mice. We propose to integrate an edge detector into a superpixel algorithm and customize the method for multi-channel images. The enhanced superpixel method outperforms the original and another advanced superpixel algorithm in terms of both boundary recall and under-segmentation error. Our framework was applied to cross-section and lateral section images of regenerated muscle fibers from confetti-fluorescent mice. Compared with "ground-truth" segmentations, our framework yielded median Dice similarity coefficients of 0.92 and higher. Our segmentation framework is flexible and provides very good segmentations of multi-color muscle fibers. We anticipate our methods will be useful for segmenting a variety of tissues in confetti fluorecent mice and in mice with similar multi-color labels.

Differential Ion Mobility Separations in up to 100 % Helium Using Microchips

PubMed Central

Shvartsburg, Alexandre A.; Ibrahim, Yehia M.; Smith, Richard D.

2014-01-01

The performance of differential IMS (FAIMS) analyzers is much enhanced by gases comprising He, especially He/N2 mixtures. However, electrical breakdown has limited the He fraction to ~50 %–75 %, depending on the field strength. By the Paschen law, the threshold field for breakdown increases at shorter distances. This allows FAIMS using chips with microscopic channels to utilize much stronger field intensities (E) than “full-size” analyzers with wider gaps. Here we show that those chips can employ higher He fractions up to 100 %. Use of He-rich gases improves the resolution and resolution/sensitivity balance substantially, although less than for full-size analyzers. The optimum He fraction is ~80 %, in line with first-principles theory. Hence, one can now measure the dependences of ion mobility on E in pure He, where ion-molecule cross section calculations are much more tractable than in other gases that form deeper and more complex interaction potentials. This capability may facilitate quantitative modeling of high-field ion mobility behavior and, thus, FAIMS separation properties, which would enable a priori extraction of structural information about the ions. PMID:24402673

Microchip Yb:CaLnAlO4 lasers with up to 91% slope efficiency.

PubMed

Loiko, Pavel; Serres, Josep Maria; Mateos, Xavier; Xu, Xiaodong; Xu, Jun; Jambunathan, Venkatesan; Navratil, Petr; Lucianetti, Antonio; Mocek, Tomas; Zhang, Xuzhao; Griebner, Uwe; Petrov, Valentin; Aguiló, Magdalena; Díaz, Francesc; Major, Arkady

2017-07-01

Multi-watt continuous-wave (CW) operation of tetragonal rare-earth calcium aluminate Yb:CaLnAlO 4 (Ln=Gd,Y)) crystals in plano-plano microchip lasers was demonstrated with an almost quantum-defect-limited slope efficiency. Pumped at 978 nm by an InGaAs laser diode, a 3.4 mm long 8 at. % Yb:CaGdAlO 4 laser generated 7.79 W at 1057-1065 nm with a slope efficiency of η=84% (with respect to the absorbed pump power). An even higher η=91% was achieved with a 2.5 mm long 3 at. % Yb:CaYAlO 4 laser, from which 5.06 W were extracted at 1048-1056 nm. Both lasers produced linearly polarized output (σ-polarization) with an almost circular diffraction-limited beam (Mx,y2<1.1). The output performance of the developed lasers was modeled, yielding an internal loss coefficient as low as 0.004-0.007  cm -1 . In addition, their spectroscopic properties were revisited.

Nanostructured gold microelectrodes for SERS and EIS measurements by incorporating ZnO nanorod growth with electroplating

PubMed Central

Zong, Xianli; Zhu, Rong; Guo, Xiaoliang

2015-01-01

In this paper, a fine gold nanostructure synthesized on selective planar microelectrodes in micro-chip is realized by using an advanced hybrid fabrication approach incorporating growth of nanorods (NRs) with gold electroplating. By this developed nanostructure, integration of in-situ surface-enhanced Raman spectroscopy (SERS) detection with electrochemical impedance spectroscopy (EIS) measurement for label-free, nondestructive, real-time and rapid monitoring on a single cell has been achieved. Moreover, parameters of Au nanostructures such as size of nanoholes/nanogaps can be controllably adjusted in the fabrication. We have demonstrated a SERS enhancement factor of up to ~2.24 × 106 and double-layer impedance decrease ratio of 90% ~ 95% at low frequency range below 200 kHz by using nanostructured microelectrodes. SERS detection and in-situ EIS measurement of a trapped single cell by using planar microelectrodes are realized to demonstrate the compatibility, multi-functions, high-sensitivity and simplicity of the micro-chip system. This dual function platform integrating SERS and EIS is of great significance in biological, biochemical and biomedical applications. PMID:26558325

Photonic crystal microchip laser

NASA Astrophysics Data System (ADS)

Gailevicius, D.; Koliadenko, V.; Purlys, V.; Peckus, M.; Taranenko, V.; Staliunas, K.

2017-02-01

The microchip lasers, being sources of coherent light, suffer from one serious drawback: low spatial quality of the beam, strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here we propose that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. We experimentally show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by factor of 2, and thus increase the brightness of radiation by a factor of 4. This comprises a new kind of laser, the "photonic crystal microchip laser", a very compact and efficient light source emitting high spatial high brightness radiation.

Photonic Crystal Microchip Laser.

PubMed

Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

2016-09-29

The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M 2 reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the "photonic crystal microchip laser", a very compact and efficient light source emitting high spatial quality high brightness radiation.

Miniature fiber Bragg grating sensor interrogator (FBG-Transceiver) system

NASA Astrophysics Data System (ADS)

Mendoza, Edgar A.; Kempen, Cornelia; Lopatin, Craig

2007-04-01

This paper describes recent progress conducted towards the development of a miniature fiber Bragg grating sensor interrogator (FBG-Transceiver TM) system based on multi-channel integrated optic sensor (InOSense TM) microchip technology. The hybrid InOSense TM microchip technology enables the integration of all of the functionalities, both passive and active, of conventional bench top FBG sensor interrogator systems, packaged in a miniaturized, low power operation, 2-cm x 5-cm package suitable for the long-term structural health monitoring in applications where size, weight, and power are critical for operation. The FBG-Transceiver system uses active optoelectronic components monolithically integrated to the InOSense TM microchip, a microprocessor controlled signal processing electronics board capable of processing the FBG sensors signals related to stress-strain and temperature as well as vibration and acoustics. The FBG-Transceiver TM system represents a new, reliable, highly robust technology that can be used to accurately monitor the status of an array of distributed fiber optic Bragg grating sensors installed in critical infrastructures. Its miniature package, low power operation, and state-of-the-art data communications architecture, all at a very affordable price makes it a very attractive solution for a large number of SHM/NDI applications in aerospace, naval and maritime industry, civil structures like bridges, buildings and dams, the oil and chemical industry, and for homeland security applications. The miniature, cost-efficient FBG-Transceiver TM system is poised to revolutionize the field of structural health monitoring and nondestructive inspection market. The sponsor of this program is NAVAIR under a DOD SBIR contract.

InSight's Second Microchip

NASA Image and Video Library

2018-01-23

Technicians at Lockheed Martin Space in Littleton, Colorado installed a microchip with 1.6 million names submitted by the public to ride along with NASA's InSight mission to Mars. The chip was installed on Jan. 23, 2018. This joins another microchip that was previously installed that included 800,000 names for a grand total of 2.4 million names going to Mars as early as May 5, 2018. The microchip including names from the NASA InSight mission's "Send Your Name to Mars" campaign was affixed to the spacecraft with a special glue. https://photojournal.jpl.nasa.gov/catalog/PIA22206

Self-correcting multi-atlas segmentation

NASA Astrophysics Data System (ADS)

Gao, Yi; Wilford, Andrew; Guo, Liang

2016-03-01

In multi-atlas segmentation, one typically registers several atlases to the new image, and their respective segmented label images are transformed and fused to form the final segmentation. After each registration, the quality of the registration is reflected by the single global value: the final registration cost. Ideally, if the quality of the registration can be evaluated at each point, independent of the registration process, which also provides a direction in which the deformation can further be improved, the overall segmentation performance can be improved. We propose such a self-correcting multi-atlas segmentation method. The method is applied on hippocampus segmentation from brain images and statistically significantly improvement is observed.

Production, Cost and Chip Characteristics of In-Woods Microchipping

Treesearch

J. Thompson; W. Sprinkle

2013-01-01

Emerging markets for biomass have increased the interest in producing microchips in the field. As a component of a large United States Department of Energy (DOE) funded project, microchipping has been trialed on a limited scale. The goal of the research was to evaluate the production, cost and chip characteristics of a mobile disc chipper configured to produce...

Development of a real-time microchip PCR system for portable plant disease diagnosis.

PubMed

Koo, Chiwan; Malapi-Wight, Martha; Kim, Hyun Soo; Cifci, Osman S; Vaughn-Diaz, Vanessa L; Ma, Bo; Kim, Sungman; Abdel-Raziq, Haron; Ong, Kevin; Jo, Young-Ki; Gross, Dennis C; Shim, Won-Bo; Han, Arum

2013-01-01

Rapid and accurate detection of plant pathogens in the field is crucial to prevent the proliferation of infected crops. Polymerase chain reaction (PCR) process is the most reliable and accepted method for plant pathogen diagnosis, however current conventional PCR machines are not portable and require additional post-processing steps to detect the amplified DNA (amplicon) of pathogens. Real-time PCR can directly quantify the amplicon during the DNA amplification without the need for post processing, thus more suitable for field operations, however still takes time and require large instruments that are costly and not portable. Microchip PCR systems have emerged in the past decade to miniaturize conventional PCR systems and to reduce operation time and cost. Real-time microchip PCR systems have also emerged, but unfortunately all reported portable real-time microchip PCR systems require various auxiliary instruments. Here we present a stand-alone real-time microchip PCR system composed of a PCR reaction chamber microchip with integrated thin-film heater, a compact fluorescence detector to detect amplified DNA, a microcontroller to control the entire thermocycling operation with data acquisition capability, and a battery. The entire system is 25 × 16 × 8 cm(3) in size and 843 g in weight. The disposable microchip requires only 8-µl sample volume and a single PCR run consumes 110 mAh of power. A DNA extraction protocol, notably without the use of liquid nitrogen, chemicals, and other large lab equipment, was developed for field operations. The developed real-time microchip PCR system and the DNA extraction protocol were used to successfully detect six different fungal and bacterial plant pathogens with 100% success rate to a detection limit of 5 ng/8 µl sample.

Development of a Real-Time Microchip PCR System for Portable Plant Disease Diagnosis

PubMed Central

Kim, Hyun Soo; Cifci, Osman S.; Vaughn-Diaz, Vanessa L.; Ma, Bo; Kim, Sungman; Abdel-Raziq, Haron; Ong, Kevin; Jo, Young-Ki; Gross, Dennis C.; Shim, Won-Bo; Han, Arum

2013-01-01

Rapid and accurate detection of plant pathogens in the field is crucial to prevent the proliferation of infected crops. Polymerase chain reaction (PCR) process is the most reliable and accepted method for plant pathogen diagnosis, however current conventional PCR machines are not portable and require additional post-processing steps to detect the amplified DNA (amplicon) of pathogens. Real-time PCR can directly quantify the amplicon during the DNA amplification without the need for post processing, thus more suitable for field operations, however still takes time and require large instruments that are costly and not portable. Microchip PCR systems have emerged in the past decade to miniaturize conventional PCR systems and to reduce operation time and cost. Real-time microchip PCR systems have also emerged, but unfortunately all reported portable real-time microchip PCR systems require various auxiliary instruments. Here we present a stand-alone real-time microchip PCR system composed of a PCR reaction chamber microchip with integrated thin-film heater, a compact fluorescence detector to detect amplified DNA, a microcontroller to control the entire thermocycling operation with data acquisition capability, and a battery. The entire system is 25×16×8 cm3 in size and 843 g in weight. The disposable microchip requires only 8-µl sample volume and a single PCR run consumes 110 mAh of power. A DNA extraction protocol, notably without the use of liquid nitrogen, chemicals, and other large lab equipment, was developed for field operations. The developed real-time microchip PCR system and the DNA extraction protocol were used to successfully detect six different fungal and bacterial plant pathogens with 100% success rate to a detection limit of 5 ng/8 µl sample. PMID:24349341

Multi-object model-based multi-atlas segmentation for rodent brains using dense discrete correspondences

NASA Astrophysics Data System (ADS)

Lee, Joohwi; Kim, Sun Hyung; Styner, Martin

2016-03-01

The delineation of rodent brain structures is challenging due to low-contrast multiple cortical and subcortical organs that are closely interfacing to each other. Atlas-based segmentation has been widely employed due to its ability to delineate multiple organs at the same time via image registration. The use of multiple atlases and subsequent label fusion techniques has further improved the robustness and accuracy of atlas-based segmentation. However, the accuracy of atlas-based segmentation is still prone to registration errors; for example, the segmentation of in vivo MR images can be less accurate and robust against image artifacts than the segmentation of post mortem images. In order to improve the accuracy and robustness of atlas-based segmentation, we propose a multi-object, model-based, multi-atlas segmentation method. We first establish spatial correspondences across atlases using a set of dense pseudo-landmark particles. We build a multi-object point distribution model using those particles in order to capture inter- and intra- subject variation among brain structures. The segmentation is obtained by fitting the model into a subject image, followed by label fusion process. Our result shows that the proposed method resulted in greater accuracy than comparable segmentation methods, including a widely used ANTs registration tool.

Correlative fluorescence and scanning transmission electron microscopy of quantum dot-labeled proteins on whole cells in liquid.

PubMed

Peckys, Diana B; Bandmann, Vera; de Jonge, Niels

2014-01-01

Correlative fluorescence microscopy combined with scanning transmission electron microscopy (STEM) of cells fully immersed in liquid is a new methodology with many application areas. Proteins, in live cells immobilized on microchips, are labeled with fluorescent quantum dot nanoparticles. In this protocol, the epidermal growth factor receptor (EGFR) is labeled. The cells are fixed after a selected labeling time, for example, 5 min as needed to form EGFR dimers. The microchip with cells is then imaged with fluorescence microscopy. Thereafter, STEM can be accomplished in two ways. The microchip with the labeled cells and one microchip with a spacer are assembled into a special microfluidic device and imaged with dedicated high-voltage STEM. Alternatively, thin edges of cells can be studied with environmental scanning electron microscopy with a STEM detector, by placing a microchip with cells in a cooled wet environment. © 2014 Elsevier Inc. All rights reserved.

Characteristics of High-Resolution Hemoglobin Measurement Microchip Integrated with Signal Processing Circuit

NASA Astrophysics Data System (ADS)

Noda, Toshihiko; Takao, Hidekuni; Ashiki, Mitsuaki; Ebi, Hiroyuki; Sawada, Kazuaki; Ishida, Makoto

2004-04-01

In this study, a microchip for measurement of hemoglobin in human blood has been proposed, fabricated and evaluated. The measurement principle of hemoglobin is based on the “cyanmethemoglobin method” that calculates the cyanmethemoglobin concentration by absorption photometry. A glass/silicon/silicon structure was used for the microchip. The middle silicon layer includes flow channels, and 45° mirrors formed at each end of the flow channels. Photodiodes and metal oxide semiconductor (MOS) integrated circuits were fabricated on the bottom silicon layer. The performance of the microchip for hemoglobin measurement was evaluated using a solution of red food color instead of a real blood sample. The fabricated microchip exhibited a similar performance to a nonminiaturized absorption cell which has the same optical path length. Signal processing output varied with solution concentration from 5.32 V to 5.55 V with very high stability due to differential signal processing.

Photonic Crystal Microchip Laser

NASA Astrophysics Data System (ADS)

Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

2016-09-01

The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the “photonic crystal microchip laser”, a very compact and efficient light source emitting high spatial quality high brightness radiation.

Photonic Crystal Microchip Laser

PubMed Central

Gailevicius, Darius; Koliadenko, Volodymyr; Purlys, Vytautas; Peckus, Martynas; Taranenko, Victor; Staliunas, Kestutis

2016-01-01

The microchip lasers, being very compact and efficient sources of coherent light, suffer from one serious drawback: low spatial quality of the beam strongly reducing the brightness of emitted radiation. Attempts to improve the beam quality, such as pump-beam guiding, external feedback, either strongly reduce the emission power, or drastically increase the size and complexity of the lasers. Here it is proposed that specially designed photonic crystal in the cavity of a microchip laser, can significantly improve the beam quality. Experiments show that a microchip laser, due to spatial filtering functionality of intracavity photonic crystal, improves the beam quality factor M2 reducing it by a factor of 2, and increase the brightness of radiation by a factor of 3. This comprises a new kind of laser, the “photonic crystal microchip laser”, a very compact and efficient light source emitting high spatial quality high brightness radiation. PMID:27683066

Coupling Microdialysis Sampling to Microchip Electrophoresis in a Reversibly Sealed Device

PubMed Central

Mecker, Laura C.; Martin, R. Scott

2007-01-01

In this paper, we describe the fabrication and characterization of a reversibly sealed microchip device that is used to couple microdialysis sampling to microchip electrophoresis. The ability to interface microdialysis sampling and microchip electrophoresis in a device that is amenable to reversible sealing is advantageous from a repeated use standpoint. Commercially available tubing coming from the microdialysis probe is directly inserted into the chip and flow from the probe is interfaced to the electrophoresis portion of the device through integrated pneumatic valves. Fluorescence detection was used to characterize the poly(dimethylsiloxane)-based device in terms of injection reproducibility. It was found that the entire system (microdialysis probe and microchip device) has a concentration response lag time of 170 sec. Microdialysis sampling followed by an electrophoretic separation of amino acids derivatized with naphthalene-2,3-dicarboxaldehyde/cyanide was also demonstrated. PMID:18836517

Acupuncture injection for field amplified sample stacking and glass microchip-based capillary gel electrophoresis.

PubMed

Ha, Ji Won; Hahn, Jong Hoon

2017-02-01

Acupuncture sample injection is a simple method to deliver well-defined nanoliter-scale sample plugs in PDMS microfluidic channels. This acupuncture injection method in microchip CE has several advantages, including minimization of sample consumption, the capability of serial injections of different sample solutions into the same microchannel, and the capability of injecting sample plugs into any desired position of a microchannel. Herein, we demonstrate that the simple and cost-effective acupuncture sample injection method can be used for PDMS microchip-based field amplified sample stacking in the most simplified straight channel by applying a single potential. We achieved the increase in electropherogram signals for the case of sample stacking. Furthermore, we present that microchip CGE of ΦX174 DNA-HaeⅢ digest can be performed with the acupuncture injection method on a glass microchip while minimizing sample loss and voltage control hardware. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Parallel separations using capillary electrophoresis on a multilane microchip with multiplexed laser-induced fluorescence detection.

PubMed

Nikcevic, Irena; Piruska, Aigars; Wehmeyer, Kenneth R; Seliskar, Carl J; Limbach, Patrick A; Heineman, William R

2010-08-01

Parallel separations using CE on a multilane microchip with multiplexed LIF detection is demonstrated. The detection system was developed to simultaneously record data on all channels using an expanded laser beam for excitation, a camera lens to capture emission, and a CCD camera for detection. The detection system enables monitoring of each channel continuously and distinguishing individual lanes without significant crosstalk between adjacent lanes. Multiple analytes can be determined in parallel lanes within a single microchip in a single run, leading to increased sample throughput. The pK(a) determination of small molecule analytes is demonstrated with the multilane microchip.

Parallel separations using capillary electrophoresis on a multilane microchip with multiplexed laser induced fluorescence detection

PubMed Central

Nikcevic, Irena; Piruska, Aigars; Wehmeyer, Kenneth R.; Seliskar, Carl J.; Limbach, Patrick A.; Heineman, William R.

2010-01-01

Parallel separations using capillary electrophoresis on a multilane microchip with multiplexed laser induced fluorescence detection is demonstrated. The detection system was developed to simultaneously record data on all channels using an expanded laser beam for excitation, a camera lens to capture emission, and a CCD camera for detection. The detection system enables monitoring of each channel continuously and distinguishing individual lanes without significant crosstalk between adjacent lanes. Multiple analytes can be analyzed on parallel lanes within a single microchip in a single run, leading to increased sample throughput. The pKa determination of small molecule analytes is demonstrated with the multilane microchip. PMID:20737446

Intelligent multi-spectral IR image segmentation

NASA Astrophysics Data System (ADS)

Lu, Thomas; Luong, Andrew; Heim, Stephen; Patel, Maharshi; Chen, Kang; Chao, Tien-Hsin; Chow, Edward; Torres, Gilbert

2017-05-01

This article presents a neural network based multi-spectral image segmentation method. A neural network is trained on the selected features of both the objects and background in the longwave (LW) Infrared (IR) images. Multiple iterations of training are performed until the accuracy of the segmentation reaches satisfactory level. The segmentation boundary of the LW image is used to segment the midwave (MW) and shortwave (SW) IR images. A second neural network detects the local discontinuities and refines the accuracy of the local boundaries. This article compares the neural network based segmentation method to the Wavelet-threshold and Grab-Cut methods. Test results have shown increased accuracy and robustness of this segmentation scheme for multi-spectral IR images.

Simultaneous segmentation of the bone and cartilage surfaces of a knee joint in 3D

NASA Astrophysics Data System (ADS)

Yin, Y.; Zhang, X.; Anderson, D. D.; Brown, T. D.; Hofwegen, C. Van; Sonka, M.

2009-02-01

We present a novel framework for the simultaneous segmentation of multiple interacting surfaces belonging to multiple mutually interacting objects. The method is a non-trivial extension of our previously reported optimal multi-surface segmentation. Considering an example application of knee-cartilage segmentation, the framework consists of the following main steps: 1) Shape model construction: Building a mean shape for each bone of the joint (femur, tibia, patella) from interactively segmented volumetric datasets. Using the resulting mean-shape model - identification of cartilage, non-cartilage, and transition areas on the mean-shape bone model surfaces. 2) Presegmentation: Employment of iterative optimal surface detection method to achieve approximate segmentation of individual bone surfaces. 3) Cross-object surface mapping: Detection of inter-bone equidistant separating sheets to help identify corresponding vertex pairs for all interacting surfaces. 4) Multi-object, multi-surface graph construction and final segmentation: Construction of a single multi-bone, multi-surface graph so that two surfaces (bone and cartilage) with zero and non-zero intervening distances can be detected for each bone of the joint, according to whether or not cartilage can be locally absent or present on the bone. To define inter-object relationships, corresponding vertex pairs identified using the separating sheets were interlinked in the graph. The graph optimization algorithm acted on the entire multiobject, multi-surface graph to yield a globally optimal solution. The segmentation framework was tested on 16 MR-DESS knee-joint datasets from the Osteoarthritis Initiative database. The average signed surface positioning error for the 6 detected surfaces ranged from 0.00 to 0.12 mm. When independently initialized, the signed reproducibility error of bone and cartilage segmentation ranged from 0.00 to 0.26 mm. The results showed that this framework provides robust, accurate, and reproducible segmentation of the knee joint bone and cartilage surfaces of the femur, tibia, and patella. As a general segmentation tool, the developed framework can be applied to a broad range of multi-object segmentation problems.

Multi-atlas segmentation enables robust multi-contrast MRI spleen segmentation for splenomegaly

NASA Astrophysics Data System (ADS)

Huo, Yuankai; Liu, Jiaqi; Xu, Zhoubing; Harrigan, Robert L.; Assad, Albert; Abramson, Richard G.; Landman, Bennett A.

2017-02-01

Non-invasive spleen volume estimation is essential in detecting splenomegaly. Magnetic resonance imaging (MRI) has been used to facilitate splenomegaly diagnosis in vivo. However, achieving accurate spleen volume estimation from MR images is challenging given the great inter-subject variance of human abdomens and wide variety of clinical images/modalities. Multi-atlas segmentation has been shown to be a promising approach to handle heterogeneous data and difficult anatomical scenarios. In this paper, we propose to use multi-atlas segmentation frameworks for MRI spleen segmentation for splenomegaly. To the best of our knowledge, this is the first work that integrates multi-atlas segmentation for splenomegaly as seen on MRI. To address the particular concerns of spleen MRI, automated and novel semi-automated atlas selection approaches are introduced. The automated approach interactively selects a subset of atlases using selective and iterative method for performance level estimation (SIMPLE) approach. To further control the outliers, semi-automated craniocaudal length based SIMPLE atlas selection (L-SIMPLE) is proposed to introduce a spatial prior in a fashion to guide the iterative atlas selection. A dataset from a clinical trial containing 55 MRI volumes (28 T1 weighted and 27 T2 weighted) was used to evaluate different methods. Both automated and semi-automated methods achieved median DSC > 0.9. The outliers were alleviated by the L-SIMPLE (≍1 min manual efforts per scan), which achieved 0.9713 Pearson correlation compared with the manual segmentation. The results demonstrated that the multi-atlas segmentation is able to achieve accurate spleen segmentation from the multi-contrast splenomegaly MRI scans.

Multi-atlas Segmentation Enables Robust Multi-contrast MRI Spleen Segmentation for Splenomegaly.

PubMed

Huo, Yuankai; Liu, Jiaqi; Xu, Zhoubing; Harrigan, Robert L; Assad, Albert; Abramson, Richard G; Landman, Bennett A

2017-02-11

Non-invasive spleen volume estimation is essential in detecting splenomegaly. Magnetic resonance imaging (MRI) has been used to facilitate splenomegaly diagnosis in vivo. However, achieving accurate spleen volume estimation from MR images is challenging given the great inter-subject variance of human abdomens and wide variety of clinical images/modalities. Multi-atlas segmentation has been shown to be a promising approach to handle heterogeneous data and difficult anatomical scenarios. In this paper, we propose to use multi-atlas segmentation frameworks for MRI spleen segmentation for splenomegaly. To the best of our knowledge, this is the first work that integrates multi-atlas segmentation for splenomegaly as seen on MRI. To address the particular concerns of spleen MRI, automated and novel semi-automated atlas selection approaches are introduced. The automated approach interactively selects a subset of atlases using selective and iterative method for performance level estimation (SIMPLE) approach. To further control the outliers, semi-automated craniocaudal length based SIMPLE atlas selection (L-SIMPLE) is proposed to introduce a spatial prior in a fashion to guide the iterative atlas selection. A dataset from a clinical trial containing 55 MRI volumes (28 T1 weighted and 27 T2 weighted) was used to evaluate different methods. Both automated and semi-automated methods achieved median DSC > 0.9. The outliers were alleviated by the L-SIMPLE (≈1 min manual efforts per scan), which achieved 0.9713 Pearson correlation compared with the manual segmentation. The results demonstrated that the multi-atlas segmentation is able to achieve accurate spleen segmentation from the multi-contrast splenomegaly MRI scans.

A Real Time System for Multi-Sensor Image Analysis through Pyramidal Segmentation

DTIC Science & Technology

1992-01-30

A Real Time Syte for M~ulti- sensor Image Analysis S. E I0 through Pyramidal Segmentation/ / c •) L. Rudin, S. Osher, G. Koepfler, J.9. Morel 7. ytu...experiments with reconnaissance photography, multi- sensor satellite imagery, medical CT and MRI multi-band data have shown a great practi- cal potential...C ,SF _/ -- / WSM iS-I-0-d41-40450 $tltwt, kw" I (nor.- . Z-97- A real-time system for multi- sensor image analysis through pyramidal segmentation

Band-broadening suppressed effect in long turned geometry channel and high-sensitive analysis of DNA sample by using floating electrokinetic supercharging on a microchip.

PubMed

Xu, Zhongqi; Murata, Kenji; Arai, Akihiro; Hirokawa, Takeshi

2010-03-12

A featured microchip owning three big reservoirs and long turned geometry channel was designed to improve the detection limit of DNA fragments by using floating electrokinetic supercharging (FEKS) method. The novel design matches the FEKS preconcentration needs of a large sample volume introduction with electrokinetic injection (EKI), as well as long duration of isotachophoresis (ITP) process to enrich low concentration sample. In the curved channel [ approximately 45.6 mm long between port 1 (P1) and the intersection point of two channels], EKI and ITP were performed while the side port 3 (P3) was electrically floated. The turn-induced band broadening with or without ITP process was investigated by a computer simulation (using CFD-ACE+ software) when the analytes traveling through the U-shaped geometry. It was found that the channel curvature determined the extent of band broadening, however, which could be effectively eliminated by the way of ITP. After the ITP-stacked zones passed the intersection point from P1, they were rapidly destacked for separation and detection from ITP to zone electrophoresis by using leading ions from P3. The FEKS carried on the novel chip successfully contributed to higher sensitivities of DNA fragments in comparison with our previous results realized on either a single channel or a cross microchip. The analysis of low concentration 50 bp DNA step ladders (0.23 mugml after 1500-fold diluted) was achieved with normal UV detection at 260 nm. The obtained limit of detections (LODs) were on average 100 times better than using conventional pinched injection, down to several ngml for individual DNA fragment.

A reusable device for electrochemical applications of hydrogel supported black lipid membranes.

PubMed

Mech-Dorosz, Agnieszka; Heiskanen, Arto; Bäckström, Sania; Perry, Mark; Muhammad, Haseena B; Hélix-Nielsen, Claus; Emnéus, Jenny

2015-02-01

Black lipid membranes (BLMs) are significant in studies of membrane transport, incorporated proteins/ion transporters, and hence in construction of biosensor devices. Although BLMs provide an accepted mimic of cellular membranes, they are inherently fragile. Techniques are developed to stabilize them, such as hydrogel supports. In this paper, we present a reusable device for studies on hydrogel supported (hs) BLMs. These are formed across an ethylene tetrafluoroethylene (ETFE) aperture array supported by the hydrogel, which is during in situ polymerization covalently "sandwiched" between the ETFE substrate and a gold electrode microchip, thus allowing direct electrochemical studies with the integrated working electrodes. Using electrochemical impedance spectroscopy (EIS), X-ray photoelectron spectroscopy and contact angle measurements, we demonstrate the optimized chemical modifications of the gold electrode microchips and plasma modification of the ETFE aperture arrays facilitating covalent "sandwiching" of the hydrogel. Both fluorescence microscopy and EIS were used to demonstrate the induced spontaneous thinning of a deposited lipid solution, leading to formation of stabilized hsBLMs on average in 10 min. The determined specific membrane capacitance and resistance were shown to vary in the range 0.31-0.49 μF/cm(2) and 45-65 kΩ cm(2), respectively, corresponding to partially solvent containing BLMs with an average life time of 60-80 min. The characterized hsBLM formation and devised equivalent circuit models lead to a schematic model to illustrate lipid molecule distribution in hydrogel-supported apertures. The functionality of stabilized hsBLMs and detection sensitivity of the platform were verified by monitoring the effect of the ion transporter valinomycin.

Monolithic thermally bonded Er3+, Yb3+:glass/Co2+:MgAl2O4 microchip lasers

NASA Astrophysics Data System (ADS)

Mlynczak, Jaroslaw; Belghachem, Nabil

2015-12-01

The highest ever reported 10 kW peak power in monolithic thermally bonded Er3+, Yb3+:glass/Co2+:MgAl2O4 microchip laser was achieved. To show the superiority of monolithic microchip lasers over those with external mirrors the laser generation characteristics of the same samples in both cases were compared.

[Comparison of susceptibility artifacts generated by microchips with different geometry at 1.5 Tesla magnet resonance imaging. A phantom pilot study referring to the ASTM standard test method F2119-07].

PubMed

Dengg, S; Kneissl, S

2013-01-01

Ferromagnetic material in microchips, used for animal identification, causes local signal increase, signal void or distortion (susceptibility artifact) on MR images. To measure the impact of microchip geometry on the artifact's size, an MRI phantom study was performed. Microchips of the labels Datamars®, Euro-I.D.® and Planet-ID® (n  =  15) were placed consecutively in a phantom and examined with respect to the ASTM Standard Test Method F2119-07 using spin echo (TR 500 ms, TE 20 ms), gradient echo (TR 300 ms, TE 15 ms, flip angel 30°) and otherwise constant imaging parameters (slice thickness 3 mm, field of view 250 x 250 mm, acquisition matrix 256 x 256 pixel, bandwidth 32 kHz) at 1.5 Tesla. Image acquisition was undertaken with a microchip positioned in the x- and z-direction and in each case with a phase-encoding direction in the y- and z-direction. The artifact size was determined with a) a measurement according to the test method F2119-07 using a homogeneous point operation, b) signal intensity measurement according to Matsuura et al. and c) pixel counts in the artifact according to Port and Pomper. There was a significant difference in artifact size between the three microchips tested (Wilcoxon p = 0.032). A two- to three-fold increase in microchip volume generated an up to 76% larger artifact, depending on the sequence type, phase-encoding direction and chip position to B0. The smaller the microchip geometry, the less is the susceptibility artifact. Spin echoes (SE) generated smaller artifacts than gradient echoes (GE). In relation to the spatial measurement of the artifact, the switch in phase-encoding direction had less influence on the artifact size in GE- than in SE-sequences. However, the artifact shape and direction of SE-sequences can be changed by altering the phase. The artifact size, caused by the microchip, plays a major clinical role in the evaluation of MRI from the head, shoulder and neck regions.

Zeta potential of microfluidic substrates: 1. Theory, experimental techniques, and effects on separations.

PubMed

Kirby, Brian J; Hasselbrink, Ernest F

2004-01-01

This paper summarizes theory, experimental techniques, and the reported data pertaining to the zeta potential of silica and silicon with attention to use as microfluidic substrate materials, particularly for microchip chemical separations. Dependence on cation concentration, buffer and cation type, pH, cation valency, and temperature are discussed. The Debye-Hückel limit, which is often correctly treated as a good approximation for describing the ion concentration in the double layer, can lead to serious errors if it is extended to predict the dependence of zeta potential on the counterion concentration. For indifferent univalent electrolytes (e.g., sodium and potassium), two simple scalings for the dependence of zeta potential on counterion concentration can be derived in high- and low-zeta limits of the nonlinear Poisson-Boltzman equation solution in the double layer. It is shown that for most situations relevant to microchip separations, the high-zeta limit is most applicable, leading to the conclusion that the zeta potential on silica substrates is approximately proportional to the logarithm of the molar counterion concentration. The zeta vs. pH dependence measurements from several experiments are compared by normalizing the zeta based on concentration.

Jansen-MIDAS: A multi-level photomicrograph segmentation software based on isotropic undecimated wavelets.

PubMed

de Siqueira, Alexandre Fioravante; Cabrera, Flávio Camargo; Nakasuga, Wagner Massayuki; Pagamisse, Aylton; Job, Aldo Eloizo

2018-01-01

Image segmentation, the process of separating the elements within a picture, is frequently used for obtaining information from photomicrographs. Segmentation methods should be used with reservations, since incorrect results can mislead when interpreting regions of interest (ROI). This decreases the success rate of extra procedures. Multi-Level Starlet Segmentation (MLSS) and Multi-Level Starlet Optimal Segmentation (MLSOS) were developed to be an alternative for general segmentation tools. These methods gave rise to Jansen-MIDAS, an open-source software. A scientist can use it to obtain several segmentations of hers/his photomicrographs. It is a reliable alternative to process different types of photomicrographs: previous versions of Jansen-MIDAS were used to segment ROI in photomicrographs of two different materials, with an accuracy superior to 89%. © 2017 Wiley Periodicals, Inc.

Novel Hg2+-Induced Nephropathy in Rats and Mice Lacking Mrp2: Evidence of Axial Heterogeneity in the Handling of Hg2+ Along the Proximal Tubule

PubMed Central

Zalups, Rudolfs K.; Joshee, Lucy; Bridges, Christy C.

2014-01-01

The role of the multi-resistance protein 2 (Mrp2) in the nephropathy induced by inorganic mercuric mercury (Hg2+) was studied in rats (TR−) and mice (Mrp2−/−), which lack functional Mrp2, and control animals. Animals were exposed to nephrotoxic doses of HgCl2. Forty-eight or 24 hours after exposure, tissues were harvested and analyzed for Hg content and markers of injury. Histological analyses revealed that the proximal tubular segments affected pathologically by Hg2+ were significantly different between Mrp2-deficient animals and controls. In the absence of Mrp2, cellular injury localized almost exclusively in proximal tubular segments in the subcapsular (S1) to midcortical regions (early S2) of the kidney. In control animals, cellular death occurred mainly in the proximal tubular segments in the inner cortex (late S2) and outer stripe of the outer medulla (S3). These differences in renal pathology indicate that axial heterogeneity exists along the proximal tubule with respect to how mercuric ions are handled. Total renal and hepatic accumulation of mercury was also greater in animals lacking Mrp2 than in controls, indicating that Mrp2 normally plays a significant role in eliminating mercuric ions from within proximal tubular cells and hepatocytes. Analyses of plasma creatinine, BUN, and renal expression of Kim-1 and Ngal tend to support the severity of the nephropathies detected histologically. Collectively, our findings indicate that a fraction of mercuric ions is normally secreted by Mrp2 in early portions of proximal tubules into the lumen and then is absorbed downstream in straight portions, where mercuric species typically induce toxic effects. PMID:25145654

Microchip electrophoresis for wine analysis.

PubMed

Gomez, Federico J V; Silva, M Fernanda

2016-12-01

The present critical review provides a summary of representative articles describing the analysis of wine by microchip electrophoresis. Special emphasis has been given to those compounds able to provide background information to achieve the differentiation of wines according to botanical origin, provenance, vintage and quality or assure wine authentication. This review focuses on capillary electrophoresis (CE) microchips dedicated to the analysis of wine covering all the contributions concerning this area. The most relevant compounds in wine analysis such as phenols, organic acids, inorganic species, aldehydes, sugars, alcohols, and neuroactive amines were considered. Moreover, a special section is dedicated to the potential of CE microchip for wine classification. Indeed, potential directions for the future are discussed.

A hydrodynamic microchip for formation of continuous cell chains

NASA Astrophysics Data System (ADS)

Khoshmanesh, Khashayar; Zhang, Wei; Tang, Shi-Yang; Nasabi, Mahyar; Soffe, Rebecca; Tovar-Lopez, Francisco J.; Rajadas, Jayakumar; Mitchell, Arnan

2014-05-01

Here, we demonstrate the unique features of a hydrodynamic based microchip for creating continuous chains of model yeast cells. The system consists of a disk shaped microfluidic structure, containing narrow orifices that connect the main channel to an array of spoke channels. Negative pressure provided by a syringe pump draws fluid from the main channel through the narrow orifices. After cleaning process, a thin layer of water is left between the glass substrate and the polydimethylsiloxane microchip, enabling leakage beneath the channel walls. A mechanical clamp is used to adjust the operation of the microchip. Relaxing the clamp allows leakage of liquid beneath the walls in a controllable fashion, leading to formation of a long cell chain evenly distributed along the channel wall. The unique features of the microchip are demonstrated by creating long chains of yeast cells and model 15 μm polystyrene particles along the side wall and analysing the hydrogen peroxide induced death of patterned cells.

Microchip transponder thermometry for monitoring core body temperature of antelope during capture.

PubMed

Rey, Benjamin; Fuller, Andrea; Hetem, Robyn S; Lease, Hilary M; Mitchell, Duncan; Meyer, Leith C R

2016-01-01

Hyperthermia is described as the major cause of morbidity and mortality associated with capture, immobilization and restraint of wild animals. Therefore, accurately determining the core body temperature of wild animals during capture is crucial for monitoring hyperthermia and the efficacy of cooling procedures. We investigated if microchip thermometry can accurately reflect core body temperature changes during capture and cooling interventions in the springbok (Antidorcas marsupialis), a medium-sized antelope. Subcutaneous temperature measured with a temperature-sensitive microchip was a weak predictor of core body temperature measured by temperature-sensitive data loggers in the abdominal cavity (R(2)=0.32, bias >2 °C). Temperature-sensitive microchips in the gluteus muscle, however, provided an accurate estimate of core body temperature (R(2)=0.76, bias=0.012 °C). Microchips inserted into muscle therefore provide a convenient and accurate method to measure body temperature continuously in captured antelope, allowing detection of hyperthermia and the efficacy of cooling procedures. Copyright © 2015 Elsevier Ltd. All rights reserved.

A low timing jitter picosecond microchip laser pumped by pulsed LD

NASA Astrophysics Data System (ADS)

Wang, Sha; Wang, Yan-biao; Feng, Guoying; Zhou, Shou-huan

2016-07-01

SESAM passively Q-switched microchip laser is a very promising instrument to replace mode locked lasers to obtain picosecond pulses. The biggest drawback of a passively Q-switched microchip laser is its un-avoided large timing jitter, especially when the pump intensity is low, i.e. at low laser repetition rate range. In order to obtain a low timing jitter passively Q-switched picosecond microchip laser in the whole laser repetition rate range, a 1000 kHz pulsed narrow bandwidth Fiber Bragg Grating (FBG) stablized laser diode was used as the pump source. By tuning the pump intensity, we could control the output laser frequency. In this way, we achieved a very low timing jitter passively Q-switched picosecond laser at 2.13 mW, 111.1 kHz. The relative timing jitter was only 0.0315%, which was around 100 times smaller compared with a cw LD pumped microchip working at hundred kilohertz repetition rate frequency range.

12  mJ Yb:YAG/Cr:YAG microchip laser.

PubMed

Guo, Xiaoyang; Tokita, Shigeki; Kawanaka, Junji

2018-02-01

We have developed a quasi-continuous wave diode end-pumped cryogenically cooled Yb:YAG/Cr:YAG passively Q-switched microchip laser. A maximum energy of 12.1 mJ with 3.7 MW of peak power was obtained. To the best of our knowledge, this is the highest energy and peak power obtained by an Yb:YAG/Cr:YAG microchip laser so far.

Sea-land segmentation for infrared remote sensing images based on superpixels and multi-scale features

NASA Astrophysics Data System (ADS)

Lei, Sen; Zou, Zhengxia; Liu, Dunge; Xia, Zhenghuan; Shi, Zhenwei

2018-06-01

Sea-land segmentation is a key step for the information processing of ocean remote sensing images. Traditional sea-land segmentation algorithms ignore the local similarity prior of sea and land, and thus fail in complex scenarios. In this paper, we propose a new sea-land segmentation method for infrared remote sensing images to tackle the problem based on superpixels and multi-scale features. Considering the connectivity and local similarity of sea or land, we interpret the sea-land segmentation task in view of superpixels rather than pixels, where similar pixels are clustered and the local similarity are explored. Moreover, the multi-scale features are elaborately designed, comprising of gray histogram and multi-scale total variation. Experimental results on infrared bands of Landsat-8 satellite images demonstrate that the proposed method can obtain more accurate and more robust sea-land segmentation results than the traditional algorithms.

Consistent cortical reconstruction and multi-atlas brain segmentation.

PubMed

Huo, Yuankai; Plassard, Andrew J; Carass, Aaron; Resnick, Susan M; Pham, Dzung L; Prince, Jerry L; Landman, Bennett A

2016-09-01

Whole brain segmentation and cortical surface reconstruction are two essential techniques for investigating the human brain. Spatial inconsistences, which can hinder further integrated analyses of brain structure, can result due to these two tasks typically being conducted independently of each other. FreeSurfer obtains self-consistent whole brain segmentations and cortical surfaces. It starts with subcortical segmentation, then carries out cortical surface reconstruction, and ends with cortical segmentation and labeling. However, this "segmentation to surface to parcellation" strategy has shown limitations in various cohorts such as older populations with large ventricles. In this work, we propose a novel "multi-atlas segmentation to surface" method called Multi-atlas CRUISE (MaCRUISE), which achieves self-consistent whole brain segmentations and cortical surfaces by combining multi-atlas segmentation with the cortical reconstruction method CRUISE. A modification called MaCRUISE(+) is designed to perform well when white matter lesions are present. Comparing to the benchmarks CRUISE and FreeSurfer, the surface accuracy of MaCRUISE and MaCRUISE(+) is validated using two independent datasets with expertly placed cortical landmarks. A third independent dataset with expertly delineated volumetric labels is employed to compare segmentation performance. Finally, 200MR volumetric images from an older adult sample are used to assess the robustness of MaCRUISE and FreeSurfer. The advantages of MaCRUISE are: (1) MaCRUISE constructs self-consistent voxelwise segmentations and cortical surfaces, while MaCRUISE(+) is robust to white matter pathology. (2) MaCRUISE achieves more accurate whole brain segmentations than independently conducting the multi-atlas segmentation. (3) MaCRUISE is comparable in accuracy to FreeSurfer (when FreeSurfer does not exhibit global failures) while achieving greater robustness across an older adult population. MaCRUISE has been made freely available in open source. Copyright © 2016 Elsevier Inc. All rights reserved.

A scalable correlator for multichannel diffuse correlation spectroscopy.

PubMed

Stapels, Christopher J; Kolodziejski, Noah J; McAdams, Daniel; Podolsky, Matthew J; Fernandez, Daniel E; Farkas, Dana; Christian, James F

2016-02-01

Diffuse correlation spectroscopy (DCS) is a technique which enables powerful and robust non-invasive optical studies of tissue micro-circulation and vascular blood flow. The technique amounts to autocorrelation analysis of coherent photons after their migration through moving scatterers and subsequent collection by single-mode optical fibers. A primary cost driver of DCS instruments are the commercial hardware-based correlators, limiting the proliferation of multi-channel instruments for validation of perfusion analysis as a clinical diagnostic metric. We present the development of a low-cost scalable correlator enabled by microchip-based time-tagging, and a software-based multi-tau data analysis method. We will discuss the capabilities of the instrument as well as the implementation and validation of 2- and 8-channel systems built for live animal and pre-clinical settings.

Segment Fixed Priority Scheduling for Self Suspending Real Time Tasks

DTIC Science & Technology

2016-08-11

Segment-Fixed Priority Scheduling for Self-Suspending Real -Time Tasks Junsung Kim, Department of Electrical and Computer Engineering, Carnegie...4 2.1 Application of a Multi-Segment Self-Suspending Real -Time Task Model ............................. 5 3 Fixed Priority Scheduling...1 Figure 2: A multi-segment self-suspending real -time task model

Multi-object segmentation using coupled nonparametric shape and relative pose priors

NASA Astrophysics Data System (ADS)

Uzunbas, Mustafa Gökhan; Soldea, Octavian; Çetin, Müjdat; Ünal, Gözde; Erçil, Aytül; Unay, Devrim; Ekin, Ahmet; Firat, Zeynep

2009-02-01

We present a new method for multi-object segmentation in a maximum a posteriori estimation framework. Our method is motivated by the observation that neighboring or coupling objects in images generate configurations and co-dependencies which could potentially aid in segmentation if properly exploited. Our approach employs coupled shape and inter-shape pose priors that are computed using training images in a nonparametric multi-variate kernel density estimation framework. The coupled shape prior is obtained by estimating the joint shape distribution of multiple objects and the inter-shape pose priors are modeled via standard moments. Based on such statistical models, we formulate an optimization problem for segmentation, which we solve by an algorithm based on active contours. Our technique provides significant improvements in the segmentation of weakly contrasted objects in a number of applications. In particular for medical image analysis, we use our method to extract brain Basal Ganglia structures, which are members of a complex multi-object system posing a challenging segmentation problem. We also apply our technique to the problem of handwritten character segmentation. Finally, we use our method to segment cars in urban scenes.

Ion conduction in crystalline superionic solids and its applications

NASA Astrophysics Data System (ADS)

Chandra, Angesh

2014-06-01

Superionic solids an area of multidisciplinary research activity, incorporates to study the physical, chemical and technological aspects of rapid ion movements within the bulk of the special class of ionic materials. It is an emerging area of materials science, as these solids show tremendous technological scopes to develop wide variety of solid state electrochemical devices such as batteries, fuel cells, supercapacitors, sensors, electrochromic displays (ECDs), memories, etc. These devices have wide range of applicabilities viz. power sources for IC microchips to transport vehicles, novel sensors for controlling atmospheric pollution, new kind of memories for computers, smart windows/display panels, etc. The field grew with a rapid pace since then, especially with regards to designing new materials as well as to explore their device potentialities. Amongst the known superionic solids, fast Ag+ ion conducting crystalline solid electrolytes are attracted special attention due to their relatively higher room temperature conductivity as well as ease of materials handling/synthesis. Ion conduction in these electrolytes is very much interesting part of today. In the present review article, the ion conducting phenomenon and some device applications of crystalline/polycrystalline superionic solid electrolytes have been reviewed in brief. Synthesis and characterization tools have also been discussed in the present review article.

Spectroscopy and microchip laser operation of Tm, Ho:KYW crystals with different Ho concentrations

NASA Astrophysics Data System (ADS)

Gusakova, N. V.; Kurilchik, S. V.; Yasukevich, A. S.; Kisel, V. E.; Dashkevich, V. I.; Orlovich, V. A.; Pavlyuk, A. A.; Vatnik, S. M.; Bagaev, S. N.; Kuleshov, N. V.

2018-02-01

The spectroscopic properties of Tm, Ho:KYW crystals with different Ho concentrations were investigated. The diode-pumped microchip laser operation of Tm (5 at.%), Ho (0.5 at.%):KYW and Tm (5 at.%), Ho (1 at.%):KYW was demonstrated. The highest, to our knowledge, output power of 480 mW with slope efficiency of 31% for CW Tm (5 at.%), Ho (0.5 at.%):KYW microchip laser was obtained.

Continuous-wave and Q-switched microchip laser performance of Yb:Y3Sc2Al3O12 crystals.

PubMed

Dong, Jun; Ueda, Ken-ichi; Kaminskii, Alexander A

2008-04-14

Optical properties of Yb:Y(3)Sc(2)Al(3)O(12) crystal were investigated and compared with those from Yb:YAG crystals. The broad absorption and emission spectra of Yb:Y(3)Sc(2)Al(3)O(12) show that this crystal is very suitable for laser-diode pumping and ultrafast laser pulse generation. Laser-diode pumped continuous-wave and passively Q-switched Yb:Y(3)Sc(2)Al(3)O(12) lasers with Cr(4+):YAG crystals as saturable absorber have been demonstrated for the first time. Continuous-wave output power of 1.12 W around 1032 nm (multi-longitudinal modes) was measured with an optical-to-optical efficiency of 30%. Laser pulses with pulse energy of over 31 microJ and pulse width of 2.5 ns were measured at repetition rate of over 12.7 kHz; a corresponding peak power of over 12 kW was obtained. The longitudinal mode selection by a thin plate of Cr(4+):YAG as an intracavity etalon was also observed in passively Q-switched Yb:Y(3)Sc(2)Al(2)O(12) microchip lasers.

Corpus callosum segmentation using deep neural networks with prior information from multi-atlas images

NASA Astrophysics Data System (ADS)

Park, Gilsoon; Hong, Jinwoo; Lee, Jong-Min

2018-03-01

In human brain, Corpus Callosum (CC) is the largest white matter structure, connecting between right and left hemispheres. Structural features such as shape and size of CC in midsagittal plane are of great significance for analyzing various neurological diseases, for example Alzheimer's disease, autism and epilepsy. For quantitative and qualitative studies of CC in brain MR images, robust segmentation of CC is important. In this paper, we present a novel method for CC segmentation. Our approach is based on deep neural networks and the prior information generated from multi-atlas images. Deep neural networks have recently shown good performance in various image processing field. Convolutional neural networks (CNN) have shown outstanding performance for classification and segmentation in medical image fields. We used convolutional neural networks for CC segmentation. Multi-atlas based segmentation model have been widely used in medical image segmentation because atlas has powerful information about the target structure we want to segment, consisting of MR images and corresponding manual segmentation of the target structure. We combined the prior information, such as location and intensity distribution of target structure (i.e. CC), made from multi-atlas images in CNN training process for more improving training. The CNN with prior information showed better segmentation performance than without.

A linearly-polarized Nd:YVO4/KTP microchip green laser.

PubMed

Jung, C; Yu, B-A; Kim, I-S; Lee, Y L; Yu, N E; Ko, D-K

2009-10-26

We described the principle and the fabrication of a Nd:YVO(4)/KTP microchip for the linearly-polarized green laser and verified its availability by manufacturing and characterizing the green laser using the microchip. Under the driving condition having the modulation frequency of 60 Hz and the duty ratio of 25%, the laser showed the stable linear polarization, the maximum average power of 37 mW, yielding the high electrical-to-optical efficiency of 10.9%.

A Sol-Gel-Modified Poly(methyl methacrylate) Electrophoresis Microchip with a Hydrophilic Channel Wall

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Gang; Xu, Xuejiao; Lin, Yuehe

2007-07-27

A sol-gel method was employed to fabricate a poly(methyl methacrylate) (PMMA) electrophoresis microchip that contains a hydrophilic channel wall. To fabricate such a device, tetraethoxysilane (TEOS) was injected into the PMMA channel and was allowed to diffuse into the surface layer for 24 h. After removing the excess TEOS, the channel was filled with an acidic solution for 3 h. Subsequently, the channel was flushed with water and was pretreated in an oven to obtain a sol-gel-modified PMMA microchip. The water contact angle for the sol-gel-modified PMMA was 27.4° compared with 66.3° for the pure PMMA. In addition, the electro-osmoticmore » flow increased from 2.13×10-4 cm2 V-1 s-1 for the native-PMMA channel to 4.86×10-4 cm2 V-1 s-1 for the modified one. The analytical performance of the sol-gel-modified PMMA microchip was demonstrated for the electrophoretic separation of several purines, coupled with amperometric detection. The separation efficiency of uric acid increased to 74 882.3 m-1 compared with 14 730.5 m-1 for native-PMMA microchips. The result of this simple modification is a significant improvement in the performance of PMMA for microchip electrophoresis and microfluidic applications.« less

Microchip assays for screening monoclonal antibody product quality.

PubMed

Chen, Xiaoyu; Tang, Kaiyan; Lee, Maximilian; Flynn, Gregory C

2008-12-01

Microchip CE-SDS was evaluated as a high-throughput alternative to conventional CE-SDS for monitoring monoclonal antibody protein quality. A commercial instrument (LabChip) 90) was used to separate dodecyl sulfate coated proteins through a sieving polymer based on the proteins' sizes. Under reducing conditions, the microchip CE-SDS separation was similar to that of conventional CE-SDS, providing reasonable resolution of the non-glycosylated and the glycosylated heavy chains. The fluorescence detection on LabChip 90 using non-covalent fluorescent labeling method was about as sensitive as the 220 nm UV detection used in a conventional CE instrument. A simple glycan typing assay was developed for the reducing microchip CE-SDS format. Antibodies, either pure or in crude cell culture media are treated with Endoglycosidase H, which specifically cleaves the hybrid and high mannose type glycans. A heavy chain migration shift on reducing CE-SDS resulting from the loss of glycan is used to measure the level of high mannose/hybrid type glycans as a percentage of the total glycans. Microchip CE-SDS, under both non-reducing and reducing conditions, can be used in a variety of antibody product screening assays. The microchip analyses provide sufficient resolution and sensitivity for this purpose but on a time scale approximately 70 times faster (41 s versus 50 min per sample) than conventional CE separation under typical operational conditions.

Printed Flexible Plastic Microchip for Viral Load Measurement through Quantitative Detection of Viruses in Plasma and Saliva

PubMed Central

Shafiee, Hadi; Kanakasabapathy, Manoj Kumar; Juillard, Franceline; Keser, Mert; Sadasivam, Magesh; Yuksekkaya, Mehmet; Hanhauser, Emily; Henrich, Timothy J.; Kuritzkes, Daniel R.; Kaye, Kenneth M.; Demirci, Utkan

2015-01-01

We report a biosensing platform for viral load measurement through electrical sensing of viruses on a flexible plastic microchip with printed electrodes. Point-of-care (POC) viral load measurement is of paramount importance with significant impact on a broad range of applications, including infectious disease diagnostics and treatment monitoring specifically in resource-constrained settings. Here, we present a broadly applicable and inexpensive biosensing technology for accurate quantification of bioagents, including viruses in biological samples, such as plasma and artificial saliva, at clinically relevant concentrations. Our microchip fabrication is simple and mass-producible as we print microelectrodes on flexible plastic substrates using conductive inks. We evaluated the microchip technology by detecting and quantifying multiple Human Immunodeficiency Virus (HIV) subtypes (A, B, C, D, E, G, and panel), Epstein-Barr Virus (EBV), and Kaposi’s Sarcoma-associated Herpes Virus (KSHV) in a fingerprick volume (50 µL) of PBS, plasma, and artificial saliva samples for a broad range of virus concentrations between 102 copies/mL and 107 copies/mL. We have also evaluated the microchip platform with discarded, de-identified HIV-infected patient samples by comparing our microchip viral load measurement results with reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) as the gold standard method using Bland-Altman Analysis. PMID:26046668

Improved hydrostatic pressure sample injection by tilting the microchip towards the disposable miniaturized CE device.

PubMed

Wang, Wei; Zhou, Fang; Zhao, Liang; Zhang, Jian-Rong; Zhu, Jun-Jie

2008-02-01

A simple method of hydrostatic pressure sample injection towards a disposable microchip CE device was developed. The liquid level in the sample reservoir was higher than that in the sample waste reservoir (SWR) by tilting microchip and hydrostatic pressure was generated, the sample was driven to pass through injection channel into SWR. After sample loading, the microchip was levelled for separation under applied high separation voltage. Effects of tilted angle, initial liquid height and injection duration on electrophoresis were investigated. With enough injection duration, the injection result was little affected by tilted angle and initial liquid heights in the reservoirs. Injection duration for obtaining a stable sample plug was mainly dependent on the tilted angle rather than the initial height of liquid. Experimental results were consistent with theoretical prediction. Fluorescence observation and electrochemical detection of dopamine and catechol were employed to verify the feasibility of tilted microchip hydrostatic pressure injection. Good reproducibility of this injection method was obtained. Because the instrumentation was simplified and no additional hardware was needed in this technology, the proposed method would be potentially useful in disposable devices.

A simple strategy for in situ fabrication of a smart hydrogel microvalve within microchannels for thermostatic control.

PubMed

Lin, Shuo; Wang, Wei; Ju, Xiao-Jie; Xie, Rui; Chu, Liang-Yin

2014-08-07

Self-regulation of temperature in microchip systems is crucial for their applications in biomedical fields such as cell culture and biomolecule synthesis as well as those cases that require constant temperature conditions. Here we report on a simple and versatile approach for in situ fabrication of a smart hydrogel microvalve within a microchip for thermostatic control. The thermo-responsive hydrogel microvalve enables the "on-off" switch by sensing temperature fluctuations to control the fluid flux as well as the fluid heat exchange for self-regulation of the temperature at a constant range. Such temperature self-regulation is demonstrated by integrating the microvalve-incorporated microchip into the flow circulation loop of a micro-heat-exchanging system for thermostatic control. Moreover, the microvalve-incorporated microchip is employed for culturing cells under temperature self-regulation. The smart microvalve shows great potential as a temperature controller for applications that require thermostatic conditions. This approach offers a facile and flexible strategy for in situ fabricating hydrogel microvalves within microchips as chemostats and microreactors for biomedical applications.

Mechanically Resilient Polymeric Films Doped with a Lithium Compound

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Kinder, James D. (Inventor)

2005-01-01

This invention is a series of mechanically resilient polymeric films, comprising rod-coil block polyimide copolymers, which are doped with a lithium compound providing lithium ion conductivity, that are easy to fabricate into mechanically resilient films with acceptable ionic or protonic conductivity at a variety of temperatures. The copolymers consists of short-rigid polyimide rod segments alternating with polyether coil segments. The rods and coil segments can be linear, branched or mixtures of linear and branched segments. The highly incompatible rods and coil segments phase separate, providing nanoscale channels for ion conduction. The polyimide segments provide dimensional and mechanical stability and can be functionalized in a number of ways to provide specialized functions for a given application. These rod-coil black polyimide copolymers are particularly useful in the preparation of ion conductive membranes for use in the manufacture of fuel cells and lithium based polymer batteries.

Automatic abdominal multi-organ segmentation using deep convolutional neural network and time-implicit level sets.

PubMed

Hu, Peijun; Wu, Fa; Peng, Jialin; Bao, Yuanyuan; Chen, Feng; Kong, Dexing

2017-03-01

Multi-organ segmentation from CT images is an essential step for computer-aided diagnosis and surgery planning. However, manual delineation of the organs by radiologists is tedious, time-consuming and poorly reproducible. Therefore, we propose a fully automatic method for the segmentation of multiple organs from three-dimensional abdominal CT images. The proposed method employs deep fully convolutional neural networks (CNNs) for organ detection and segmentation, which is further refined by a time-implicit multi-phase evolution method. Firstly, a 3D CNN is trained to automatically localize and delineate the organs of interest with a probability prediction map. The learned probability map provides both subject-specific spatial priors and initialization for subsequent fine segmentation. Then, for the refinement of the multi-organ segmentation, image intensity models, probability priors as well as a disjoint region constraint are incorporated into an unified energy functional. Finally, a novel time-implicit multi-phase level-set algorithm is utilized to efficiently optimize the proposed energy functional model. Our method has been evaluated on 140 abdominal CT scans for the segmentation of four organs (liver, spleen and both kidneys). With respect to the ground truth, average Dice overlap ratios for the liver, spleen and both kidneys are 96.0, 94.2 and 95.4%, respectively, and average symmetric surface distance is less than 1.3 mm for all the segmented organs. The computation time for a CT volume is 125 s in average. The achieved accuracy compares well to state-of-the-art methods with much higher efficiency. A fully automatic method for multi-organ segmentation from abdominal CT images was developed and evaluated. The results demonstrated its potential in clinical usage with high effectiveness, robustness and efficiency.

Comparison of rectal, microchip transponder, and infrared thermometry techniques for obtaining body temperature in the laboratory rabbit (Oryctolagus cuniculus).

PubMed

Chen, Patty H; White, Charles E

2006-01-01

This study compared rabbit rectal thermometry with 4 other thermometry techniques: an implantable microchip temperature transponder, an environmental noncontact infrared thermometer, a tympanic infrared thermometer designed for use on humans, and a tympanic infrared thermometer designed for use on animals. The microchip transponder was implanted between the shoulder blades; the environmental noncontact infrared thermometer recorded results from the base of the right pinna and the left inner thigh, and the tympanic infrared thermometer temperatures were taken from the right ear. Results from each technique were compared to determine agreement between the test modality and the rectal temperature. The practicality and reliability of the modalities were reviewed also. According to this study, the implantable microchip transponder measurements agreed most closely with the rectal temperature.

Further improvement of hydrostatic pressure sample injection for microchip electrophoresis.

PubMed

Luo, Yong; Zhang, Qingquan; Qin, Jianhua; Lin, Bingcheng

2007-12-01

Hydrostatic pressure sample injection method is able to minimize the number of electrodes needed for a microchip electrophoresis process; however, it neither can be applied for electrophoretic DNA sizing, nor can be implemented on the widely used single-cross microchip. This paper presents an injector design that makes the hydrostatic pressure sample injection method suitable for DNA sizing. By introducing an assistant channel into the normal double-cross injector, a rugged DNA sample plug suitable for sizing can be successfully formed within the cross area during the sample loading. This paper also demonstrates that the hydrostatic pressure sample injection can be performed in the single-cross microchip by controlling the radial position of the detection point in the separation channel. Rhodamine 123 and its derivative as model sample were successfully separated.

Microchip-associated fibrosarcoma in a cat.

PubMed

Carminato, Antonio; Vascellari, Marta; Marchioro, Wendy; Melchiotti, Erica; Mutinelli, Franco

2011-12-01

A 9-year-old, neutered male cat was presented for a subcutaneous mass on the neck. After surgical removal of the mass, a pet identification microchip was found within the tumour. Histological examination of the mass revealed typical features of the feline postinjection sarcoma. The cat had never received injections at the tumour site; all routine vaccinations were administered in the hindlimbs. Few cases of sarcomas developing at the site of microchip application have been reported in animals, although the contributory role of vaccine administrations has not been ruled out. This is the first report of a microchip-associated fibrosarcoma in a cat. Adherence to American Association of Feline Practitioners vaccination guidelines, avoiding the interscapular area, enabled confirmation of the definitive aetiology of the neoplasia. © 2011 The Authors. Veterinary Dermatology. © 2011 ESVD and ACVD.

Rectangular pulsed LD pumped saturable output coupler (SOC) Q-switched microchip laser

NASA Astrophysics Data System (ADS)

Wang, Yan-biao; Wang, Sha; Feng, Guo-ying; Zhou, Shou-huan

2017-02-01

We studied the cw LD and rectangular pulsed LD pumped saturable output coupler (SOC) passively Q-switched Nd:YVO4 transmission microchip laser experimentally. We demonstrated that the SOC passively Q-switched Nd:YVO4 transmission microchip laser pumped by a highly stabilized narrow bandwidth pulsed LD has a much lower timing jitter than pumped by a continuous wave (CW) LD, especially at low output frequency regime. By changing the pump beam size in the rectangular shape pulsed pump scheme, the output frequency can be achieved from 333.3 kHz to 71.4 kHz, while the relative timing jitter decreased from 0.09865% to 0.03115% accordingly. Additionally, the microchip laser has a good stability of output power, the power fluctuation below 2%.

A Multi-Objective Decision Making Approach for Solving the Image Segmentation Fusion Problem.

PubMed

Khelifi, Lazhar; Mignotte, Max

2017-08-01

Image segmentation fusion is defined as the set of methods which aim at merging several image segmentations, in a manner that takes full advantage of the complementarity of each one. Previous relevant researches in this field have been impeded by the difficulty in identifying an appropriate single segmentation fusion criterion, providing the best possible, i.e., the more informative, result of fusion. In this paper, we propose a new model of image segmentation fusion based on multi-objective optimization which can mitigate this problem, to obtain a final improved result of segmentation. Our fusion framework incorporates the dominance concept in order to efficiently combine and optimize two complementary segmentation criteria, namely, the global consistency error and the F-measure (precision-recall) criterion. To this end, we present a hierarchical and efficient way to optimize the multi-objective consensus energy function related to this fusion model, which exploits a simple and deterministic iterative relaxation strategy combining the different image segments. This step is followed by a decision making task based on the so-called "technique for order performance by similarity to ideal solution". Results obtained on two publicly available databases with manual ground truth segmentations clearly show that our multi-objective energy-based model gives better results than the classical mono-objective one.

Local SIMPLE multi-atlas-based segmentation applied to lung lobe detection on chest CT

NASA Astrophysics Data System (ADS)

Agarwal, M.; Hendriks, E. A.; Stoel, B. C.; Bakker, M. E.; Reiber, J. H. C.; Staring, M.

2012-02-01

For multi atlas-based segmentation approaches, a segmentation fusion scheme which considers local performance measures may be more accurate than a method which uses a global performance measure. We improve upon an existing segmentation fusion method called SIMPLE and extend it to be localized and suitable for multi-labeled segmentations. We demonstrate the algorithm performance on 23 CT scans of COPD patients using a leave-one- out experiment. Our algorithm performs significantly better (p < 0.01) than majority voting, STAPLE, and SIMPLE, with a median overlap of the fissure of 0.45, 0.48, 0.55 and 0.6 for majority voting, STAPLE, SIMPLE, and the proposed algorithm, respectively.

Apparatus and method for performing microfluidic manipulations for chemical analysis

DOEpatents

Ramsey, J. Michael

1999-01-01

A microchip apparatus and method provide fluidic manipulations for a variety of applications, including sample injection for microchip liquid chromatography. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis is performed in channels formed in the substrate. Injections are made by electro-osmotically pumping sample through the injection channel that crosses the separation channel, followed by a switching of the potentials to force a plug into the separation channel.

Apparatus and method for performing microfluidic manipulations for chemical analysis

DOEpatents

Ramsey, J. Michael

2002-01-01

A microchip apparatus and method provide fluidic manipulations for a variety of applications, including sample injection for microchip liquid chromatography. The microchip is fabricated using standard photolitographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis is performed in channels formed in the substrate. Injections are made by electro-osmotically pumping sample through the injection channel that crosses the separation channel, followed by a switching of the potentials to force a plug into the separation channel.

12 mJ Yb:YAG/Cr:YAG microchip laser

NASA Astrophysics Data System (ADS)

Guo, Xiaoyang; Tokita, Shigeki; Kawanaka, Junji

2018-02-01

By cryogenically cooling the Yb:YAG/Cr:YAG medium, one can break through the damage limit of Yb:YAG/Cr:YAG passively Q-switched microchip lasers at room temperature and thus achieve a shorter minimum pulse duration. In the proof of principle experiment we carried out, a 160.6 ps pulse duration was obtained. To the best of our knowledge, this is the first realization of sub-200 ps pulse operation for an Yb:YAG/Cr:YAG microchip laser

Practical application of pulsed "eye-safe" microchip laser to laser rangefinders

NASA Astrophysics Data System (ADS)

Młyńczak, J.; Kopczyński, K.; Mierczyk, Z.; Zygmunt, M.; Natkański, S.; Muzal, M.; Wojtanowski, J.; Kirwil, P.; Jakubaszek, M.; Knysak, P.; Piotrowski, W.; Zarzycka, A.; Gawlikowski, A.

2013-09-01

The paper describes practical application of pulsed microchip laser generating at 1535-nm wavelength to a laser rangefinder. The complete prototype of a laser rangefinder was built and investigated in real environmental conditions. The measured performance of the device is discussed. To build the prototype of a laser rangefinder at a reasonable price and shape a number of basic considerations had to be done. These include the mechanical and optical design of a microchip laser and the opto-mechanical construction of the rangefinder.

Decoupling of ion conductivity from segmental dynamics in oligomeric ethylene oxide functionalized oxanorbornene dicarboximide homopolymers

DOE PAGES

Adams, Marisa; Richmond, Victoria; Smith, Douglas; ...

2017-03-24

Here, in order to design more effective solid polymer electrolytes, it is important to decouple ion conductivityfrom polymer segmental motion. To that end, novel polymers based on oxanorbornene dicarboximidemonomers with varying lengths of oligomeric ethylene oxide side chains have been synthesized usingring opening metathesis polymerization. These unique polymers have a fairly rigid and bulky backboneand were used to investigate the decoupling of ion motion from polymer segmental dynamics. Ionconductivity was measured using broadband dielectric spectroscopy for varying levels of added lithiumsalt. The conductivity data demonstrate six to seven orders of separation in timescale of ion conductivityfrom polymer segmental motion formore » polymers with shorter ethylene oxide side chains. However,commensurate changes in the glass transition temperatures T g reduce the effect of decoupling in ionconductivity and lead to lower conductivity at ambient conditions. These results suggest that both anincrease in decoupling and a reduction in T g might be required to develop solid polymer electrolytes withhigh ion conductivity at room temperature.« less

Joint multi-object registration and segmentation of left and right cardiac ventricles in 4D cine MRI

NASA Astrophysics Data System (ADS)

Ehrhardt, Jan; Kepp, Timo; Schmidt-Richberg, Alexander; Handels, Heinz

2014-03-01

The diagnosis of cardiac function based on cine MRI requires the segmentation of cardiac structures in the images, but the problem of automatic cardiac segmentation is still open, due to the imaging characteristics of cardiac MR images and the anatomical variability of the heart. In this paper, we present a variational framework for joint segmentation and registration of multiple structures of the heart. To enable the simultaneous segmentation and registration of multiple objects, a shape prior term is introduced into a region competition approach for multi-object level set segmentation. The proposed algorithm is applied for simultaneous segmentation of the myocardium as well as the left and right ventricular blood pool in short axis cine MRI images. Two experiments are performed: first, intra-patient 4D segmentation with a given initial segmentation for one time-point in a 4D sequence, and second, a multi-atlas segmentation strategy is applied to unseen patient data. Evaluation of segmentation accuracy is done by overlap coefficients and surface distances. An evaluation based on clinical 4D cine MRI images of 25 patients shows the benefit of the combined approach compared to sole registration and sole segmentation.

Multi-scales region segmentation for ROI separation in digital mammograms

NASA Astrophysics Data System (ADS)

Zhang, Dapeng; Zhang, Di; Li, Yue; Wang, Wei

2017-02-01

Mammography is currently the most effective imaging modality used by radiologists for the screening of breast cancer. Segmentation is one of the key steps in the process of developing anatomical models for calculation of safe medical dose of radiation. This paper explores the potential of the statistical region merging segmentation technique for Breast segmentation in digital mammograms. First, the mammograms are pre-processing for regions enhancement, then the enhanced images are segmented using SRM with multi scales, finally these segmentations are combined for region of interest (ROI) separation and edge detection. The proposed algorithm uses multi-scales region segmentation in order to: separate breast region from background region, region edge detection and ROIs separation. The experiments are performed using a data set of mammograms from different patients, demonstrating the validity of the proposed criterion. Results show that, the statistical region merging segmentation algorithm actually can work on the segmentation of medical image and more accurate than another methods. And the outcome shows that the technique has a great potential to become a method of choice for segmentation of mammograms.

Estimating the concentration of gold nanoparticles incorporated on natural rubber membranes using multi-level starlet optimal segmentation

NASA Astrophysics Data System (ADS)

de Siqueira, A. F.; Cabrera, F. C.; Pagamisse, A.; Job, A. E.

2014-12-01

This study consolidates multi-level starlet segmentation (MLSS) and multi-level starlet optimal segmentation (MLSOS) techniques for photomicrograph segmentation, based on starlet wavelet detail levels to separate areas of interest in an input image. Several segmentation levels can be obtained using MLSS; after that, Matthews correlation coefficient is used to choose an optimal segmentation level, giving rise to MLSOS. In this paper, MLSOS is employed to estimate the concentration of gold nanoparticles with diameter around 47 nm, reduced on natural rubber membranes. These samples were used for the construction of SERS/SERRS substrates and in the study of the influence of natural rubber membranes with incorporated gold nanoparticles on the physiology of Leishmania braziliensis. Precision, recall, and accuracy are used to evaluate the segmentation performance, and MLSOS presents an accuracy greater than 88 % for this application.

Image Segmentation Method Using Fuzzy C Mean Clustering Based on Multi-Objective Optimization

NASA Astrophysics Data System (ADS)

Chen, Jinlin; Yang, Chunzhi; Xu, Guangkui; Ning, Li

2018-04-01

Image segmentation is not only one of the hottest topics in digital image processing, but also an important part of computer vision applications. As one kind of image segmentation algorithms, fuzzy C-means clustering is an effective and concise segmentation algorithm. However, the drawback of FCM is that it is sensitive to image noise. To solve the problem, this paper designs a novel fuzzy C-mean clustering algorithm based on multi-objective optimization. We add a parameter λ to the fuzzy distance measurement formula to improve the multi-objective optimization. The parameter λ can adjust the weights of the pixel local information. In the algorithm, the local correlation of neighboring pixels is added to the improved multi-objective mathematical model to optimize the clustering cent. Two different experimental results show that the novel fuzzy C-means approach has an efficient performance and computational time while segmenting images by different type of noises.

Design and Experimental Validation of a Simple Controller for a Multi-Segment Magnetic Crawler Robot

DTIC Science & Technology

2015-04-01

Ave, Cambridge, MA USA 02139; bSpace and Naval Warfare (SPAWAR) Systems Center Pacific, San Diego, CA USA 92152 ABSTRACT A novel, multi-segmented...high-level, autonomous control computer. A low-level, embedded microcomputer handles the commands to the driving motors. This paper presents the...to be demonstrated.14 The Unmanned Systems Group at SPAWAR Systems Center Pacific has developed a multi-segment magnetic crawler robot (MSMR

Ionomers for Ion-Conducting Energy Materials

NASA Astrophysics Data System (ADS)

Colby, Ralph

For ionic actuators and battery separators, it is vital to utilize single-ion conducting ionomers that avoid the detrimental polarization of other ions. Single-ion conducting ionomers are synthesized based on DFT calculations, with low glass transition temperatures (facile dynamics) to prepare ion-conducting membranes for battery separators that conduct Li+ or Na+. Characterization by X-ray scattering, dielectric spectroscopy, FTIR, NMR and linear viscoelasticity collectively develop a coherent picture of ionic aggregation and both counterion and polymer dynamics. 7Li NMR diffusion measurements find that diffusion is faster than expected by conductivity using the Nernst-Einstein equation, which means that the majority of Li diffusion occurs by ion pairs moving with the polymer segmental motion. Segmental motion only contributes to ionic conduction in the rare event that one of these ion pairs has an extra Li (a positive triple ion). This leads us to a new metric for ion-conducting soft materials, the product of the cation number density p0 and their diffusion coefficient D; p0D is the diffusive flux of lithium ions. This new metric has a maximum at intermediate ion content that corresponds to the overlap of ion pair polarizability volumes. At higher ion contents, the ion pairs interact strongly and form larger aggregation states that retard segmental motion of both mobile ion pairs and triple ions.

3D multi-scale FCN with random modality voxel dropout learning for Intervertebral Disc Localization and Segmentation from Multi-modality MR Images.

PubMed

Li, Xiaomeng; Dou, Qi; Chen, Hao; Fu, Chi-Wing; Qi, Xiaojuan; Belavý, Daniel L; Armbrecht, Gabriele; Felsenberg, Dieter; Zheng, Guoyan; Heng, Pheng-Ann

2018-04-01

Intervertebral discs (IVDs) are small joints that lie between adjacent vertebrae. The localization and segmentation of IVDs are important for spine disease diagnosis and measurement quantification. However, manual annotation is time-consuming and error-prone with limited reproducibility, particularly for volumetric data. In this work, our goal is to develop an automatic and accurate method based on fully convolutional networks (FCN) for the localization and segmentation of IVDs from multi-modality 3D MR data. Compared with single modality data, multi-modality MR images provide complementary contextual information, which contributes to better recognition performance. However, how to effectively integrate such multi-modality information to generate accurate segmentation results remains to be further explored. In this paper, we present a novel multi-scale and modality dropout learning framework to locate and segment IVDs from four-modality MR images. First, we design a 3D multi-scale context fully convolutional network, which processes the input data in multiple scales of context and then merges the high-level features to enhance the representation capability of the network for handling the scale variation of anatomical structures. Second, to harness the complementary information from different modalities, we present a random modality voxel dropout strategy which alleviates the co-adaption issue and increases the discriminative capability of the network. Our method achieved the 1st place in the MICCAI challenge on automatic localization and segmentation of IVDs from multi-modality MR images, with a mean segmentation Dice coefficient of 91.2% and a mean localization error of 0.62 mm. We further conduct extensive experiments on the extended dataset to validate our method. We demonstrate that the proposed modality dropout strategy with multi-modality images as contextual information improved the segmentation accuracy significantly. Furthermore, experiments conducted on extended data collected from two different time points demonstrate the efficacy of our method on tracking the morphological changes in a longitudinal study. Copyright © 2018 Elsevier B.V. All rights reserved.

Ceramic capillary electrophoresis chip for the measurement of inorganic ions in water samples.

PubMed

Fercher, Georg; Haller, Anna; Smetana, Walter; Vellekoop, Michael J

2010-05-01

We present a microchip capillary electrophoresis (CE) device build-up in low temperature co-fired ceramics (LTCC) multilayer technology for the analysis of major inorganic ions in water samples in less than 80 s. Contactless conductivity measurement is employed as a robust alternative to direct-contact conductivity detection schemes. The measurement electrodes are placed in a planar way at the top side of the CE chip and are realized by screen printing. Laser-cutting of channel and double-T injector structures is used to minimize irregularities and wall defects, elevating plate numbers per meter up to values of 110,000. Lowest limit of detection is 6 microM. The cost efficient LTCC module is attractive particularly for portable instruments in environmental applications because of its chemical inertness, hermeticity and easy three-dimensional integration capabilities of fluidic, electrical and mechanical components.

50 CFR 21.21 - Import and export permits.

Code of Federal Regulations, 2011 CFR

2011-10-01

... with an implanted microchip for identification. (d) Falconry birds covered under a CITES “pet passport... and Wildlife Service leg band issued by the Service, including any raptor with an implanted microchip...

Integration of a Graphite/PMMA CompositeElectrode into a Poly(methyl methacrylate) (PMMA) Substrate for Electrochemical Detection in Microchips

PubMed Central

Regel, Anne; Lunte, Susan

2013-01-01

Traditional fabrication methods for polymer microchips, the bonding of two substrates together to form the microchip, can make the integration of carbon electrodes difficult. We have developed a simple and inexpensive method to integrate graphite/PMMA composite electrodes (GPCEs) into a PMMA substrate. These substrates can be bonded to other PMMA layers using a solvent-assisted thermal bonding method. The optimal composition of the GPCEs for electrochemical detection was determined using cyclic voltammetry with dopamine as a test analyte. Using the optimized GPCEs in an all-PMMA flow cell with flow injection analysis, it was possible to detect 50 nM dopamine under the best conditions. These electrodes were also evaluated for the detection of dopamine and catechol following separation by microchip electrophoresis (ME). PMID:23670816

A review of microdialysis coupled to microchip electrophoresis for monitoring biological events

PubMed Central

Saylor, Rachel A.; Lunte, Susan M.

2015-01-01

Microdialysis is a powerful sampling technique that enables monitoring of dynamic processes in vitro and in vivo. The combination of microdialysis with chromatographic or electrophoretic methods yields along with selective detection methods yields a “separation-based sensor” capable of monitoring multiple analytes in near real time. Analysis of microdialysis samples requires techniques that are fast (<1 min), have low volume requirements (nL–pL), and, ideally, can be employed on-line. Microchip electrophoresis fulfills these requirements and also permits the possibility of integrating sample preparation and manipulation with detection strategies directly on-chip. Microdialysis coupled to microchip electrophoresis has been employed for monitoring biological events in vivo and in vitro. This review discusses technical considerations for coupling microdialysis sampling and microchip electrophoresis, including various interface designs, and current applications in the field. PMID:25637011

Integration of Cell Phone Imaging with Microchip ELISA to Detect Ovarian Cancer HE4 Biomarker in Urine at the Point-of-Care

PubMed Central

Wang, ShuQi; Zhao, Xiaohu; Khimji, Imran; Akbas, Ragip; Qiu, Weiliang; Edwards, Dale; Cramer, Daniel W.; Ye, Bin; Demirci, Utkan

2013-01-01

Ovarian cancer is asymptomatic at early stages and most patients present with advanced levels of disease. Lack of cost-effective methods that can achieve frequent, simple and non-invasive testing hinders early detection and causes high mortality in ovarian cancer patients. Here, we report a simple and inexpensive microchip ELISA-based detection module that employs a portable detection system, i.e., a cell phone/charge-coupled device (CCD) to quantify an ovarian cancer biomarker, HE4, in urine. Integration of a mobile application with a cell phone enabled immediate processing of microchip ELISA results, which eliminated the need for a bulky, expensive spectrophotometer. The HE4 level detected by a cell phone or a lensless CCD system was significantly elevated in urine samples from cancer patients (n = 19) than normal healthy controls (n = 20) (p < 0.001). Receiver operating characteristic (ROC) analyses showed that the microchip ELISA coupled with a cell phone running an automated analysis application had a sensitivity of 89.5% at a specificity of 90%. Under the same specificity, the microchip ELISA coupled with a CCD had a sensitivity of 84.2%. In conclusion, integration of microchip ELISA with cell phone/CCD-based colorimetric measurement technology can be used to detect HE4 biomarker at the point-of-care (POC), paving the way to create bedside technologies for diagnostics and treatment monitoring. PMID:21881677

Polymeric microchip for the simultaneous determination of anions and cations by hydrodynamic injection using a dual-channel sequential injection microchip electrophoresis system.

PubMed

Gaudry, Adam J; Nai, Yi Heng; Guijt, Rosanne M; Breadmore, Michael C

2014-04-01

A dual-channel sequential injection microchip capillary electrophoresis system with pressure-driven injection is demonstrated for simultaneous separations of anions and cations from a single sample. The poly(methyl methacrylate) (PMMA) microchips feature integral in-plane contactless conductivity detection electrodes. A novel, hydrodynamic "split-injection" method utilizes background electrolyte (BGE) sheathing to gate the sample flows, while control over the injection volume is achieved by balancing hydrodynamic resistances using external hydrodynamic resistors. Injection is realized by a unique flow-through interface, allowing for automated, continuous sampling for sequential injection analysis by microchip electrophoresis. The developed system was very robust, with individual microchips used for up to 2000 analyses with lifetimes limited by irreversible blockages of the microchannels. The unique dual-channel geometry was demonstrated by the simultaneous separation of three cations and three anions in individual microchannels in under 40 s with limits of detection (LODs) ranging from 1.5 to 24 μM. From a series of 100 sequential injections the %RSDs were determined for every fifth run, resulting in %RSDs for migration times that ranged from 0.3 to 0.7 (n = 20) and 2.3 to 4.5 for peak area (n = 20). This system offers low LODs and a high degree of reproducibility and robustness while the hydrodynamic injection eliminates electrokinetic bias during injection, making it attractive for a wide range of rapid, sensitive, and quantitative online analytical applications.

Nonlinear resonances in linear segmented Paul trap of short central segment.

PubMed

Kłosowski, Łukasz; Piwiński, Mariusz; Pleskacz, Katarzyna; Wójtewicz, Szymon; Lisak, Daniel

2018-03-23

Linear segmented Paul trap system has been prepared for ion mass spectroscopy experiments. A non-standard approach to stability of trapped ions is applied to explain some effects observed with ensembles of calcium ions. Trap's stability diagram is extended to 3-dimensional one using additional ∆a besides standard q and a stability parameters. Nonlinear resonances in (q,∆a) diagrams are observed and described with a proposed model. The resonance lines have been identified using simple simulations and comparing the numerical and experimental results. The phenomenon can be applied in electron-impact ionization experiments for mass-identification of obtained ions or purification of their ensembles. This article is protected by copyright. All rights reserved.

LINKS: learning-based multi-source IntegratioN frameworK for Segmentation of infant brain images.

PubMed

Wang, Li; Gao, Yaozong; Shi, Feng; Li, Gang; Gilmore, John H; Lin, Weili; Shen, Dinggang

2015-03-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination processes. In the first year of life, the image contrast between white and gray matters of the infant brain undergoes dramatic changes. In particular, the image contrast is inverted around 6-8months of age, and the white and gray matter tissues are isointense in both T1- and T2-weighted MR images and thus exhibit the extremely low tissue contrast, which poses significant challenges for automated segmentation. Most previous studies used multi-atlas label fusion strategy, which has the limitation of equally treating the different available image modalities and is often computationally expensive. To cope with these limitations, in this paper, we propose a novel learning-based multi-source integration framework for segmentation of infant brain images. Specifically, we employ the random forest technique to effectively integrate features from multi-source images together for tissue segmentation. Here, the multi-source images include initially only the multi-modality (T1, T2 and FA) images and later also the iteratively estimated and refined tissue probability maps of gray matter, white matter, and cerebrospinal fluid. Experimental results on 119 infants show that the proposed method achieves better performance than other state-of-the-art automated segmentation methods. Further validation was performed on the MICCAI grand challenge and the proposed method was ranked top among all competing methods. Moreover, to alleviate the possible anatomical errors, our method can also be combined with an anatomically-constrained multi-atlas labeling approach for further improving the segmentation accuracy. Copyright © 2014 Elsevier Inc. All rights reserved.

LINKS: Learning-based multi-source IntegratioN frameworK for Segmentation of infant brain images

PubMed Central

Wang, Li; Gao, Yaozong; Shi, Feng; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

2014-01-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination processes. In the first year of life, the image contrast between white and gray matters of the infant brain undergoes dramatic changes. In particular, the image contrast is inverted around 6-8 months of age, and the white and gray matter tissues are isointense in both T1- and T2-weighted MR images and thus exhibit the extremely low tissue contrast, which poses significant challenges for automated segmentation. Most previous studies used multi-atlas label fusion strategy, which has the limitation of equally treating the different available image modalities and is often computationally expensive. To cope with these limitations, in this paper, we propose a novel learning-based multi-source integration framework for segmentation of infant brain images. Specifically, we employ the random forest technique to effectively integrate features from multi-source images together for tissue segmentation. Here, the multi-source images include initially only the multi-modality (T1, T2 and FA) images and later also the iteratively estimated and refined tissue probability maps of gray matter, white matter, and cerebrospinal fluid. Experimental results on 119 infants show that the proposed method achieves better performance than other state-of-the-art automated segmentation methods. Further validation was performed on the MICCAI grand challenge and the proposed method was ranked top among all competing methods. Moreover, to alleviate the possible anatomical errors, our method can also be combined with an anatomically-constrained multi-atlas labeling approach for further improving the segmentation accuracy. PMID:25541188

Integrated multi-choice goal programming and multi-segment goal programming for supplier selection considering imperfect-quality and price-quantity discounts in a multiple sourcing environment

NASA Astrophysics Data System (ADS)

Chang, Ching-Ter; Chen, Huang-Mu; Zhuang, Zheng-Yun

2014-05-01

Supplier selection (SS) is a multi-criteria and multi-objective problem, in which multi-segment (e.g. imperfect-quality discount (IQD) and price-quantity discount (PQD)) and multi-aspiration level problems may be significantly important; however, little attention had been given to dealing with both of them simultaneously in the past. This study proposes a model for integrating multi-choice goal programming and multi-segment goal programming to solve the above-mentioned problems by providing the following main contributions: (1) it allows decision-makers to set multiple aspiration levels on the right-hand side of each goal to suit real-world situations, (2) the PQD and IQD conditions are considered in the proposed model simultaneously and (3) the proposed model can solve a SS problem with n suppliers where each supplier offers m IQD with r PQD intervals, where only ? extra binary variables are required. The usefulness of the proposed model is explained using a real case. The results indicate that the proposed model not only can deal with a SS problem with multi-segment and multi-aspiration levels, but also can help the decision-maker to find the appropriate order quantities for each supplier by considering cost, quality and delivery.

Elastomeric Microchip Electrospray Emitter for Stable Cone-Jet Mode Operation in the Nano-Flow Regime

PubMed Central

Kelly, Ryan T.; Tang, Keqi; Irimia, Daniel; Toner, Mehmet; Smith, Richard D.

2009-01-01

Despite widespread interest in combining lab-on-a-chip technologies with mass spectrometry (MS)-based analyses, the coupling of microfluidics to electrospray ionization (ESI)-MS remains challenging. We report a robust, integrated poly(dimethylsiloxane) microchip interface for ESI-MS using simple and widely accessible microfabrication procedures. The interface uses an auxiliary channel to provide electrical contact for the stable cone-jet electrospray without sample loss or dilution. The electric field at the channel terminus is enhanced by two vertical cuts that cause the interface to taper to a line rather than to a point, and the formation of a small Taylor cone at the channel exit ensures sub-nL post-column dead volumes. Cone-jet mode electrospray was demonstrated for up to 90% aqueous solutions and for extended durations. Comparable ESI-MS sensitivities were achieved using both microchip and conventional fused silica capillary emitters, but stable cone-jet mode electrosprays could be established over a far broader range of flow rates (from 50-1000 nL/min) and applied potentials using the microchip emitters. This attribute of the microchip emitter should simplify electrospray optimization and make the stable electrospray more resistant to external perturbations. PMID:18419138

A compactly integrated laser-induced fluorescence detector for microchip electrophoresis.

PubMed

Li, Hai-Fang; Lin, Jin-Ming; Su, Rong-Guo; Uchiyama, Katsumi; Hobo, Toshiyuki

2004-06-01

A simple and easy-to-use integrated laser-induced fluorescence detector for microchip electrophoresis was constructed and evaluated. The fluid channels and optical fiber channels in the glass microchip were fabricated using standard photolithographic techniques and wet chemical etching. A 473 nm diode-pumped laser was used as the excitation source, and the collimation and collection optics and mirrors were discarded by using a multimode optical fiber to couple the excitation light straight into the microchannel and placing the microchip directly on the top of the photomultiplier tube. A combination of filter systems was incorporated into a poly(dimethylsiloxane) layer, which was reversibly sealed to the bottom of the microchip to eliminate the scattering excitation light reaching to the photomultiplier tube. Fluorescein/calcein samples were taken as model analytes to evaluate the performance with respect to design factors. The detection limits were 0.05 microM for fluorescein and 0.18 microM for calcein, respectively. The suitability of this simple detector for fluorescence detection was demonstrated by baseline separation of fluorescein isothiocyanate (FITC)-labeled arginine, phenylalanine, and glycine and FITC within 30 s at separation length of 3.8 cm and electrical field strength of 600 V/cm.

A sea-land segmentation algorithm based on multi-feature fusion for a large-field remote sensing image

NASA Astrophysics Data System (ADS)

Li, Jing; Xie, Weixin; Pei, Jihong

2018-03-01

Sea-land segmentation is one of the key technologies of sea target detection in remote sensing images. At present, the existing algorithms have the problems of low accuracy, low universality and poor automatic performance. This paper puts forward a sea-land segmentation algorithm based on multi-feature fusion for a large-field remote sensing image removing island. Firstly, the coastline data is extracted and all of land area is labeled by using the geographic information in large-field remote sensing image. Secondly, three features (local entropy, local texture and local gradient mean) is extracted in the sea-land border area, and the three features combine a 3D feature vector. And then the MultiGaussian model is adopted to describe 3D feature vectors of sea background in the edge of the coastline. Based on this multi-gaussian sea background model, the sea pixels and land pixels near coastline are classified more precise. Finally, the coarse segmentation result and the fine segmentation result are fused to obtain the accurate sea-land segmentation. Comparing and analyzing the experimental results by subjective vision, it shows that the proposed method has high segmentation accuracy, wide applicability and strong anti-disturbance ability.

3D Multi-segment foot kinematics in children: A developmental study in typically developing boys.

PubMed

Deschamps, Kevin; Staes, Filip; Peerlinck, Kathelijne; Van Geet, Christel; Hermans, Cedric; Matricali, Giovanni Arnoldo; Lobet, Sebastien

2017-02-01

The relationship between age and 3D rotations objectivized with multisegment foot models has not been quantified until now. The purpose of this study was therefore to investigate the relationship between age and multi-segment foot kinematics in a cross-sectional database. Barefoot multi-segment foot kinematics of thirty two typically developing boys, aged 6-20 years, were captured with the Rizzoli Multi-segment Foot Model. One-dimensional statistical parametric mapping linear regression was used to examine the relationship between age and 3D inter-segment rotations of the dominant leg during the full gait cycle. Age was significantly correlated with sagittal plane kinematics of the midfoot and the calcaneus-metatarsus inter-segment angle (p<0.0125). Age was also correlated with the transverse plane kinematics of the calcaneus-metatarsus angle (p<0.0001). Gait labs should consider age related differences and variability if optimal decision making is pursued. It remains unclear if this is of interest for all foot models, however, the current study highlights that this is of particular relevance for foot models which incorporate a separate midfoot segment. Copyright © 2016 Elsevier B.V. All rights reserved.

Multi-Atlas Segmentation using Partially Annotated Data: Methods and Annotation Strategies.

PubMed

Koch, Lisa M; Rajchl, Martin; Bai, Wenjia; Baumgartner, Christian F; Tong, Tong; Passerat-Palmbach, Jonathan; Aljabar, Paul; Rueckert, Daniel

2017-08-22

Multi-atlas segmentation is a widely used tool in medical image analysis, providing robust and accurate results by learning from annotated atlas datasets. However, the availability of fully annotated atlas images for training is limited due to the time required for the labelling task. Segmentation methods requiring only a proportion of each atlas image to be labelled could therefore reduce the workload on expert raters tasked with annotating atlas images. To address this issue, we first re-examine the labelling problem common in many existing approaches and formulate its solution in terms of a Markov Random Field energy minimisation problem on a graph connecting atlases and the target image. This provides a unifying framework for multi-atlas segmentation. We then show how modifications in the graph configuration of the proposed framework enable the use of partially annotated atlas images and investigate different partial annotation strategies. The proposed method was evaluated on two Magnetic Resonance Imaging (MRI) datasets for hippocampal and cardiac segmentation. Experiments were performed aimed at (1) recreating existing segmentation techniques with the proposed framework and (2) demonstrating the potential of employing sparsely annotated atlas data for multi-atlas segmentation.

Automatic multi-organ segmentation using learning-based segmentation and level set optimization.

PubMed

Kohlberger, Timo; Sofka, Michal; Zhang, Jingdan; Birkbeck, Neil; Wetzl, Jens; Kaftan, Jens; Declerck, Jérôme; Zhou, S Kevin

2011-01-01

We present a novel generic segmentation system for the fully automatic multi-organ segmentation from CT medical images. Thereby we combine the advantages of learning-based approaches on point cloud-based shape representation, such a speed, robustness, point correspondences, with those of PDE-optimization-based level set approaches, such as high accuracy and the straightforward prevention of segment overlaps. In a benchmark on 10-100 annotated datasets for the liver, the lungs, and the kidneys we show that the proposed system yields segmentation accuracies of 1.17-2.89 mm average surface errors. Thereby the level set segmentation (which is initialized by the learning-based segmentations) contributes with an 20%-40% increase in accuracy.

Automated brain tumor segmentation using spatial accuracy-weighted hidden Markov Random Field.

PubMed

Nie, Jingxin; Xue, Zhong; Liu, Tianming; Young, Geoffrey S; Setayesh, Kian; Guo, Lei; Wong, Stephen T C

2009-09-01

A variety of algorithms have been proposed for brain tumor segmentation from multi-channel sequences, however, most of them require isotropic or pseudo-isotropic resolution of the MR images. Although co-registration and interpolation of low-resolution sequences, such as T2-weighted images, onto the space of the high-resolution image, such as T1-weighted image, can be performed prior to the segmentation, the results are usually limited by partial volume effects due to interpolation of low-resolution images. To improve the quality of tumor segmentation in clinical applications where low-resolution sequences are commonly used together with high-resolution images, we propose the algorithm based on Spatial accuracy-weighted Hidden Markov random field and Expectation maximization (SHE) approach for both automated tumor and enhanced-tumor segmentation. SHE incorporates the spatial interpolation accuracy of low-resolution images into the optimization procedure of the Hidden Markov Random Field (HMRF) to segment tumor using multi-channel MR images with different resolutions, e.g., high-resolution T1-weighted and low-resolution T2-weighted images. In experiments, we evaluated this algorithm using a set of simulated multi-channel brain MR images with known ground-truth tissue segmentation and also applied it to a dataset of MR images obtained during clinical trials of brain tumor chemotherapy. The results show that more accurate tumor segmentation results can be obtained by comparing with conventional multi-channel segmentation algorithms.

Apparatus and method for performing microfluidic manipulations for chemical analysis and synthesis

DOEpatents

Ramsey, J. Michael

2000-01-01

A microchip laboratory system and method provide fluid manipulations for a variety of applications, including sample injection for microchip chemical separations. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis and electrochromatography are performed in channels formed in the substrate. Analytes are loaded into a four-way intersection of channels by electrokinetically pumping the analyte through the intersection, followed by switching of the potentials to force an analyte plug into the separation channel.

Apparatus and method for performing microfluidic manipulations for chemical analysis and synthesis

DOEpatents

Ramsey, J. Michael

2000-01-01

A microchip laboratory system and method proved fluid manipulations for a variety of applications, including sample injection for microchip chemical separations. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis and electrochromatography are performed in channels formed in the substrate. Analytes are loaded into a four-way intersection of channels by electrokinetically pumping the analyte through the intersection, followed by switching of the potentials to force an analyte plug into the separation channel.

Apparatus and method for performing microfluidic manipulations for chemical analysis and synthesis

DOEpatents

Ramsey, J. Michael

2002-01-01

A microchip laboratory system and method provide fluid manipulations for a variety of applications, including sample injection for microchip chemical separations. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis and electrochromatography are performed in channels formed in the substrate. Analytes are loaded into a four-way intersection of channels by electrokinetically pumping the analyte through the intersection, followed by switching of the potentials to force an analyte plug into the separation channel.

Apparatus and method for performing microfluidic manipulations for chemical analysis and synthesis

DOEpatents

Ramsey, J. Michael

1999-01-01

A microchip laboratory system and method provide fluid manipulations for a variety of applications, including sample injection for microchip chemical separations. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis and electrochromatography are performed in channels formed in the substrate. Analytes are loaded into a four-way intersection of channels by electrokinetically pumping the analyte through the intersection, followed by switching of the potentials to force an analyte plug into the separation channel.

Application of Microchip Electrophoresis for Clinical Tests

NASA Astrophysics Data System (ADS)

Yatsushiro, Shouki; Kataoka, Masatoshi

Microchip electrophoresis has recently attracted much attention in the field of nuclear acid analysis due to its high efficiency, ease of operation, low consumption of samples and reagents, and relatively low costs. In addition, the analysis has expanded to an analytical field like not only the analysis of DNA but also the analysis of RNA, the protein, the sugar chain, and the cellular function, etc. In this report, we showed that high-performance monitoring systems for human blood glucose levels and α-amylase activity in human plasma using microchip electrophoresis.

Apparatus and method for performing microfluidic manipulations for chemical analysis and synthesis

DOEpatents

Ramsey, J.M.

1999-01-12

A microchip laboratory system and method provide fluid manipulations for a variety of applications, including sample injection for microchip chemical separations. The microchip is fabricated using standard photolithographic procedures and chemical wet etching, with the substrate and cover plate joined using direct bonding. Capillary electrophoresis and electrochromatography are performed in channels formed in the substrate. Analytes are loaded into a four-way intersection of channels by electrokinetically pumping the analyte through the intersection, followed by switching of the potentials to force an analyte plug into the separation channel. 46 figs.

> 6 MW peak power at 532 nm from passively Q-switched Nd:YAG/Cr4+:YAG microchip laser.

PubMed

Bhandari, Rakesh; Taira, Takunori

2011-09-26

Megawatt peak power, giant pulse microchip lasers are attractive for wavelength conversion, provided their output is linearly polarized. We use a [110] cut Cr(4+):YAG for passively Q-switched Nd:YAG microchip laser to obtain a stable, linearly polarized output. Further, we optimize the conditions for second harmonic generation at 532 nm wavelength to achieve > 6 MW peak power, 1.7 mJ, 265 ps, 100 Hz pulses with a conversion efficiency of 85%. © 2011 Optical Society of America

PCR amplification on microarrays of gel immobilized oligonucleotides

DOEpatents

Strizhkov, Boris; Tillib, Sergei; Mikhailovich, Vladimir; Mirzabekov, Andrei

2003-11-04

The invention relates two general methods for performing PCR amplification, combined with the detection and analysis of the PCR products on a microchip. In the first method, the amplification occurs both outside and within a plurality of gel pads on a microchip, with at least one oligonucleotide primer immobilized in a gel pad. In the second method, PCR amplification also takes place within gel pads on a microchip, but the pads are surrounded by a hydrophobic liquid such as that which separates the individual gel pads into environments which resemble micro-miniaturized test tubes.

Plasmon-enhanced versatile optical nonlinearities in a Au-Ag-Au multi-segmental hybrid structure.

PubMed

Yao, Lin-Hua; Zhang, Jun-Pei; Dai, Hong-Wei; Wang, Ming-Shan; Zhang, Lu-Man; Wang, Xia; Han, Jun-Bo

2018-06-27

A Au-Ag-Au multi-segmental hybrid structure has been synthesized by using an electrodeposition method based on an anodic aluminum oxide (AAO) membrane. The third-order optical nonlinearities, second harmonic generation (SHG) and photoluminescence (PL) properties containing ultrafast supercontinuum generation and plasmon mediated thermal emission have been investigated. Significant optical enhancements have been obtained near surface plasmon resonance wavelength in all the abovementioned nonlinear processes. Comparative studies between the Au-Ag-Au multi-segmental hybrid structure and the corresponding single-component Au and Ag hybrid structures demonstrate that the Au-Ag-Au multi-segmental hybrid structure has much larger optical nonlinearities than its counterparts. These results demonstrate that the Au-Ag-Au hybrid structure is a promising candidate for applications in plasmonic devices and enhancement substrates.

Segmentation and object-oriented classification of wetlands in a karst Florida landscape using multi-season Landsat-7 ETM+ Imagery

EPA Science Inventory

Segmentation and object-oriented processing of single-season and multi-season Landsat-7 ETM+ data was utilized for the classification of wetlands in a 1560 km2 study area of north central Florida. This segmentation and object-oriented classification outperformed the traditional ...

A general microchip surface modification approach using a spin-coated polymer resist film doped with hydroxypropyl cellulose.

PubMed

Sun, Xiuhua; Yang, Weichun; Geng, Yanli; Woolley, Adam T

2009-04-07

We have developed a simple and effective method for surface modification of polymer microchips by entrapping hydroxypropyl cellulose (HPC) in a spin-coated thin film on the surface. Poly(methyl methacrylate-8.5-methacrylic acid), a widely available commercial resist formulation, was utilized as a matrix for dissolving HPC and providing adherence to native polymer surfaces. Various amounts of HPC (0.1-2.0%) dissolved in the copolymer and spun on polymer surfaces were evaluated. The modified surfaces were characterized by contact angle measurement, X-ray photoelectron spectroscopy and atomic force microscopy. The developed method was applied on both poly(methyl methacrylate) and cyclic olefin copolymer microchips. A fluorescently labeled myoglobin digest, binary protein mixture, and human serum sample were all separated in these surface-modified polymer microdevices. Our work exhibits an easy and reliable way to achieve favorable biomolecular separation performance in polymer microchips.

A general microchip surface modification approach using a spin-coated polymer resist film doped with hydroxypropyl cellulose

PubMed Central

Sun, Xiuhua; Yang, Weichun; Geng, Yanli; Woolley, Adam T.

2009-01-01

We have developed a simple and effective method for surface modification of polymer microchips by entrapping hydroxypropyl cellulose (HPC) in a spin-coated thin film on the surface. Poly(methyl methacrylate-8.5-methacrylic acid), a widely available commercial resist formulation, was utilized as a matrix for dissolving HPC and providing adherence to native polymer surfaces. Various amounts of HPC (0.1–2.0%) dissolved in the copolymer and spun on polymer surfaces were evaluated. The modified surfaces were characterized by contact angle measurement, X-ray photoelectron spectroscopy and atomic force microscopy. The developed method was applied on both poly(methyl methacrylate) and cyclic olefin copolymer microchips. A fluorescently labeled myoglobin digest, binary protein mixture, and human serum sample were all separated in these surface-modified polymer microdevices. Our work exhibits an easy and reliable way to achieve favorable biomolecular separation performance in polymer microchips. PMID:19294306

Recent progress in microchip electrophoresis-mass spectrometry.

PubMed

Kitagawa, Fumihiko; Otsuka, Koji

2011-06-25

This review highlights the methodological and instrumental developments in microchip electrophoresis (MCE)-mass spectrometry (MS) from 1997. In MCE-MS, the development of ionization interface is one of the most important issues to realize highly sensitive detection and high separation efficiency. Among several interfaces, electrospray ionization (ESI) has been mainly employed to MCE-MS since a simple structure of the ESI interface is suitable for coupling with the microchips. Although the number of publications is still limited, laser desorption ionization (LDI) interface has also been developed for MCE-MS. The characteristics of the ESI and LDI interfaces applied to the electrophoresis microchips are presented in this review. The scope of applications in MCE-MS covers mainly biogenic compounds such as bioactive amines, peptides, tryptic digests and proteins. This review provides a comprehensive table listing the applications in MCE-MS. Copyright © 2010 Elsevier B.V. All rights reserved.

A Cr4+:YAG passively Q-switched Nd:YVO4 microchip laser for controllable high-order Hermite-Gaussian modes

NASA Astrophysics Data System (ADS)

Dong, Jun; He, Yu; Bai, Sheng-Chuang; Ueda, Ken-ichi; Kaminskii, Alexander A.

2016-09-01

A nanosecond, high peak power, passively Q-switched laser for controllable Hermite-Gaussian (HG) modes has been achieved by manipulating the saturated inversion population inside the gain medium. The stable HG modes are generated in a Cr4+:YAG passively Q-switched Nd:YVO4 microchip laser by applying a tilted pump beam. The asymmetrical saturated inversion population distribution inside the Nd:YVO4 crystal for desirable HG modes is manipulated by choosing the proper pump beam diameter and varying pump power. A HG9,8 mode passively Q-switched Nd:YVO4 microchip laser with average output power of 265 mW has been obtained. Laser pulses with a pulse width of 7.3 ns and peak power of over 1.7 kW working at 21 kHz have been generated in the passively Q-switched Nd:YVO4 microchip laser.

Integration of On-Chip Peristaltic Pumps and Injection Valves with Microchip Electrophoresis and Electrochemical Detection

PubMed Central

Bowen, Amanda L; Martin, R. Scott

2010-01-01

A microfluidic approach that integrates peristaltic pumping from an on-chip reservoir with injection valves, microchip electrophoresis and electrochemical detection is described. Fabrication and operation of both the peristaltic pumps and injection valves were optimized to ensure efficient pumping and discrete injections. The final device uses the peristaltic pumps to continuously direct sample from a reservoir containing a mixture of analytes to injection valves that are coupled with microchip electrophoresis and amperometric detection. The separation and direct detection of dopamine and norepinephrine were possible with this approach and the utility of the device was demonstrated by monitoring the stimulated release of these neurotransmitters from a layer of cells introduced into the microchip. It is also shown that this pumping/reservoir approach can be expanded to multiple reservoirs and pumps, where one reservoir can be addressed individually or multiple reservoirs sampled simultaneously. PMID:20665914

Multi-fractal texture features for brain tumor and edema segmentation

NASA Astrophysics Data System (ADS)

Reza, S.; Iftekharuddin, K. M.

2014-03-01

In this work, we propose a fully automatic brain tumor and edema segmentation technique in brain magnetic resonance (MR) images. Different brain tissues are characterized using the novel texture features such as piece-wise triangular prism surface area (PTPSA), multi-fractional Brownian motion (mBm) and Gabor-like textons, along with regular intensity and intensity difference features. Classical Random Forest (RF) classifier is used to formulate the segmentation task as classification of these features in multi-modal MRIs. The segmentation performance is compared with other state-of-art works using a publicly available dataset known as Brain Tumor Segmentation (BRATS) 2012 [1]. Quantitative evaluation is done using the online evaluation tool from Kitware/MIDAS website [2]. The results show that our segmentation performance is more consistent and, on the average, outperforms other state-of-the art works in both training and challenge cases in the BRATS competition.

Multi-atlas segmentation of subcortical brain structures via the AutoSeg software pipeline

PubMed Central

Wang, Jiahui; Vachet, Clement; Rumple, Ashley; Gouttard, Sylvain; Ouziel, Clémentine; Perrot, Emilie; Du, Guangwei; Huang, Xuemei; Gerig, Guido; Styner, Martin

2014-01-01

Automated segmenting and labeling of individual brain anatomical regions, in MRI are challenging, due to the issue of individual structural variability. Although atlas-based segmentation has shown its potential for both tissue and structure segmentation, due to the inherent natural variability as well as disease-related changes in MR appearance, a single atlas image is often inappropriate to represent the full population of datasets processed in a given neuroimaging study. As an alternative for the case of single atlas segmentation, the use of multiple atlases alongside label fusion techniques has been introduced using a set of individual “atlases” that encompasses the expected variability in the studied population. In our study, we proposed a multi-atlas segmentation scheme with a novel graph-based atlas selection technique. We first paired and co-registered all atlases and the subject MR scans. A directed graph with edge weights based on intensity and shape similarity between all MR scans is then computed. The set of neighboring templates is selected via clustering of the graph. Finally, weighted majority voting is employed to create the final segmentation over the selected atlases. This multi-atlas segmentation scheme is used to extend a single-atlas-based segmentation toolkit entitled AutoSeg, which is an open-source, extensible C++ based software pipeline employing BatchMake for its pipeline scripting, developed at the Neuro Image Research and Analysis Laboratories of the University of North Carolina at Chapel Hill. AutoSeg performs N4 intensity inhomogeneity correction, rigid registration to a common template space, automated brain tissue classification based skull-stripping, and the multi-atlas segmentation. The multi-atlas-based AutoSeg has been evaluated on subcortical structure segmentation with a testing dataset of 20 adult brain MRI scans and 15 atlas MRI scans. The AutoSeg achieved mean Dice coefficients of 81.73% for the subcortical structures. PMID:24567717

SegAN: Adversarial Network with Multi-scale L1 Loss for Medical Image Segmentation.

PubMed

Xue, Yuan; Xu, Tao; Zhang, Han; Long, L Rodney; Huang, Xiaolei

2018-05-03

Inspired by classic Generative Adversarial Networks (GANs), we propose a novel end-to-end adversarial neural network, called SegAN, for the task of medical image segmentation. Since image segmentation requires dense, pixel-level labeling, the single scalar real/fake output of a classic GAN's discriminator may be ineffective in producing stable and sufficient gradient feedback to the networks. Instead, we use a fully convolutional neural network as the segmentor to generate segmentation label maps, and propose a novel adversarial critic network with a multi-scale L 1 loss function to force the critic and segmentor to learn both global and local features that capture long- and short-range spatial relationships between pixels. In our SegAN framework, the segmentor and critic networks are trained in an alternating fashion in a min-max game: The critic is trained by maximizing a multi-scale loss function, while the segmentor is trained with only gradients passed along by the critic, with the aim to minimize the multi-scale loss function. We show that such a SegAN framework is more effective and stable for the segmentation task, and it leads to better performance than the state-of-the-art U-net segmentation method. We tested our SegAN method using datasets from the MICCAI BRATS brain tumor segmentation challenge. Extensive experimental results demonstrate the effectiveness of the proposed SegAN with multi-scale loss: on BRATS 2013 SegAN gives performance comparable to the state-of-the-art for whole tumor and tumor core segmentation while achieves better precision and sensitivity for Gd-enhance tumor core segmentation; on BRATS 2015 SegAN achieves better performance than the state-of-the-art in both dice score and precision.

Fast electrophoretic analysis of individual mitochondria using microchip capillary electrophoresis with laser induced fluorescence detection.

PubMed

Duffy, Ciarán F; MacCraith, Brian; Diamond, Dermot; O'Kennedy, Richard; Arriaga, Edgar A

2006-08-01

The analysis of mitochondria by capillary electrophoresis usually takes longer than 20 min per replicate which may compromise the quality of the mitochondria due to degradation. In addition, low sample consumption may be beneficial in the analysis of rare or difficult samples. In this report, we demonstrate the ability to analyze individual mitochondrial events in picoliter-volume samples (approximately 80 pL) taken from a bovine liver preparation using microchip capillary electrophoresis with laser-induced fluorescence detection (micro-chip CE-LIF). Using a commercial "double-T" glass microchip, the sample was electrokinetically loaded in the "double-T" intersection and then subjected to electrophoretic separation along the main separation channel. In order to decrease interactions of mitochondria with channel walls during the analysis, poly(vinyl alcohol) was used as a dynamic coating. This procedure eliminates the need for complicated covalent surface modifications within the channels that were previously used in capillary electrophoresis methods. For analysis, mitochondria, isolated from bovine liver tissue, were selectively labelled using 10-nonyl acridine orange (NAO). The results consist of electropherograms where each mitochondrial event is a narrow spike (240 +/- 44 ms). While the spike intensity is representative of its NAO content, its migration time is used to calculate and describe its electrophoretic mobility, which is a property still largely unexplored for intracellular organelles. The five-fold decrease in separation time (4 min for microchip versus 20 min for capillary electrophoresis) makes microchip electrophoretic separations of organelles a faster, sensitive, low-sample volume alternative for the characterization of individual organelle properties and for investigations of subcellular heterogeneity.

Evaluation of pain and inflammation associated with hot iron branding and microchip transponder injection in horses.

PubMed

Lindegaard, Casper; Vaabengaard, Dorte; Christophersen, Mogens T; Ekstøm, Claus T; Fjeldborg, Julie

2009-07-01

To compare effects of hot iron branding and microchip transponder injection regarding aversive behavioral reactions indicative of pain and inflammation in horses. 7 adult horses. In a randomized controlled clinical crossover study, behavioral reactions to hot iron branding and microchip transponder injection were scored by 4 observers. Local and systemic inflammation including allodynia were assessed and compared by use of physiologic and biochemical responses obtained repeatedly for the 168-hour study period. Serum cortisol concentration was measured repeatedly throughout the first 24 hours of the study. Sham treatments were performed 1 day before and 7 days after treatments. Hot iron branding elicited a significantly stronger aversive reaction indicative of pain than did microchip transponder injection (odds ratio [OR], 12.83). Allodynia quantified by means of skin sensitivity to von Frey monofilaments was significantly greater after hot iron branding than after microchip transponder injection (OR, 2.59). Neither treatment induced signs of spontaneously occurring pain that were observed during the remaining study period, and neither treatment induced increased serum cortisol concentrations. Comparison with sham treatments indicated no memory of an unpleasant event. The hot iron branding areas had significantly increased skin temperature and swelling (OR, 14.6). Systemic inflammation as measured via serum amyloid A concentration was not detected after any of the treatments. Microchip transponder injection induced less signs of pain and inflammation and did not seem to pose a higher long-term risk than hot iron branding. Consequently, results indicated that hot iron branding does inflict more pain and should be abandoned where possible.

Analytical Chemistry and the Microchip.

ERIC Educational Resources Information Center

Lowry, Robert K.

1986-01-01

Analytical techniques used at various points in making microchips are described. They include: Fourier transform infrared spectrometry (silicon purity); optical emission spectroscopy (quantitative thin-film composition); X-ray photoelectron spectroscopy (chemical changes in thin films); wet chemistry, instrumental analysis (process chemicals);…

Science and Technology of Bio-Inert Thin Films as Hermetic-Encapsulating Coatings for Implantable Biomedical Devices: Application to Implantable Microchip in the Eye for the Artificial Retina

NASA Astrophysics Data System (ADS)

Auciello, Orlando; Shi, Bing

Extensive research has been devoted to the development of neuron prostheses and hybrid bionic systems to establish links between the nervous system and electronic or robotic prostheses with the main focus of restoring motor and sensory functions in blind patients. Artificial retinas, one type of neural prostheses we are currently working on, aim to restore some vision in blind patients caused by retinitis picmentosa or macular degeneration, and in the future to restore vision at the level of face recognition, if not more. Currently there is no hermetic microchip-size coating that provides a reliable, long-term (years) performance as encapsulating coating for the artificial retina Si microchip to be implanted inside the eye. This chapter focuses on the critical topics relevant to the development of a robust, long-term artificial retina device, namely the science and technology of hermetic bio-inert encapsulating coatings to protect a Si microchip implanted in the human eye from being attacked by chemicals existing in the eye's saline environment. The work discussed in this chapter is related to the development of a novel ultrananocrystalline diamond (UNCD) hermetic coating, which exhibited no degradation in rabbit eyes. The material synthesis, characterization, and electrochemical properties of these hermetic coatings are reviewed for application as encapsulating coating for the artificial retinal microchips implantable inside the human eye. Our work has shown that UNCD coatings may provide a reliable hermetic bio-inert coating technology for encapsulation of Si microchips implantable in the eye specifically and in the human body in general. Electrochemical tests of the UNCD films grown under CH4/Ar/H2 (1%) plasma exhibit the lowest leakage currents (˜7 × 10-7 A/cm2) in a saline solution simulating the eye environment. This leakage is incompatible with the functionality of the first-generation artificial retinal microchip. However, the growth of UNCD on top of the Si microchip passivated by a silicon nitride layer or the oxide layers is also under investigation in our group as introduced in this chapter. The electrochemically induced leakage will be reduced by at least one to three orders of magnitude to the range of 10-10 A/cm2, which is compatible with reliable, long-term implants.

Polyelectrolyte Properties in Mono and Multi-Valent Ionic Media: Brushes and Complex Coacervates

NASA Astrophysics Data System (ADS)

Farina, Robert M.

Materials composed of polyelectrolytes have unique and interesting physical properties resulting primarily from their charged monomer segments. Polyelectrolytes, which exist in many different biological and industrial forms, have also been shown to be highly responsive to external environmental changes. Here, two specific polyelectrolyte systems, brushes and complex coacervates, are discussed in regards to how their properties can be tailored by adjusting the surrounding ionic environment with mono and multi-valent ions. End-tethered polyelectrolyte brushes, which constitute an interesting and substantial portion of polyelectrolyte applications, are well known for their ability to provide excellent lubrication and low friction when coated onto surfaces (e.g. articular cartilage and medical devices), as well as for their ability to stabilize colloidal particles in solution (e.g. paint and cosmetic materials). These properties have been extensively studied with brushes in pure mono-valent ionic media. However, polyelectrolyte brush interactions with multi-valent ions in solution are much less understood, although highly relevant considering mono and multi-valent counterions are present in most applications. Even at very low concentrations of multi-valent ions in solution, dramatic polyelectrolyte brush physical property changes can occur, resulting in collapsed chains which also adhere to one another via multi-valent bridging. Here, the strong polyelectrolyte poly(sodium styrene sulfonate) was studied using the Surface Forces Apparatus (SFA) and electrochemistry in order to investigate brush height and intermolecular interactions between two brushes as a function of multi-valent counterion population inside a brush. Complex coacervates are formed when polyanions and polycations are mixed together in proper conditions of an aqueous solution. This mixing results in a phase separation of a polymer-rich, coacervate phase composed of a chain network held together via electrostatic interactions. Complex coacervates are highly regarded for their extremely low interfacial energy resulting in an ability to spread and adhere to surfaces under water, utilized by marine organisms (e.g. mussels and tubeworms), as well as many encapsulation applications (e.g. pigment encapsulation for carbon-less paper and electronic paper displays). Here, the interfacial energy of coacervates composed of oppositely charged polypeptides, poly(L-lysine) and poly(L-glutamic acid), was investigated using the SFA in regards to changes in bulk mono-valent salt concentrations.

Design and Fabrication of High Gain Multi-element Multi-segment Quarter-sector Cylindrical Dielectric Resonator Antenna

NASA Astrophysics Data System (ADS)

Ranjan, Pinku; Gangwar, Ravi Kumar

2017-12-01

A novel design and analysis of quarter cylindrical dielectric resonator antenna (q-CDRA) with multi-element and multi-segment (MEMS) approach has been presented. The MEMS q-CDRA has been designed by splitting four identical quarters from a solid cylinder and then multi-segmentation approach has been utilized to design q-CDRA. The proposed antenna has been designed for enhancement in bandwidth as well as for high gain. For bandwidth enhancement, multi-segmentation method has been explained for the selection of dielectric constant of materials. The performance of the proposed MEMS q-CDRA has been demonstrated with design guideline of MEMS approach. To validate the antenna performance, three segments q-CDRA has been fabricated and analyzed practically. The simulated results have been in good agreement with measured one. The MEMS q-CDRA has wide impedance bandwidth (|S11|≤-10 dB) of 133.8 % with monopole-like radiation pattern. The proposed MEMS q-CDRA has been operating at TM01δ mode with the measured gain of 6.65 dBi and minimum gain of 4.5 dBi in entire operating frequency band (5.1-13.7 GHz). The proposed MEMS q-CDRA may find appropriate applications in WiMAX and WLAN band.

Multi-scale image segmentation method with visual saliency constraints and its application

NASA Astrophysics Data System (ADS)

Chen, Yan; Yu, Jie; Sun, Kaimin

2018-03-01

Object-based image analysis method has many advantages over pixel-based methods, so it is one of the current research hotspots. It is very important to get the image objects by multi-scale image segmentation in order to carry out object-based image analysis. The current popular image segmentation methods mainly share the bottom-up segmentation principle, which is simple to realize and the object boundaries obtained are accurate. However, the macro statistical characteristics of the image areas are difficult to be taken into account, and fragmented segmentation (or over-segmentation) results are difficult to avoid. In addition, when it comes to information extraction, target recognition and other applications, image targets are not equally important, i.e., some specific targets or target groups with particular features worth more attention than the others. To avoid the problem of over-segmentation and highlight the targets of interest, this paper proposes a multi-scale image segmentation method with visually saliency graph constraints. Visual saliency theory and the typical feature extraction method are adopted to obtain the visual saliency information, especially the macroscopic information to be analyzed. The visual saliency information is used as a distribution map of homogeneity weight, where each pixel is given a weight. This weight acts as one of the merging constraints in the multi- scale image segmentation. As a result, pixels that macroscopically belong to the same object but are locally different can be more likely assigned to one same object. In addition, due to the constraint of visual saliency model, the constraint ability over local-macroscopic characteristics can be well controlled during the segmentation process based on different objects. These controls will improve the completeness of visually saliency areas in the segmentation results while diluting the controlling effect for non- saliency background areas. Experiments show that this method works better for texture image segmentation than traditional multi-scale image segmentation methods, and can enable us to give priority control to the saliency objects of interest. This method has been used in image quality evaluation, scattered residential area extraction, sparse forest extraction and other applications to verify its validation. All applications showed good results.

Multi-atlas-based segmentation of the parotid glands of MR images in patients following head-and-neck cancer radiotherapy

NASA Astrophysics Data System (ADS)

Cheng, Guanghui; Yang, Xiaofeng; Wu, Ning; Xu, Zhijian; Zhao, Hongfu; Wang, Yuefeng; Liu, Tian

2013-02-01

Xerostomia (dry mouth), resulting from radiation damage to the parotid glands, is one of the most common and distressing side effects of head-and-neck cancer radiotherapy. Recent MRI studies have demonstrated that the volume reduction of parotid glands is an important indicator for radiation damage and xerostomia. In the clinic, parotid-volume evaluation is exclusively based on physicians' manual contours. However, manual contouring is time-consuming and prone to inter-observer and intra-observer variability. Here, we report a fully automated multi-atlas-based registration method for parotid-gland delineation in 3D head-and-neck MR images. The multi-atlas segmentation utilizes a hybrid deformable image registration to map the target subject to multiple patients' images, applies the transformation to the corresponding segmented parotid glands, and subsequently uses the multiple patient-specific pairs (head-and-neck MR image and transformed parotid-gland mask) to train support vector machine (SVM) to reach consensus to segment the parotid gland of the target subject. This segmentation algorithm was tested with head-and-neck MRIs of 5 patients following radiotherapy for the nasopharyngeal cancer. The average parotid-gland volume overlapped 85% between the automatic segmentations and the physicians' manual contours. In conclusion, we have demonstrated the feasibility of an automatic multi-atlas based segmentation algorithm to segment parotid glands in head-and-neck MR images.

Hierarchical combinatorial deep learning architecture for pancreas segmentation of medical computed tomography cancer images.

PubMed

Fu, Min; Wu, Wenming; Hong, Xiafei; Liu, Qiuhua; Jiang, Jialin; Ou, Yaobin; Zhao, Yupei; Gong, Xinqi

2018-04-24

Efficient computational recognition and segmentation of target organ from medical images are foundational in diagnosis and treatment, especially about pancreas cancer. In practice, the diversity in appearance of pancreas and organs in abdomen, makes detailed texture information of objects important in segmentation algorithm. According to our observations, however, the structures of previous networks, such as the Richer Feature Convolutional Network (RCF), are too coarse to segment the object (pancreas) accurately, especially the edge. In this paper, we extend the RCF, proposed to the field of edge detection, for the challenging pancreas segmentation, and put forward a novel pancreas segmentation network. By employing multi-layer up-sampling structure replacing the simple up-sampling operation in all stages, the proposed network fully considers the multi-scale detailed contexture information of object (pancreas) to perform per-pixel segmentation. Additionally, using the CT scans, we supply and train our network, thus get an effective pipeline. Working with our pipeline with multi-layer up-sampling model, we achieve better performance than RCF in the task of single object (pancreas) segmentation. Besides, combining with multi scale input, we achieve the 76.36% DSC (Dice Similarity Coefficient) value in testing data. The results of our experiments show that our advanced model works better than previous networks in our dataset. On the other words, it has better ability in catching detailed contexture information. Therefore, our new single object segmentation model has practical meaning in computational automatic diagnosis.

25 CFR 542.8 - What are the minimum internal control standards for pull tabs?

Code of Federal Regulations, 2011 CFR

2011-04-01

... microchip reader, the reader shall be tested periodically to determine that it is correctly reading the bar code or microchip. (iii) If the electronic equipment returns a voucher or a payment slip to the player...

R&D 100, 2016: T-Quake – Quantum-Mechanical Transmitter/Receiver Microchip

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tauke-Pedretti, Anna; Camacho, Ryan; Thayer, Gayle

2016-11-07

Applying advanced microfabrication techniques and innovative microdesign, the Sandia Enabled Communications and Authentication Network (SECANT) team has designed and produced photonic microchips capable of sending, receiving, and processing quantum signals for applications in cyber and physical security.

Reduction of timing jitter in passively Q-switched microchip lasers using self-injection seeding.

PubMed

Steinmetz, Alexander; Nodop, Dirk; Martin, Andreas; Limpert, Jens; Tünnermann, Andreas

2010-09-01

We present an efficient, simple, and passive technique for the reduction of timing jitter in passively Q-switched microchip lasers via self-injection seeding using a fiber delay line. The presented approach mitigates one inherent issue of passively Q-switched lasers without the need for active stabilization. At a repetition rate of a few hundred kilohertz and pulse duration of approximately 200 ps delivered by a microchip laser, the rms jitter is reduced from several nanoseconds down to 20 ps, hence, significantly below the pulse duration of the laser source.

Sub-nanosecond Yb:KLu(WO₄)₂ microchip laser.

PubMed

Loiko, P; Serres, J M; Mateos, X; Yumashev, K; Yasukevich, A; Petrov, V; Griebner, U; Aguiló, M; Díaz, F

2016-06-01

A diode-pumped Yb:KLu(WO₄)₂ microchip laser passively Q-switched by a Cr⁴⁺:YAG saturable absorber generated a maximum average output power of 590 mW at 1031 nm with a slope efficiency of 55%. The pulse characteristics were 690 ps/47.6 μJ at a pulse repetition frequency of 12.4 kHz. The output beam had an excellent circular profile with M²<1.05. Yb:KLu(WO₄)₂ is very promising for ultrathin sub-ns microchip lasers.

Deformation-induced release of ATP from erythrocytes in a poly(dimethylsiloxane)-based microchip with channels that mimic resistance vessels.

PubMed

Price, Alexander K; Fischer, David J; Martin, R Scott; Spence, Dana M

2004-08-15

The ability of nitric oxide to relax smooth muscle cells surrounding resistance vessels in vivo is well documented. Here, we describe a series of studies designed to quantify amounts of adenosine triphosphate (ATP), a known stimulus of NO production in endothelial cells, released from erythrocytes that are mechanically deformed as these cells traverse microbore channels in lithographically patterned microchips. Results indicate that micromolar amounts of ATP are released from erythrocytes flowing through channels having cross sectional dimensions of 60 x 38 micron (2.22 +/- 0.50 microM ATP). Microscopic images indicate that erythrocytes, when being pumped through the microchip channels, migrate toward the center of the channels, leaving a cell-free or skimming layer at the walls of the channel, a profile known to exist in circulatory vessels in vivo. A comparison of the amounts of ATP released from RBCs mechanically deformed in microbore tubing (2.54 +/- 0.15 microM) vs a microchip (2.59 +/- 0.32 microM) suggests that channels in microchips may serve as functional biomimics of the microvasculature. Control studies involving diamide, a membrane-stiffening agent, suggest that the RBC-derived ATP is not due to cell lysis but rather physical deformation.

Microchip ELISA coupled with cell phone to detect ovarian cancer HE4 biomarker in urine.

PubMed

Wang, ShuQi; Akbas, Ragip; Demirci, Utkan

2015-01-01

Ovarian cancer is a leading cause of death from gynecologic cancers in the USA, and early diagnosis can potentially increase 5-year survival rate. Detection of biomarkers derived from hyperplasia of epithelial tissue by enzyme-linked immunosorbent assay (ELISA) proves to be a practical way of early diagnosis of ovarian cancer. However, ELISA is commonly performed in a laboratory setting, and it cannot be used in a clinical setting for on-site consultation. We have shown a microchip ELISA that detects HE4, an ovarian cancer biomarker, from urine using a cell phone integrated with a mobile application for imaging and data analysis. In microchip ELISA, HE4 from urine was first absorbed on the surface; the primary and secondary antibodies were subsequently anchored on the surface via immuno-reaction; and addition of substrate led to color development because of enzymatic labeling. The microchip after color development was imaged using a cell phone, and the color intensity was analyzed by an integrated mobile application. By comparing with an ELISA standard curve, the concentration of HE4 was reported on the cell phone screen. The presented microchip ELISA coupled with a cell phone is portable as opposed to traditional ELISA, and this method can facilitate the detection of ovarian cancer at the point-of-care (POC).

Laser and Optical Subsystem for NASA's Cold Atom Laboratory

NASA Astrophysics Data System (ADS)

Kohel, James; Kellogg, James; Elliott, Ethan; Krutzik, Markus; Aveline, David; Thompson, Robert

2016-05-01

We describe the design and validation of the laser and optics subsystem for NASA's Cold Atom Laboratory (CAL), a multi-user facility being developed at NASA's Jet Propulsion Laboratory for studies of ultra-cold quantum gases in the microgravity environment of the International Space Station. Ultra-cold atoms will be generated in CAL by employing a combination of laser cooling techniques and evaporative cooling in a microchip-based magnetic trap. Laser cooling and absorption imaging detection of bosonic mixtures of 87 Rb and 39 K or 41 K will be accomplished using a high-power (up to 500 mW ex-fiber), frequency-agile dual wavelength (767 nm and 780 nm) laser and optical subsystem. The CAL laser and optical subsystem also includes the capability to generate high-power multi-frequency optical pulses at 784.87 nm to realize a dual-species Bragg atom interferometer. Currently at Humboldt-Universität zu Berlin.

A segmented ion engine design for solar electric propulsion systems

NASA Technical Reports Server (NTRS)

Brophy, John R.

1992-01-01

A new ion engine design, called a segmented ion engine, is described which is capable of reducing the required ion source life time for small body rendezvous missions from 18,000 h to about 8,000 h. The use of SAND ion optics for the engine accelerator system makes it possible to substantially reduce the cost of demonstrating the required engine endurance. It is concluded that a flight test of a 5-kW xenon ion propulsion system on the ELITE spacecraft would enormously reduce the cost and risk of using ion propulsion on a planetary vehicle by addressing systems level issues associated with flying a spacecraft radically different from conventional planetary vehicles.

Multi-purpose CMOS sensor interface for low-power applications

NASA Astrophysics Data System (ADS)

Wouters, P.; de Cooman, M.; Puers, R.

1994-08-01

A dedicated low-power CMOS transponder microchip is presented as part of a novel telemetry implant for biomedical applications. This mixed analog-digital circuit contains an identification code and collects information on physiological parameters, i.e., body temperature and physical activity, and on the status of the battery. To minimize the amount of data to be transmitted, a dedicated signal processing algorithm is embedded within its circuitry. All telemetry functions (encoding, modulation, generation of the carrier) are implemented on the integrated circuit. Emphasis is on a high degree of flexibility towards sensor inputs and internal data management, extreme miniaturization, and low-power consumption to allow a long implantation lifetime.

Sensitive Amino Acid Composition and Chirality Analysis with the Mars Organic Analyzer (MOA)

NASA Technical Reports Server (NTRS)

Skelley, Alison M.; Scherer, James R.; Aubrey, Andrew D.; Grover, William H.; Ivester, Robin H. C.; Ehrenfreund, Pascale; Grunthaner, Frank J.; Bada, Jeffrey L.; Mathies, Richard A.

2005-01-01

Detection of life on Mars requires definition of a suitable biomarker and development of sensitive yet compact instrumentation capable of performing in situ analyses. Our studies are focused on amino acid analysis because amino acids are more resistant to decomposition than other biomolecules, and because amino acid chirality is a well-defined biomarker. Amino acid composition and chirality analysis has been previously demonstrated in the lab using microfabricated capillary electrophoresis (CE) chips. To analyze amino acids in the field, we have developed the Mars Organic Analyzer (MOA), a portable analysis system that consists of a compact instrument and a novel multi-layer CE microchip.

Engineering of multi-segmented light tunnel and flattop focus with designed axial lengths and gaps

NASA Astrophysics Data System (ADS)

Yu, Yanzhong; Huang, Han; Zhou, Mianmian; Zhan, Qiwen

2018-01-01

Based on the radiation pattern from a sectional-uniform line source antenna, a three-dimensional (3D) focus engineering technique for the creation of multi-segmented light tunnel and flattop focus with designed axial lengths and gaps is proposed. Under a 4Pi focusing system, the fields radiated from sectional-uniform magnetic and electromagnetic current line source antennas are employed to generate multi-segmented optical tube and flattop focus, respectively. Numerical results demonstrate that the produced light tube and flattop focus remain homogeneous along the optical axis; and their lengths of the nth segment and the nth gap between consecutive segments can be easily adjusted and only depend on the sizes of the nth section and the nth blanking between adjacent sectional antennas. The optical tube is a pure azimuthally polarized field but for the flattop focus the longitudinal polarization is dominant on the optical axis. To obtain the required pupil plane illumination for constructing the above focal field with prescribed characteristics, the inverse problem of the antenna radiation field is solved. These peculiar focusing fields might find potential applications in multi-particle acceleration, multi-particle trapping and manipulation.

Rod-Coil Block Polyimide Copolymers

NASA Technical Reports Server (NTRS)

Meador, Mary Ann B. (Inventor); Kinder, James D. (Inventor)

2005-01-01

This invention is a series of rod-coil block polyimide copolymers that are easy to fabricate into mechanically resilient films with acceptable ionic or protonic conductivity at a variety of temperatures. The copolymers consist of short-rigid polyimide rod segments alternating with polyether coil segments. The rods and coil segments can be linear, branched or mixtures of linear and branched segments. The highly incompatible rods and coil segments phase separate, providing nanoscale channels for ion conduction. The polyimide segments provide dimensional and mechanical stability and can be functionalized in a number of ways to provide specialized functions for a given application. These rod-coil black polyimide copolymers are particularly useful in the preparation of ion conductive membranes for use in the manufacture of fuel cells and lithium based polymer batteries.

On the importance of FIB-SEM specific segmentation algorithms for porous media

DOE Office of Scientific and Technical Information (OSTI.GOV)

Salzer, Martin, E-mail: martin.salzer@uni-ulm.de; Thiele, Simon, E-mail: simon.thiele@imtek.uni-freiburg.de; Zengerle, Roland, E-mail: zengerle@imtek.uni-freiburg.de

2014-09-15

A new algorithmic approach to segmentation of highly porous three dimensional image data gained by focused ion beam tomography is described which extends the key-principle of local threshold backpropagation described in Salzer et al. (2012). The technique of focused ion beam tomography has shown to be capable of imaging the microstructure of functional materials. In order to perform a quantitative analysis on the corresponding microstructure a segmentation task needs to be performed. However, algorithmic segmentation of images obtained with focused ion beam tomography is a challenging problem for highly porous materials if filling the pore phase, e.g. with epoxy resin,more » is difficult. The gray intensities of individual voxels are not sufficient to determine the phase represented by them and usual thresholding methods are not applicable. We thus propose a new approach to segmentation that pays respect to the specifics of the imaging process of focused ion beam tomography. As an application of our approach, the segmentation of three dimensional images for a cathode material used in polymer electrolyte membrane fuel cells is discussed. We show that our approach preserves significantly more of the original nanostructure than a thresholding approach. - Highlights: • We describe a new approach to the segmentation of FIB-SEM images of porous media. • The first and last occurrences of structures are detected by analysing the z-profiles. • The algorithm is validated by comparing it to a manual segmentation. • The new approach shows significantly less artifacts than a thresholding approach. • A structural analysis also shows improved results for the obtained microstructure.« less

Multi-scale structural analysis of gas diffusion layers

NASA Astrophysics Data System (ADS)

Göbel, Martin; Godehardt, Michael; Schladitz, Katja

2017-07-01

The macroscopic properties of materials are strongly determined by their micro structure. Here, transport properties of gas diffusion layers (GDL) for fuel cells are considered. In order to simulate flow and thermal properties, detailed micro structural information is essential. 3D images obtained by high-resolution computed tomography using synchrotron radiation and scanning electron microscopy (SEM) combined with focused ion beam (FIB) serial slicing were used. A recent method for reconstruction of porous structures from FIB-SEM images and sophisticated morphological image transformations were applied to segment the solid structural components. The essential algorithmic steps for segmenting the different components in the tomographic data-sets are described and discussed. In this paper, two types of GDL, based on a non-woven substrate layer and a paper substrate layer were considered, respectively. More than three components are separated within the synchrotron radiation computed tomography data. That is, fiber system, polytetrafluoroethylene (PTFE) binder/impregnation, micro porous layer (MPL), inclusions within the latter, and pore space are segmented. The usage of the thus derived 3D structure data in different simulation applications can be demonstrated. Simulations of macroscopic properties such as thermal conductivity, depending on the flooding state of the GDL are possible.

Region-based multi-step optic disk and cup segmentation from color fundus image

NASA Astrophysics Data System (ADS)

Xiao, Di; Lock, Jane; Manresa, Javier Moreno; Vignarajan, Janardhan; Tay-Kearney, Mei-Ling; Kanagasingam, Yogesan

2013-02-01

Retinal optic cup-disk-ratio (CDR) is a one of important indicators of glaucomatous neuropathy. In this paper, we propose a novel multi-step 4-quadrant thresholding method for optic disk segmentation and a multi-step temporal-nasal segmenting method for optic cup segmentation based on blood vessel inpainted HSL lightness images and green images. The performance of the proposed methods was evaluated on a group of color fundus images and compared with the manual outlining results from two experts. Dice scores of detected disk and cup regions between the auto and manual results were computed and compared. Vertical CDRs were also compared among the three results. The preliminary experiment has demonstrated the robustness of the method for automatic optic disk and cup segmentation and its potential value for clinical application.

Segmentation of white rat sperm image

NASA Astrophysics Data System (ADS)

Bai, Weiguo; Liu, Jianguo; Chen, Guoyuan

2011-11-01

The segmentation of sperm image exerts a profound influence in the analysis of sperm morphology, which plays a significant role in the research of animals' infertility and reproduction. To overcome the microscope image's properties of low contrast and highly polluted noise, and to get better segmentation results of sperm image, this paper presents a multi-scale gradient operator combined with a multi-structuring element for the micro-spermatozoa image of white rat, as the multi-scale gradient operator can smooth the noise of an image, while the multi-structuring element can retain more shape details of the sperms. Then, we use the Otsu method to segment the modified gradient image whose gray scale processed is strong in sperms and weak in the background, converting it into a binary sperm image. As the obtained binary image owns impurities that are not similar with sperms in the shape, we choose a form factor to filter those objects whose form factor value is larger than the select critical value, and retain those objects whose not. And then, we can get the final binary image of the segmented sperms. The experiment shows this method's great advantage in the segmentation of the micro-spermatozoa image.

A Novel Protocol to Analyze Short- and Long-Chain Fatty Acids Using Nonaqueous Microchip Capillary Electrophoresis

NASA Technical Reports Server (NTRS)

Cable, M. L.; Stockton, A. M.; Mora, Maria F; Willis, P. A.

2013-01-01

We propose a new protocol to identify and quantify both short- and long-chain saturated fatty acids in samples of astrobiological interest using non-aqueous microchip capillary electrophoresis (micronNACE) with laser induced fluorescence (LIF).

R&D 100, 2016: T-Quake – Quantum-Mechanical Transmitter/Receiver Microchip

ScienceCinema

Tauke-Pedretti, Anna; Camacho, Ryan; Thayer, Gayle

2018-06-13

Applying advanced microfabrication techniques and innovative microdesign, the Sandia Enabled Communications and Authentication Network (SECANT) team has designed and produced photonic microchips capable of sending, receiving, and processing quantum signals for applications in cyber and physical security.

50 CFR 23.56 - What U.S. CITES document conditions do I need to follow?

Code of Federal Regulations, 2011 CFR

2011-10-01

... CITES document correspond. If a microchip is used, we may, if necessary, ask the importer, exporter, or re-exporter to have equipment on hand to read the microchip at the time of import, export, or re...

50 CFR 23.56 - What U.S. CITES document conditions do I need to follow?

Code of Federal Regulations, 2010 CFR

2010-10-01

... CITES document correspond. If a microchip is used, we may, if necessary, ask the importer, exporter, or re-exporter to have equipment on hand to read the microchip at the time of import, export, or re...

On-Campus Projects: Inventing a Microchip.

ERIC Educational Resources Information Center

Basta, Nicholas

1985-01-01

In response to growth of microelectronics and changes in microchip design/manufacturing technology, universities are supporting class projects for students. Approximately 50 schools now conduct such programs which have resulted from earlier National Science Foundation sponsorship. Major advantages for the students include designing experience,…

TU-AB-202-11: Tumor Segmentation by Fusion of Multi-Tracer PET Images Using Copula Based Statistical Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lapuyade-Lahorgue, J; Ruan, S; Li, H

Purpose: Multi-tracer PET imaging is getting more attention in radiotherapy by providing additional tumor volume information such as glucose and oxygenation. However, automatic PET-based tumor segmentation is still a very challenging problem. We propose a statistical fusion approach to joint segment the sub-area of tumors from the two tracers FDG and FMISO PET images. Methods: Non-standardized Gamma distributions are convenient to model intensity distributions in PET. As a serious correlation exists in multi-tracer PET images, we proposed a new fusion method based on copula which is capable to represent dependency between different tracers. The Hidden Markov Field (HMF) model ismore » used to represent spatial relationship between PET image voxels and statistical dynamics of intensities for each modality. Real PET images of five patients with FDG and FMISO are used to evaluate quantitatively and qualitatively our method. A comparison between individual and multi-tracer segmentations was conducted to show advantages of the proposed fusion method. Results: The segmentation results show that fusion with Gaussian copula can receive high Dice coefficient of 0.84 compared to that of 0.54 and 0.3 of monomodal segmentation results based on individual segmentation of FDG and FMISO PET images. In addition, high correlation coefficients (0.75 to 0.91) for the Gaussian copula for all five testing patients indicates the dependency between tumor regions in the multi-tracer PET images. Conclusion: This study shows that using multi-tracer PET imaging can efficiently improve the segmentation of tumor region where hypoxia and glucidic consumption are present at the same time. Introduction of copulas for modeling the dependency between two tracers can simultaneously take into account information from both tracers and deal with two pathological phenomena. Future work will be to consider other families of copula such as spherical and archimedian copulas, and to eliminate partial volume effect by considering dependency between neighboring voxels.« less

Multi-ion, multi-event test of ion cyclotron resonance heating

NASA Technical Reports Server (NTRS)

Persoon, Ann M.

1993-01-01

The multi-ion, multi-event study of ion cyclotron resonance heating has been funded to study ion energization through ion cyclotron resonance with low frequency broadband electromagnetic turbulence. The modeling algorithm for the ion cyclotron resonance heating (ICRH) of oxygen ions was presented in Crew et al. (1990). Crew and his co-authors developed a two-parameter representation of selected oxygen conic distributions and modelled the conic formation in terms of resonance heating. The first year of this study seeks to extend the work of Crew and his co-authors by testing the applicability of the ICRH mechanism to helium ion conic distributions, using data obtained from the Energetic Ion Composition Spectrometer and the Plasma Wave Instrument on Dynamics Explorer 1.

Microchip capillary gel electrophoresis using programmed field strength gradients for the ultra-fast analysis of genetically modified organisms in soybeans.

PubMed

Kim, Yun-Jeong; Chae, Joon-Seok; Chang, Jun Keun; Kang, Seong Ho

2005-08-12

We have developed a novel method for the ultra-fast analysis of genetically modified organisms (GMOs) in soybeans by microchip capillary gel electrophoresis (MCGE) using programmed field strength gradients (PFSG) in a conventional glass double-T microchip. Under the programmed electric field strength and 0.3% poly(ethylene oxide) sieving matrix, the GMO in soybeans was analyzed within only 11 s of the microchip. The MCGE-PFSG method was a program that changes the electric field strength during GMO analysis, and was also applied to the ultra-fast analysis of PCR products. Compared to MCGE using a conventional and constantly applied electric field, the MCGE-PFSG analysis generated faster results without the loss of resolving power and reproducibility for specific DNA fragments (100- and 250-bp DNA) of GM-soybeans. The MCGE-PFSG technique may prove to be a new tool in the GMO analysis due to its speed, simplicity, and high efficiency.

A three-layer PMMA electrophoresis microchip with Pt microelectrodes insulated by a thin film for contactless conductivity detection.

PubMed

Liu, Junshan; Wang, Junyao; Chen, Zuanguang; Yu, Yong; Yang, Xiujuan; Zhang, Xianbin; Xu, Zheng; Liu, Chong

2011-03-07

A three-layer poly (methyl methacrylate) (PMMA) electrophoresis microchip integrated with Pt microelectrodes for contactless conductivity detection is presented. A 50 μm-thick PMMA film is used as the insulating layer and placed between the channel plate (containing the microchannel) and the electrode plate (containing the microelectrode). The three-layer structure facilitates the achievement of a thin insulating layer, obviates the difficulty of integrating microelectrodes on a thin film, and does not compromise the integration of microchips. To overcome the thermal and chemical incompatibilities of polymers and photolithographic techniques, a modified lift-off process was developed to integrate Pt microelectrodes onto the PMMA substrate. A novel two-step bonding method was created to assemble the complete PMMA microchip. A low limit of detection of 1.25 μg ml(-1) for Na(+) and high separation efficiency of 77,000 and 48,000 plates/m for Na(+) and K(+) were obtained when operating the detector at a low excitation frequency of 60 kHz.

Detection of enteropathogenic Escherichia coli by microchip capillary electrophoresis.

PubMed

Law, Wai S; Li, Sam F Y; Kricka, Larry J

2009-01-01

There is always a need to detect the presence of microorganisms, either as contaminants in food and pharmaceutical industries or bioindicators for disease diagnosis. Hence, it is important to develop efficient, rapid, and simple methods to detect microorganisms. Traditional culturing method is unsatisfactory due to its long incubation time. Molecular methods, although capable of providing a high degree of specificity, are not always useful in providing quick tests of presence or absence of microorganisms. Microchip elec-trophoresis has been recently employed to address problems associated with the detection of microorganisms due to its high versatility, selectivity, sensitivity, and short analysis times. In this work, the potential of PDMS-based microchip electrophoresis in the identification and characterization of microorganism was evaluated. Enteropathogenic E. coli (EPEC) was selected as the model microorganism. To obtain repeat-able separations, sample pretreatment was found to be essential. Microchip electrophoresis with laser-induced fluorescence detection could potentially revolutionize certain aspects of microbiology involving diagnosis, profiling of pathogens, environmental analysis, and many others areas of study.

Multiphoton lithography using a high-repetition rate microchip laser.

PubMed

Ritschdorff, Eric T; Shear, Jason B

2010-10-15

Multiphoton lithography (MPL) provides a means to create prototype, three-dimensional (3D) materials for numerous applications in analysis and cell biology. A major impediment to the broad adoption of MPL in research laboratories is its reliance on high peak-power light sources, a requirement that typically has been met using expensive femtosecond titanium:sapphire lasers. Development of affordable microchip laser sources has the potential to substantially extend the reach of MPL, but previous lasers have provided relatively low pulse repetition rates (low kilohertz range), thereby limiting the rate at which microforms could be produced using this direct-write approach. In this report, we examine the MPL capabilities of a new, high-repetition-rate (36.6 kHz) microchip Nd:YAG laser. We show that this laser enables an approximate 4-fold decrease in fabrication times for protein-based microforms relative to the existing state-of-the-art microchip source and demonstrate its utility for creating complex 3D microarchitectures.

Microchip electrophoresis with electrochemical detection for the determination of analytes in the dopamine metabolic pathway

PubMed Central

Saylor, Rachel A.; Reid, Erin A.; Lunte, Susan M.

2016-01-01

A method for the separation and detection of analytes in the dopamine metabolic pathway was developed using microchip electrophoresis with electrochemical detection. The microchip consisted of a 5 cm PDMS separation channel in a simple-t configuration. Analytes in the dopamine metabolic pathway were separated using a background electrolyte composed of 15 mM phosphate at pH 7.4, 15 mM SDS, and 2.5 mM boric acid. Two different microchip substrates using different electrode materials were compared for the analysis: a PDMS/PDMS device with a carbon fiber electrode and a PDMS/glass hybrid device with a pyrolyzed photoresist film carbon electrode. While the PDMS/PDMS device generated high separation efficiencies and good resolution, more reproducible migration times were obtained with the PDMS/glass hybrid device, making it a better choice for biological applications. Lastly, the optimized method was used to monitor L-DOPA metabolism in a rat brain slice. PMID:25958983

Effect of Chain Rigidity on the Decoupling of Ion Motion from Segmental Relaxation in Polymerized Ionic Liquids: Ambient and Elevated Pressure Studies

DOE PAGES

Wojnarowska, Zaneta; Feng, Hongbo; Fu, Yao; ...

2017-08-21

Conductivity in polymer electrolytes has been generally discussed with the assumption that the segmental motions control charge transport. However, much less attention has been paid to the mechanism of ion conductivity where the motions of ions are less dependent (decoupled) on segmental dynamics. We present that this phenomenon is observed in ionic materials as they approach their glass transition temperature and becomes essential for design and development of highly conducting solid polymer electrolytes. In this paper, we study the effect of chain rigidity on the decoupling of ion transport from segmental motion in three polymerized ionic liquids (polyILs) containing themore » same cation–anion pair but differing in flexibility of the polymer backbones and side groups. Analysis of dielectric and rheology data reveals that decoupling is strong in vinyl-based rigid polymers while almost negligible in novel siloxane-based flexible polyILs. To explain this behavior, we investigated ion and chain dynamics at ambient and elevated pressure. Our results suggest that decoupling has a direct relationship to the frustration in chain packing and free volume. Finally, these conclusions are also supported by coarse-grained molecular dynamics simulations.« less

Effect of Chain Rigidity on the Decoupling of Ion Motion from Segmental Relaxation in Polymerized Ionic Liquids: Ambient and Elevated Pressure Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wojnarowska, Zaneta; Feng, Hongbo; Fu, Yao

Conductivity in polymer electrolytes has been generally discussed with the assumption that the segmental motions control charge transport. However, much less attention has been paid to the mechanism of ion conductivity where the motions of ions are less dependent (decoupled) on segmental dynamics. We present that this phenomenon is observed in ionic materials as they approach their glass transition temperature and becomes essential for design and development of highly conducting solid polymer electrolytes. In this paper, we study the effect of chain rigidity on the decoupling of ion transport from segmental motion in three polymerized ionic liquids (polyILs) containing themore » same cation–anion pair but differing in flexibility of the polymer backbones and side groups. Analysis of dielectric and rheology data reveals that decoupling is strong in vinyl-based rigid polymers while almost negligible in novel siloxane-based flexible polyILs. To explain this behavior, we investigated ion and chain dynamics at ambient and elevated pressure. Our results suggest that decoupling has a direct relationship to the frustration in chain packing and free volume. Finally, these conclusions are also supported by coarse-grained molecular dynamics simulations.« less

Research on segmentation based on multi-atlas in brain MR image

NASA Astrophysics Data System (ADS)

Qian, Yuejing

2018-03-01

Accurate segmentation of specific tissues in brain MR image can be effectively achieved with the multi-atlas-based segmentation method, and the accuracy mainly depends on the image registration accuracy and fusion scheme. This paper proposes an automatic segmentation method based on the multi-atlas for brain MR image. Firstly, to improve the registration accuracy in the area to be segmented, we employ a target-oriented image registration method for the refinement. Then In the label fusion, we proposed a new algorithm to detect the abnormal sparse patch and simultaneously abandon the corresponding abnormal sparse coefficients, this method is made based on the remaining sparse coefficients combined with the multipoint label estimator strategy. The performance of the proposed method was compared with those of the nonlocal patch-based label fusion method (Nonlocal-PBM), the sparse patch-based label fusion method (Sparse-PBM) and majority voting method (MV). Based on our experimental results, the proposed method is efficient in the brain MR images segmentation compared with MV, Nonlocal-PBM, and Sparse-PBM methods.

Multi-atlas based segmentation using probabilistic label fusion with adaptive weighting of image similarity measures.

PubMed

Sjöberg, C; Ahnesjö, A

2013-06-01

Label fusion multi-atlas approaches for image segmentation can give better segmentation results than single atlas methods. We present a multi-atlas label fusion strategy based on probabilistic weighting of distance maps. Relationships between image similarities and segmentation similarities are estimated in a learning phase and used to derive fusion weights that are proportional to the probability for each atlas to improve the segmentation result. The method was tested using a leave-one-out strategy on a database of 21 pre-segmented prostate patients for different image registrations combined with different image similarity scorings. The probabilistic weighting yields results that are equal or better compared to both fusion with equal weights and results using the STAPLE algorithm. Results from the experiments demonstrate that label fusion by weighted distance maps is feasible, and that probabilistic weighted fusion improves segmentation quality more the stronger the individual atlas segmentation quality depends on the corresponding registered image similarity. The regions used for evaluation of the image similarity measures were found to be more important than the choice of similarity measure. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

All-fiber pulse shortening of passively Q-switched microchip laser pulses down to sub-200 fs.

PubMed

Lehneis, R; Steinmetz, A; Limpert, J; Tünnermann, A

2014-10-15

We present an all-fiber concept that generates ultrashort pulses using a passively Q-switched microchip seed laser. A proof-of-principle configuration combines nonlinear pulse compression applying a chirped fiber-Bragg-grating, dispersion-free pulse shortening by means of a fiber-integrated spectral filtering, and a final hollow-core-fiber compression to reach the sub-200-fs pulse-duration region. In a compact all-fiber pulse-shortening unit, initial 100 ps long microchip pulses at 1064 nm wavelength have been shortened to 174 fs and shifted to 1034 nm while preserving a high temporal quality.

Wavelength-tunable, sub-picosecond pulses from a passively Q-switched microchip laser system.

PubMed

Lehneis, R; Steinmetz, A; Limpert, J; Tünnermann, A

2013-07-15

We present a novel concept to generate sub-picosecond pulses from a passively Q-switched Nd:YVO4 microchip laser system with an adjustable wavelength shift up to a few tens of nanometers around the original emission wavelength of 1064 nm. This concept comprises two stages: one that carries out a nonlinear compression of fiber-amplified microchip pulses and a subsequent stage in which the compressed pulses are coupled into a further waveguide structure followed by a bandpass filter. In a proof-of-principle experiment, pedestal-free 0.62 ps long pulses have been demonstrated with a wavelength shift to 1045 nm.

Direct generation of vector vortex beams with switchable radial and azimuthal polarizations in a monolithic Nd:YAG microchip laser

NASA Astrophysics Data System (ADS)

He, Hong-Sen; Chen, Zhen; Dong, Jun

2017-05-01

A hollow focus lens (HFL) has been designed to effectively produce a focused annular beam for high-intensity pumping. By applying the central-dark pump beam, a monolithic Nd:YAG microchip laser without any extra optical elements is demonstrated to generate vector vortex beams with switchable radially polarized (RP) and azimuthally polarized (AP) states by easily controlling the pump power. The order and handedness of the output vortex beam remain stable during the switching of the RP and AP states. The monolithic Nd:YAG microchip laser provides a new laser source for applications such as material processing and optical manipulation.

Laser-induced fluorescence microscopic system using an optical parametric oscillator for tunable detection in microchip analysis.

PubMed

Kumemura, Momoko; Odake, Tamao; Korenaga, Takashi

2005-06-01

A laser-induced fluorescence microscopic system based on optical parametric oscillation has been constructed as a tunable detector for microchip analysis. The detection limit of sulforhodamine B (Ex. 520 nm, Em. 570 nm) was 0.2 mumol, which was approximately eight orders of magnitude better than with a conventional fluorophotometer. The system was applied to the determination of fluorescence-labeled DNA (Ex. 494 nm, Em. 519 nm) in a microchannel and the detection limit reached a single molecule. These results showed the feasibility of this system as a highly sensitive and tunable fluorescence detector for microchip analysis.

Efficient second to ninth harmonic generation using megawatt peak power microchip laser.

PubMed

Bhandari, R; Tsuji, N; Suzuki, T; Nishifuji, M; Taira, T

2013-11-18

We report the design and use of a megawatt peak power Nd:YAG/Cr4+:YAG microchip laser for efficient second to ninth harmonic generation. We show that the sub-nanosecond pulse width region, between 100 ps and 1 ns, is ideally suited for efficient wavelength conversion. Using this feature, we report 85% second harmonic generation efficiency using lithium triborate (LBO), 60% fourth harmonic generation efficiency usingß-barium borate, and 44% IR to UV third harmonic generation efficiency using Type I and Type II LBO. Finally, we report the first demonstration of 118 nm VUV generation in xenon gas using a microchip laser.

Correlative fluorescence and electron microscopy of quantum dot labeled proteins on whole cells in liquid.

PubMed

Peckys, Diana B; Dukes, Madeline J; de Jonge, Niels

2014-01-01

Correlative fluorescence microscopy and scanning transmission electron microscopy (STEM) of cells fully immersed in liquid is a new methodology with many application areas. Proteins, in live cells immobilized on microchips, are labeled with fluorescent quantum dot (QD) nanoparticles. In this protocol, the epidermal growth factor receptor (EGFR) is labeled. The cells are fixed after a selected labeling time, for example, 5 min as needed to form EGFR dimers. The microchip with cells is then imaged with fluorescence microscopy. Thereafter, the microchip with the labeled cells and one with a spacer are assembled in a special microfluidic device and imaged with STEM.

Cryogenic Tm:YAP microchip laser

NASA Astrophysics Data System (ADS)

Hubka, Zbyněk.; Å ulc, Jan; Jelínková, Helena; Nejezchleb, Karel; Å koda, Václav

2016-04-01

The spectral characteristics of laser active media, and thus those of the laser output, are temperature dependent. Specifically, in almost every crystal host, cooling to low temperatures leads to better heat removal, a higher efficiency and output power, and a reduced lasing threshold. Tm-ion doped lasers have an emission wavelength around 2 μm and are important in medicine for soft tissue cutting and hemostasis, as well as in LIDAR or atmosphere sensing technology. This paper presents the performance-temperature dependency of a 4 at. % doped Tm:YAP microchip. During the experiment the Tm:YAP crystal was placed inside an evacuated liquid nitrogen cryostat on a cooling finger. As its temperature was varied from 80 K to 340 K, changes were observed in the absorption spectrum, ranging from 750 nm to 2000 nm and in the fluorescence spectrum from 1600 nm to 2050 nm. Fluorescence lifetime was seen to rise and fall with decreasing temperature. The laser was pumped by a 792 nm laser diode and at 80 K the maximum output peak power of the laser was 4.6 W with 23 % slope efficiency and 0.6 W threshold, compared to 2.4 W output peak power, 13 % slope efficiency and 3.3 W threshold when at 340 K. The laser emission wavelength changed from 1883 nm to 1993 nm for 80 K and 300 K, respectively.

Integrated Micro-Chip Amino Acid Chirality Detector for MOD

NASA Technical Reports Server (NTRS)

Glavin, D. P.; Bada, J. L.; Botta, O.; Kminek, G.; Grunthaner, F.; Mathies, R.

2001-01-01

Integration of a micro-chip capillary electrophoresis analyzer with a sublimation-based extraction technique, as used in the Mars Organic Detector (MOD), for the in-situ detection of amino acids and their enantiomers on solar system bodies. Additional information is contained in the original extended abstract.

Amperometric detector designs for capillary electrophoresis microchips.

PubMed

Castaño-Alvarez, Mario; Fernández-Abedul, M Teresa; Costa-García, Agustín

2006-03-24

Electrochemical (EC) detection is a sensitive and miniaturisable detection mode for capillary electrophoresis (CE) microchips. Detection cell design is very important in order to ensure electrical isolation from the high separation voltage. Amperometric detectors with different designs have been developed for coupling EC detection to CE-microchips. Different working electrode alignment: in-channel or end-channel has been tested in conjunction with several materials: gold, platinum or carbon. The end-channel detector was based on a platinum or gold wire manually aligned at the exit of the separation channel. Thick- (screen-printed carbon electrode) and thin-film (sputtered gold film) electrodes have also been employed with this configuration, but with a different design that allowed the rapid replacement of the electrode. The in-channel detector was based on a gold film within the separation channel. A gold-based dual electrode detector, which combined for the first time in- and end-channel detection, has been also tested. These amperometric detectors have been evaluated in combination to poly(methylmethacrylate) (PMMA) and Topas (thermoplastic olefin polymer of amorphous structure) CE-microchips. Topas is a new and promising cyclic olefin copolymer with high chemical resistance. Relevant parameters of the polymer microchip separation such as precision, efficiency or resolution and amperometric detection were studied with the different detector designs using p-aminophenol and L-ascorbic acid as model analytes in Tris-based buffer pH 9.0.

Activity recognition using Video Event Segmentation with Text (VEST)

NASA Astrophysics Data System (ADS)

Holloway, Hillary; Jones, Eric K.; Kaluzniacki, Andrew; Blasch, Erik; Tierno, Jorge

2014-06-01

Multi-Intelligence (multi-INT) data includes video, text, and signals that require analysis by operators. Analysis methods include information fusion approaches such as filtering, correlation, and association. In this paper, we discuss the Video Event Segmentation with Text (VEST) method, which provides event boundaries of an activity to compile related message and video clips for future interest. VEST infers meaningful activities by clustering multiple streams of time-sequenced multi-INT intelligence data and derived fusion products. We discuss exemplar results that segment raw full-motion video (FMV) data by using extracted commentary message timestamps, FMV metadata, and user-defined queries.

A novel magnet based 3D printed marker wand as basis for repeated in-shoe multi segment foot analysis: a proof of concept.

PubMed

Eerdekens, Maarten; Staes, Filip; Pilkington, Thomas; Deschamps, Kevin

2017-01-01

Application of in-shoe multi-segment foot kinematic analyses currently faces a number of challenges, including: (i) the difficulty to apply regular markers onto the skin, (ii) the necessity for an adequate shoe which fits various foot morphologies and (iii) the need for adequate repeatability throughout a repeated measure condition. The aim of this study therefore was to design novel magnet based 3D printed markers for repeated in-shoe measurements while using accordingly adapted modified shoes for a specific multi-segment foot model. Multi-segment foot kinematics of ten participants were recorded and kinematics of hindfoot, midfoot and forefoot were calculated. Dynamic trials were conducted to check for intra and inter-session repeatability when combining novel markers and modified shoes in a repeated measures design. Intraclass correlation coefficients were calculated to determine reliability. Both repeatability and reliability were proven to be good to excellent with maximum joint angle deviations of 1.11° for intra-session variability and 1.29° for same-day inter-session variability respectively and ICC values of >0.91. The novel markers can be reliably used in future research settings using in-shoe multi-segment foot kinematic analyses with multiple shod conditions.

Segmentation of Image Ensembles via Latent Atlases

PubMed Central

Van Leemput, Koen; Menze, Bjoern H.; Wells, William M.; Golland, Polina

2010-01-01

Spatial priors, such as probabilistic atlases, play an important role in MRI segmentation. However, the availability of comprehensive, reliable and suitable manual segmentations for atlas construction is limited. We therefore propose a method for joint segmentation of corresponding regions of interest in a collection of aligned images that does not require labeled training data. Instead, a latent atlas, initialized by at most a single manual segmentation, is inferred from the evolving segmentations of the ensemble. The algorithm is based on probabilistic principles but is solved using partial differential equations (PDEs) and energy minimization criteria. We evaluate the method on two datasets, segmenting subcortical and cortical structures in a multi-subject study and extracting brain tumors in a single-subject multi-modal longitudinal experiment. We compare the segmentation results to manual segmentations, when those exist, and to the results of a state-of-the-art atlas-based segmentation method. The quality of the results supports the latent atlas as a promising alternative when existing atlases are not compatible with the images to be segmented. PMID:20580305

Multi-atlas segmentation of the cartilage in knee MR images with sequential volume- and bone-mask-based registrations

NASA Astrophysics Data System (ADS)

Lee, Han Sang; Kim, Hyeun A.; Kim, Hyeonjin; Hong, Helen; Yoon, Young Cheol; Kim, Junmo

2016-03-01

In spite of its clinical importance in diagnosis of osteoarthritis, segmentation of cartilage in knee MRI remains a challenging task due to its shape variability and low contrast with surrounding soft tissues and synovial fluid. In this paper, we propose a multi-atlas segmentation of cartilage in knee MRI with sequential atlas registrations and locallyweighted voting (LWV). First, bone is segmented by sequential volume- and object-based registrations and LWV. Second, to overcome the shape variability of cartilage, cartilage is segmented by bone-mask-based registration and LWV. In experiments, the proposed method improved the bone segmentation by reducing misclassified bone region, and enhanced the cartilage segmentation by preventing cartilage leakage into surrounding similar intensity region, with the help of sequential registrations and LWV.

A method for automatic grain segmentation of multi-angle cross-polarized microscopic images of sandstone

NASA Astrophysics Data System (ADS)

Jiang, Feng; Gu, Qing; Hao, Huizhen; Li, Na; Wang, Bingqian; Hu, Xiumian

2018-06-01

Automatic grain segmentation of sandstone is to partition mineral grains into separate regions in the thin section, which is the first step for computer aided mineral identification and sandstone classification. The sandstone microscopic images contain a large number of mixed mineral grains where differences among adjacent grains, i.e., quartz, feldspar and lithic grains, are usually ambiguous, which make grain segmentation difficult. In this paper, we take advantage of multi-angle cross-polarized microscopic images and propose a method for grain segmentation with high accuracy. The method consists of two stages, in the first stage, we enhance the SLIC (Simple Linear Iterative Clustering) algorithm, named MSLIC, to make use of multi-angle images and segment the images as boundary adherent superpixels. In the second stage, we propose the region merging technique which combines the coarse merging and fine merging algorithms. The coarse merging merges the adjacent superpixels with less evident boundaries, and the fine merging merges the ambiguous superpixels using the spatial enhanced fuzzy clustering. Experiments are designed on 9 sets of multi-angle cross-polarized images taken from the three major types of sandstones. The results demonstrate both the effectiveness and potential of the proposed method, comparing to the available segmentation methods.

Neutral beam monitoring

DOEpatents

Fink, Joel H.

1981-08-18

Method and apparatus for monitoring characteristics of a high energy neutral beam. A neutral beam is generated by passing accelerated ions through a walled cell containing a low energy neutral gas, such that charge exchange neutralizes the high energy ion beam. The neutral beam is monitored by detecting the current flowing through the cell wall produced by low energy ions which drift to the wall after the charge exchange. By segmenting the wall into radial and longitudinal segments various beam conditions are further identified.

Evidence of impurity and boundary effects on magnetic monopole dynamics in spin ice

NASA Astrophysics Data System (ADS)

Revell, H. M.; Yaraskavitch, L. R.; Mason, J. D.; Ross, K. A.; Noad, H. M. L.; Dabkowska, H. A.; Gaulin, B. D.; Henelius, P.; Kycia, J. B.

2013-01-01

Electrical resistance is a crucial and well-understood property of systems ranging from computer microchips to nerve impulse propagation in the human body. Here we study the motion of magnetic charges in spin ice and find that extra spins inserted in Dy2Ti2O7 trap magnetic monopole excitations and provide the first example of how defects in a spin-ice material obstruct the flow of monopoles--a magnetic version of residual resistance. We measure the time-dependent magnetic relaxation in Dy2Ti2O7 and show that it decays with a stretched exponential followed by a very slow long-time tail. In a Monte Carlo simulation governed by Metropolis dynamics we show that surface effects and a very low level of stuffed spins (0.30%)--magnetic Dy ions substituted for non-magnetic Ti ions--cause these signatures in the relaxation. In addition, we find evidence that the rapidly diverging experimental timescale is due to a temperature-dependent attempt rate proportional to the monopole density.

Mechanisms Underlying Ionic Mobilities in Nanocomposite Polymer Electrolytes

NASA Astrophysics Data System (ADS)

Ganesan, Venkat; Hanson, Benjamin; Pryamitsyn, Victor

2014-03-01

Recently, a number of experiments have demonstrated that addition of ceramics with nanoscale dimensions can lead to substantial improvements in the low temperature conductivity of the polymeric materials. However, the origin of such behaviors, and more generally, the manner by which nanoscale fillers impact the ion mobilities remain unresolved. In this communication, we report the results of atomistic molecular dynamics simulations which used multibody polarizable force-fields to study lithium ion diffusivities in an amorphous poly(ethylene-oxide) (PEO) melt containing well-dispersed TiO2 nanoparticles. We observed that the lithium ion diffusivities decrease with increased particle loading. Our analysis suggests that the ion mobilities are correlated to the nanoparticle-induced changes in the polymer segmental dynamics. Interestingly, the changes in polymer segmental dynamics were seen to be related to the nanoparticle's influence on the polymer conformational features. Overall, our results indicate that addition of nanoparticle fillers modify polymer conformations and the polymer segmental dynamics, and thereby influence the ion mobilities of polymer electrolytes.

Fully Convolutional Neural Networks Improve Abdominal Organ Segmentation.

PubMed

Bobo, Meg F; Bao, Shunxing; Huo, Yuankai; Yao, Yuang; Virostko, Jack; Plassard, Andrew J; Lyu, Ilwoo; Assad, Albert; Abramson, Richard G; Hilmes, Melissa A; Landman, Bennett A

2018-03-01

Abdominal image segmentation is a challenging, yet important clinical problem. Variations in body size, position, and relative organ positions greatly complicate the segmentation process. Historically, multi-atlas methods have achieved leading results across imaging modalities and anatomical targets. However, deep learning is rapidly overtaking classical approaches for image segmentation. Recently, Zhou et al. showed that fully convolutional networks produce excellent results in abdominal organ segmentation of computed tomography (CT) scans. Yet, deep learning approaches have not been applied to whole abdomen magnetic resonance imaging (MRI) segmentation. Herein, we evaluate the applicability of an existing fully convolutional neural network (FCNN) designed for CT imaging to segment abdominal organs on T2 weighted (T2w) MRI's with two examples. In the primary example, we compare a classical multi-atlas approach with FCNN on forty-five T2w MRI's acquired from splenomegaly patients with five organs labeled (liver, spleen, left kidney, right kidney, and stomach). Thirty-six images were used for training while nine were used for testing. The FCNN resulted in a Dice similarity coefficient (DSC) of 0.930 in spleens, 0.730 in left kidneys, 0.780 in right kidneys, 0.913 in livers, and 0.556 in stomachs. The performance measures for livers, spleens, right kidneys, and stomachs were significantly better than multi-atlas (p < 0.05, Wilcoxon rank-sum test). In a secondary example, we compare the multi-atlas approach with FCNN on 138 distinct T2w MRI's with manually labeled pancreases (one label). On the pancreas dataset, the FCNN resulted in a median DSC of 0.691 in pancreases versus 0.287 for multi-atlas. The results are highly promising given relatively limited training data and without specific training of the FCNN model and illustrate the potential of deep learning approaches to transcend imaging modalities.

Fully convolutional neural networks improve abdominal organ segmentation

NASA Astrophysics Data System (ADS)

Bobo, Meg F.; Bao, Shunxing; Huo, Yuankai; Yao, Yuang; Virostko, Jack; Plassard, Andrew J.; Lyu, Ilwoo; Assad, Albert; Abramson, Richard G.; Hilmes, Melissa A.; Landman, Bennett A.

2018-03-01

Abdominal image segmentation is a challenging, yet important clinical problem. Variations in body size, position, and relative organ positions greatly complicate the segmentation process. Historically, multi-atlas methods have achieved leading results across imaging modalities and anatomical targets. However, deep learning is rapidly overtaking classical approaches for image segmentation. Recently, Zhou et al. showed that fully convolutional networks produce excellent results in abdominal organ segmentation of computed tomography (CT) scans. Yet, deep learning approaches have not been applied to whole abdomen magnetic resonance imaging (MRI) segmentation. Herein, we evaluate the applicability of an existing fully convolutional neural network (FCNN) designed for CT imaging to segment abdominal organs on T2 weighted (T2w) MRI's with two examples. In the primary example, we compare a classical multi-atlas approach with FCNN on forty-five T2w MRI's acquired from splenomegaly patients with five organs labeled (liver, spleen, left kidney, right kidney, and stomach). Thirty-six images were used for training while nine were used for testing. The FCNN resulted in a Dice similarity coefficient (DSC) of 0.930 in spleens, 0.730 in left kidneys, 0.780 in right kidneys, 0.913 in livers, and 0.556 in stomachs. The performance measures for livers, spleens, right kidneys, and stomachs were significantly better than multi-atlas (p < 0.05, Wilcoxon rank-sum test). In a secondary example, we compare the multi-atlas approach with FCNN on 138 distinct T2w MRI's with manually labeled pancreases (one label). On the pancreas dataset, the FCNN resulted in a median DSC of 0.691 in pancreases versus 0.287 for multi-atlas. The results are highly promising given relatively limited training data and without specific training of the FCNN model and illustrate the potential of deep learning approaches to transcend imaging modalities. 1

A Novel Ultrafast Rechargeable Multi-Ions Battery.

PubMed

Wang, Shuai; Jiao, Shuqiang; Tian, Donghua; Chen, Hao-Sen; Jiao, Handong; Tu, Jiguo; Liu, Yingjun; Fang, Dai-Ning

2017-04-01

An ultrafast rechargeable multi-ions battery is presented, in which multi-ions can electrochemically intercalate into graphite layers, exhibiting a high reversible discharge capacity of ≈100 mAh g -1 and a Coulombic efficiency of ≈99% over hundreds of cycles at a high current density. The results may open up a new paradigm for multi-ions-based electrochemical battery technologies and applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Measurement of monomolecular binding constants of neutral phenols into the beta-cyclodextrin by continuous frontal analysis in capillary and microchip electrophoresis via a competitive assay.

PubMed

Le Saux, Thomas; Hisamoto, Hideaki; Terabe, Shigeru

2006-02-03

Measurement of binding constant by chip electrophoresis is a very promising technique for the high throughput screening of non-covalent interactions. Among the different electrophoretic methods available that yield the binding parameters, continuous frontal analysis is the most appropriate for a transposition from capillary electrophoresis (CE) to microchip electrophoresis. Implementation of this methodology in microchip was exemplified by the measurement of inclusion constants of 2-naphtalenesulfonate and neutral phenols (phenol, 4-chlorophenol and 4-nitrophenol) into beta-cyclodextrin by competitive assays. The issue of competitor choice is discussed in relation to its appropriateness for proper monitoring of the interaction.

Inner structure detection by optical tomography technology based on feedback of microchip Nd:YAG lasers.

PubMed

Xu, Chunxin; Zhang, Shulian; Tan, Yidong; Zhao, Shijie

2013-05-20

We describe a new optical tomography technology based on feedback of microchip Nd:YAG lasers. In the case of feedback light frequency-shifted, light can be magnified by a fact of 10(6) in the Nd:YAG microchip lasers, which makes it possible to realize optical tomography with a greater depth than current optical tomography. The results of the measuring and imaging of kinds of samples are presented, which demonstrate the feasibility and potential of this approach in the inner structure detection. The system has a lateral resolution of ~1 μm, a vertical resolution of 15 μm and a longitudinal scanning range of over 10mm.

Integration of Multiple Components in Polystyrene-based Microfluidic Devices Part 1: Fabrication and Characterization

PubMed Central

Johnson, Alicia S.; Anderson, Kari B.; Halpin, Stephen T.; Kirkpatrick, Douglas C.; Spence, Dana M.; Martin, R. Scott

2012-01-01

In Part I of a two-part series, we describe a simple, and inexpensive approach to fabricate polystyrene devices that is based upon melting polystyrene (from either a Petri dish or powder form) against PDMS molds or around electrode materials. The ability to incorporate microchannels in polystyrene and integrate the resulting device with standard laboratory equipment such as an optical plate reader for analyte readout and micropipettors for fluid propulsion is first described. A simple approach for sample and reagent delivery to the device channels using a standard, multi-channel micropipette and a PDMS-based injection block is detailed. Integration of the microfluidic device with these off-chip functions (sample delivery and readout) enables high throughput screens and analyses. An approach to fabricate polystyrene-based devices with embedded electrodes is also demonstrated, thereby enabling the integration of microchip electrophoresis with electrochemical detection through the use of a palladium electrode (for a decoupler) and carbon-fiber bundle (for detection). The device was sealed against a PDMS-based microchannel and used for the electrophoretic separation and amperometric detection of dopamine, epinephrine, catechol, and 3,4-dihydroxyphenylacetic acid. Finally, these devices were compared against PDMS-based microchips in terms of their optical transparency and absorption of an anti-platelet drug, clopidogrel. Part I of this series lays the foundation for Part II, where these devices were utilized for various on-chip cellular analysis. PMID:23120747

Monolithic integrated optic fiber Bragg grating sensor interrogator

NASA Astrophysics Data System (ADS)

Mendoza, Edgar A.; Esterkin, Yan; Kempen, Cornelia; Sun, Songjian

2010-04-01

Fiber Bragg gratings (FBGs) are a mature sensing technology that has gained rapid acceptance in civil, aerospace, chemical and petrochemical, medicine, aviation and automotive industries. Fiber Bragg grating sensors can be use for a variety of measurements including strain, stress, vibration, acoustics, acceleration, pressure, temperature, moisture, and corrosion distributed at multiple locations within the structure using a single fiber element. The most prominent advantages of FBGs are: small size and light weight, multiple FBG transducers on a single fiber, and immunity to radio frequency interference. A major disadvantage of FBG technology is that conventional state-of-the-art fiber Bragg grating interrogation systems are typically bulky, heavy, and costly bench top instruments that are assembled from off-the-shelf fiber optic and optical components integrated with a signal electronics board into an instrument console. Based on the need for a compact FBG interrogation system, this paper describes recent progress towards the development of a miniature fiber Bragg grating sensor interrogator (FBG-TransceiverTM) system based on multi-channel monolithic integrated optic sensor microchip technology. The integrated optic microchip technology enables the monolithic integration of all of the functionalities, both passive and active, of conventional bench top FBG sensor interrogators systems, packaged in a miniaturized, low power operation, 2-cm x 5-cm small form factor (SFF) package suitable for the long-term structural health monitoring in applications where size, weight, and power are critical for operation.

Improved segmentation of cerebellar structures in children

PubMed Central

Narayanan, Priya Lakshmi; Boonazier, Natalie; Warton, Christopher; Molteno, Christopher D; Joseph, Jesuchristopher; Jacobson, Joseph L; Jacobson, Sandra W; Zöllei, Lilla; Meintjes, Ernesta M

2016-01-01

Background Consistent localization of cerebellar cortex in a standard coordinate system is important for functional studies and detection of anatomical alterations in studies of morphometry. To date, no pediatric cerebellar atlas is available. New method The probabilistic Cape Town Pediatric Cerebellar Atlas (CAPCA18) was constructed in the age-appropriate National Institute of Health Pediatric Database asymmetric template space using manual tracings of 16 cerebellar compartments in 18 healthy children (9–13 years) from Cape Town, South Africa. The individual atlases of the training subjects were also used to implement multi atlas label fusion using multi atlas majority voting (MAMV) and multi atlas generative model (MAGM) approaches. Segmentation accuracy in 14 test subjects was compared for each method to ‘gold standard’ manual tracings. Results Spatial overlap between manual tracings and CAPCA18 automated segmentation was 73% or higher for all lobules in both hemispheres, except VIIb and X. Automated segmentation using MAGM yielded the best segmentation accuracy over all lobules (mean Dice Similarity Coefficient 0.76; range 0.55–0.91). Comparison with existing methods In all lobules, spatial overlap of CAPCA18 segmentations with manual tracings was similar or higher than those obtained with SUIT (spatially unbiased infra-tentorial template), providing additional evidence of the benefits of an age appropriate atlas. MAGM segmentation accuracy was comparable to values reported recently by Park et al. (2014) in adults (across all lobules mean DSC = 0.73, range 0.40–0.89). Conclusions CAPCA18 and the associated multi atlases of the training subjects yield improved segmentation of cerebellar structures in children. PMID:26743973

Modelling of graphene Q-switched Tm lasers

NASA Astrophysics Data System (ADS)

Yasukevich, A. S.; Loiko, P.; Gusakova, N. V.; Serres, J. M.; Mateos, X.; Yumashev, K. V.; Kuleshov, N. V.; Petrov, V.; Griebner, U.; Aguiló, M.; Díaz, F.

2017-04-01

We report on a model of diode-pumped Thulium lasers passively Q-switched by a graphene saturable absorber applicable also for any other "fast" saturable absorber. It reasonably predicts the dependence of the pulse duration, pulse energy and pulse repetition frequency on the absorbed power. The model is applied in the present work for a Tm: KLuW microchip laser passively Q-switched with a multi-layer graphene saturable absorber. The laser generates 1 W at 1926 nm with a slope efficiency of 39%. Stable 190 ns /4.1 μJ pulses are achieved at a pulse repetition frequency of 260 kHz. The potential of graphene for the generation of few-ns pulses at 2 μm is discussed.

Tube Radial Distribution Flow Separation in a Microchannel Using an Ionic Liquid Aqueous Two-Phase System Based on Phase Separation Multi-Phase Flow.

PubMed

Nagatani, Kosuke; Shihata, Yoshinori; Matsushita, Takahiro; Tsukagoshi, Kazuhiko

2016-01-01

Ionic liquid aqueous two-phase systems were delivered into a capillary tube to achieve tube radial distribution flow (TRDF) or annular flow in a microspace. The phase diagram, viscosity of the phases, and TRDF image of the 1-butyl-3-methylimidazolium chloride and NaOH system were examined. The TRDF was formed with inner ionic liquid-rich and outer ionic liquid-poor phases in the capillary tube. The phase configuration was explained using the viscous dissipation principle. We also examined the distribution of rhodamine B in a three-branched microchannel on a microchip with ionic liquid aqueous two-phase systems for the first time.

Segmented frequency-domain fluorescence lifetime measurements: minimizing the effects of photobleaching within a multi-component system.

PubMed

Marwani, Hadi M; Lowry, Mark; Keating, Patrick; Warner, Isiah M; Cook, Robert L

2007-11-01

This study introduces a newly developed frequency segmentation and recombination method for frequency-domain fluorescence lifetime measurements to address the effects of changing fractional contributions over time and minimize the effects of photobleaching within multi-component systems. Frequency segmentation and recombination experiments were evaluated using a two component system consisting of fluorescein and rhodamine B. Comparison of experimental data collected in traditional and segmented fashion with simulated data, generated using different changing fractional contributions, demonstrated the validity of the technique. Frequency segmentation and recombination was also applied to a more complex system consisting of pyrene with Suwannee River fulvic acid reference and was shown to improve recovered lifetimes and fractional intensity contributions. It was observed that photobleaching in both systems led to errors in recovered lifetimes which can complicate the interpretation of lifetime results. Results showed clear evidence that the frequency segmentation and recombination method reduced errors resulting from a changing fractional contribution in a multi-component system, and allowed photobleaching issues to be addressed by commercially available instrumentation.

Polymer microchip CE of proteins either off- or on-chip labeled with chameleon dye for simplified analysis.

PubMed

Yu, Ming; Wang, Hsiang-Yu; Woolley, Adam T

2009-12-01

Microchip CE of proteins labeled either off- or on-chip with the "chameleon" CE dye 503 using poly(methyl methacrylate) microchips is presented. A simple dynamic coating using the cationic surfactant CTAB prevented nonspecific adsorption of protein and dye to the channel walls. The labeling reactions for both off- and on-chip labeling proceeded at room temperature without requiring heating steps. In off-chip labeling, a 9 ng/mL concentration detection limit for BSA, corresponding to a approximately 7 fg (100 zmol) mass detection limit, was obtained. In on-chip tagging, the free dye and protein were placed in different reservoirs of the microchip, and an extra incubation step was not needed. A 1 microg/mL concentration detection limit for BSA, corresponding to a approximately 700 fg (10 amol) mass detection limit, was obtained from this protocol. The earlier elution time of the BSA peak in on-chip labeling resulted from fewer total labels on each protein molecule. Our on-chip labeling method is an important part of automation in miniaturized devices.

Recent developments in optical detection methods for microchip separations.

PubMed

Götz, Sebastian; Karst, Uwe

2007-01-01

This paper summarizes the features and performances of optical detection systems currently applied in order to monitor separations on microchip devices. Fluorescence detection, which delivers very high sensitivity and selectivity, is still the most widely applied method of detection. Instruments utilizing laser-induced fluorescence (LIF) and lamp-based fluorescence along with recent applications of light-emitting diodes (LED) as excitation sources are also covered in this paper. Since chemiluminescence detection can be achieved using extremely simple devices which no longer require light sources and optical components for focusing and collimation, interesting approaches based on this technique are presented, too. Although UV/vis absorbance is a detection method that is commonly used in standard desktop electrophoresis and liquid chromatography instruments, it has not yet reached the same level of popularity for microchip applications. Current applications of UV/vis absorbance detection to microchip separations and innovative approaches that increase sensitivity are described. This article, which contains 85 references, focuses on developments and applications published within the last three years, points out exciting new approaches, and provides future perspectives on this field.

Precise determination of N-acetylcysteine in pharmaceuticals by microchip electrophoresis.

PubMed

Rudašová, Marína; Masár, Marián

2016-01-01

A novel microchip electrophoresis method for the rapid and high-precision determination of N-acetylcysteine, a pharmaceutically active ingredient, in mucolytics has been developed. Isotachophoresis separations were carried out at pH 6.0 on a microchip with conductivity detection. The methods of external calibration and internal standard were used to evaluate the results. The internal standard method effectively eliminated variations in various working parameters, mainly run-to-run fluctuations of an injected volume. The repeatability and accuracy of N-acetylcysteine determination in all mucolytic preparations tested (Solmucol 90 and 200, and ACC Long 600) were more than satisfactory with the relative standard deviation and relative error values <0.7 and <1.9%, respectively. A recovery range of 99-101% of N-acetylcysteine in the analyzed pharmaceuticals predetermines the proposed method for accurate analysis as well. This work, in general, indicates analytical possibilities of microchip isotachophoresis for the quantitative analysis of simplified samples such as pharmaceuticals that contain the analyte(s) at relatively high concentrations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Optimization of Electrophoresis on a Glass Microfluidic Chip and its Application in Forensic Science.

PubMed

Han, Jun P; Sun, Jing; Wang, Le; Liu, Peng; Zhuang, Bin; Zhao, Lei; Liu, Yao; Li, Cai X

2017-11-01

Microfluidic chips offer significant speed, cost, and sensitivity advantages, but numerous parameters must be optimized to provide microchip electrophoresis detection. Experiments were conducted to study the factors, including sieving matrices (the concentration and type), surface modification, analysis temperature, and electric field strengths, which all impact the effectiveness of microchip electrophoresis detection of DNA samples. Our results showed that the best resolution for ssDNA was observed using 4.5% w/v (7 M urea) lab-fabricated LPA gel, dynamic wall coating of the microchannel, electrophoresis temperatures between 55 and 60°C, and electrical fields between 350 and 450 V/cm on the microchip-based capillary electrophoresis (μCE) system. One base-pair resolution could be achieved in the 19-cm-length microchannel. Furthermore, both 9947A standard genomic DNA and DNA extracted from blood spots were demonstrated to be successfully separated with well-resolved DNA peaks in 8 min. Therefore, the microchip electrophoresis system demonstrated good potential for rapid forensic DNA analysis. © 2017 American Academy of Forensic Sciences.

Rapid sample screening method for authenticity controlling vanilla flavors using a CE microchip approach with electrochemical detection.

PubMed

Avila, Mónica; González, María Cristina; Zougagh, Mohammed; Escarpa, Alberto; Ríos, Angel

2007-11-01

Five vanilla-related flavors of food significance, vanillic alcohol (VOH), ethyl maltol (EMA), maltol (MAL), ethyl vanillin (EVA) and vanillin (VAN), were separated using CE microchips with electrochemical detection (CE-ED microchips). A +2 kV driving voltage for both injection and separation operation steps, using a borate buffer (pH 9.5, 20 mM) and 1 M nitric acid in the detection reservoir allowed the selective and sensitive detection of the target analytes in less than 200 s with reproducible control of EOF (RSD(migration times)<3%). The analysis in selected real vanilla samples was focusing on VAN and EVA because VAN is a basic fragrance compound of the vanilla aroma, whereas EVA is an unequivocal proof of adulteration of vanilla flavors. Fast detection of all relevant flavors (200 s) with an acceptable resolution (R(s) >1.5) and a high accuracy (recoveries higher than 90%) were obtained with independence of the matrices and samples examined. These results showed the reliability of the method and the potential use of CE microchips in the food control field for fraudulent purposes.

In-band-pumped Ho:KLu(WO4)2 microchip laser with 84% slope efficiency.

PubMed

Loiko, Pavel; Serres, Josep Maria; Mateos, Xavier; Yumashev, Konstantin; Kuleshov, Nikolai; Petrov, Valentin; Griebner, Uwe; Aguiló, Magdalena; Díaz, Francesc

2015-02-01

We report on a continuous-wave Ho:KLu(WO4)2 (KLuW) microchip laser with a record slope efficiency of 84%, the highest value among the holmium inband-pumped lasers, delivering 201 mW output power at 2105 nm. The Ho laser operating at room temperature on the (5)I8→(5)I7 transition is in-band-pumped by a diode-pumped Tm:KLuW microchip laser at 1946 nm. Ho:KLuW laser operation at 2061 and 2079 nm is also demonstrated with a maximum slope efficiency of 79%. The microchip laser generates an almost diffraction-limited output beam with a Gaussian profile and a M2<1.1. The laser performance of the Ng-cut Ho:KLuW crystal is very similar for pump light polarizations ‖Nm and Np. The positive thermal lens plays a key role in the laser mode stabilization and proper mode-matching. The latter, together with the low quantum defect under in-band-pumping (∼0.08), is responsible for the extraordinary high slope efficiency.

Multi-atlas pancreas segmentation: Atlas selection based on vessel structure.

PubMed

Karasawa, Ken'ichi; Oda, Masahiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Chu, Chengwen; Zheng, Guoyan; Rueckert, Daniel; Mori, Kensaku

2017-07-01

Automated organ segmentation from medical images is an indispensable component for clinical applications such as computer-aided diagnosis (CAD) and computer-assisted surgery (CAS). We utilize a multi-atlas segmentation scheme, which has recently been used in different approaches in the literature to achieve more accurate and robust segmentation of anatomical structures in computed tomography (CT) volume data. Among abdominal organs, the pancreas has large inter-patient variability in its position, size and shape. Moreover, the CT intensity of the pancreas closely resembles adjacent tissues, rendering its segmentation a challenging task. Due to this, conventional intensity-based atlas selection for pancreas segmentation often fails to select atlases that are similar in pancreas position and shape to those of the unlabeled target volume. In this paper, we propose a new atlas selection strategy based on vessel structure around the pancreatic tissue and demonstrate its application to a multi-atlas pancreas segmentation. Our method utilizes vessel structure around the pancreas to select atlases with high pancreatic resemblance to the unlabeled volume. Also, we investigate two types of applications of the vessel structure information to the atlas selection. Our segmentations were evaluated on 150 abdominal contrast-enhanced CT volumes. The experimental results showed that our approach can segment the pancreas with an average Jaccard index of 66.3% and an average Dice overlap coefficient of 78.5%. Copyright © 2017 Elsevier B.V. All rights reserved.

Time evolution of negative ion profile in a large cesiated negative ion source applicable to fusion reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshida, M., E-mail: yoshida.masafumi@jaea.go.jp; Hanada, M.; Kojima, A.

2016-02-15

To understand the physics of the cesium (Cs) recycling in the large Cs-seeded negative ion sources relevant to ITER and JT-60SA with ion extraction area of 45-60 cm × 110-120 cm, the time evolution of the negative ion profile was precisely measured in JT-60SA where the ion extraction area is longitudinally segmented into 5. The Cs was seeded from the oven at 180 °C to the ion source. After 1 g of Cs input, surface production of the negative ions appeared only in the central segment where a Cs nozzle was located. Up to 2 g of Cs, the negative ionmore » profile was longitudinally expanded over full ion extraction area. The measured time evolution of the negative ion profile has the similar tendency of distribution of the Cs atoms that is calculated. From the results, it is suggested that Cs atom distribution is correlated with the formation of the negative ion profile.« less

A disposable laser print-cut-laminate polyester microchip for multiplexed PCR via infra-red-mediated thermal control.

PubMed

Ouyang, Yiwen; Duarte, Gabriela R M; Poe, Brian L; Riehl, Paul S; dos Santos, Fernando M; Martin-Didonet, Claudia C G; Carrilho, Emanuel; Landers, James P

2015-12-11

Infrared (IR)-mediated thermal cycling system, a method proven to be a effective for sub-μL scale polymerase chain reaction (PCR) on microchips, has been integrated with DNA extraction and separation on a glass microchip in a fully integrated micro Total Analysis System by Easley et al., in 2006. IR-PCR has been demonstrated on both glass and PMMA microdevices where the fabrication (bonding) is not trivial. Polyester-toner (PeT) microfluidic devices have significant potential as cost-effective, disposable microdevices as a result of the ease of fabrication (∼$0.25 USD and <10 min per device) and availability of commercial substrates. For the first time, we demonstrate here the thermal cycling in PeT microchips on the IR-PCR system. Undesirable IR absorption by the black-toner bonding layer was eliminated with a spatial filter in the form of an aluminum foil mask. The solution heating rate for a black PeT microchip using a tungsten lamp was 10.1 ± 0.7 °C s(-1) with a cooling rate of roughly -12 ± 0.9 °C s(-1) assisted by forced air cooling. Dynamic surface passivation strategies allowed the successful amplification of a 520 bp fragment of the λ-phage genome (in 11 min) and a 1500 bp region of Azospirillum brasilense. Using a centrosymmetric chamber configuration in a multichamber PeT microchip, homogenous temperature distribution over all chambers was achieved with inter-chamber temperature differences at annealing, extension and denaturing steps of less than ±2 °C. The effectiveness of the multichamber system was demonstrated with the simultaneous amplification of a 390 bp amplicon of human β-globin gene in five PeT PCR microchambers. The relative PCR amplification efficiency with a human β-globin DNA fragment ranged from 70% to 90%, in comparison to conventional thermal cyclers, with an inter-chamber standard deviation of ∼10%. Development of PeT microchips for IR-PCR has the potential to provide rapid, low-volume amplification while also integrating PCR with extraction upstream and separation/detection downstream. Copyright © 2015. Published by Elsevier B.V.

Multi-atlas segmentation with joint label fusion and corrective learning—an open source implementation

PubMed Central

Wang, Hongzhi; Yushkevich, Paul A.

2013-01-01

Label fusion based multi-atlas segmentation has proven to be one of the most competitive techniques for medical image segmentation. This technique transfers segmentations from expert-labeled images, called atlases, to a novel image using deformable image registration. Errors produced by label transfer are further reduced by label fusion that combines the results produced by all atlases into a consensus solution. Among the proposed label fusion strategies, weighted voting with spatially varying weight distributions derived from atlas-target intensity similarity is a simple and highly effective label fusion technique. However, one limitation of most weighted voting methods is that the weights are computed independently for each atlas, without taking into account the fact that different atlases may produce similar label errors. To address this problem, we recently developed the joint label fusion technique and the corrective learning technique, which won the first place of the 2012 MICCAI Multi-Atlas Labeling Challenge and was one of the top performers in 2013 MICCAI Segmentation: Algorithms, Theory and Applications (SATA) challenge. To make our techniques more accessible to the scientific research community, we describe an Insight-Toolkit based open source implementation of our label fusion methods. Our implementation extends our methods to work with multi-modality imaging data and is more suitable for segmentation problems with multiple labels. We demonstrate the usage of our tools through applying them to the 2012 MICCAI Multi-Atlas Labeling Challenge brain image dataset and the 2013 SATA challenge canine leg image dataset. We report the best results on these two datasets so far. PMID:24319427

A comparative study on dynamic stiffness in typical finite element model and multi-body model of C6-C7 cervical spine segment.

PubMed

Wang, Yawei; Wang, Lizhen; Du, Chengfei; Mo, Zhongjun; Fan, Yubo

2016-06-01

In contrast to numerous researches on static or quasi-static stiffness of cervical spine segments, very few investigations on their dynamic stiffness were published. Currently, scale factors and estimated coefficients were usually used in multi-body models for including viscoelastic properties and damping effects, meanwhile viscoelastic properties of some tissues were unavailable for establishing finite element models. Because dynamic stiffness of cervical spine segments in these models were difficult to validate because of lacking in experimental data, we tried to gain some insights on current modeling methods through studying dynamic stiffness differences between these models. A finite element model and a multi-body model of C6-C7 segment were developed through using available material data and typical modeling technologies. These two models were validated with quasi-static response data of the C6-C7 cervical spine segment. Dynamic stiffness differences were investigated through controlling motions of C6 vertebrae at different rates and then comparing their reaction forces or moments. Validation results showed that both the finite element model and the multi-body model could generate reasonable responses under quasi-static loads, but the finite element segment model exhibited more nonlinear characters. Dynamic response investigations indicated that dynamic stiffness of this finite element model might be underestimated because of the absence of dynamic stiffen effect and damping effects of annulus fibrous, while representation of these effects also need to be improved in current multi-body model. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

An adaptive multi-feature segmentation model for infrared image

NASA Astrophysics Data System (ADS)

Zhang, Tingting; Han, Jin; Zhang, Yi; Bai, Lianfa

2016-04-01

Active contour models (ACM) have been extensively applied to image segmentation, conventional region-based active contour models only utilize global or local single feature information to minimize the energy functional to drive the contour evolution. Considering the limitations of original ACMs, an adaptive multi-feature segmentation model is proposed to handle infrared images with blurred boundaries and low contrast. In the proposed model, several essential local statistic features are introduced to construct a multi-feature signed pressure function (MFSPF). In addition, we draw upon the adaptive weight coefficient to modify the level set formulation, which is formed by integrating MFSPF with local statistic features and signed pressure function with global information. Experimental results demonstrate that the proposed method can make up for the inadequacy of the original method and get desirable results in segmenting infrared images.

The use of an ion-beam source to alter the surface morphology of biological implant materials

NASA Technical Reports Server (NTRS)

Weigand, A. J.

1978-01-01

An electron-bombardment ion-thruster was used as a neutralized-ion-beam sputtering source to texture the surfaces of biological implant materials. The materials investigated included 316 stainless steel; titanium-6% aluminum, 4% vanadium; cobalt-20% chromium, 15% tungsten; cobalt-35% nickel, 20% chromium, 10% molybdenum; polytetrafluoroethylene; polyoxymethylene; silicone and polyurethane copolymer; 32%-carbon-impregnated polyolefin; segmented polyurethane; silicone rubber; and alumina. Scanning electron microscopy was used to determine surface morphology changes of all materials after ion-texturing. Electron spectroscopy for chemical analysis was used to determine the effects of ion-texturing on the surface chemical composition of some polymers. Liquid contact angle data were obtained for ion-textured and untextured polymer samples. Results of tensile and fatigue tests of ion-textured metal alloys are presented. Preliminary data of tissue response to ion-textured surfaces of some metals, polytetrafluoroethylene, alumina, and segmented polyurethane have been obtained.

Automated unsupervised multi-parametric classification of adipose tissue depots in skeletal muscle

PubMed Central

Valentinitsch, Alexander; Karampinos, Dimitrios C.; Alizai, Hamza; Subburaj, Karupppasamy; Kumar, Deepak; Link, Thomas M.; Majumdar, Sharmila

2012-01-01

Purpose To introduce and validate an automated unsupervised multi-parametric method for segmentation of the subcutaneous fat and muscle regions in order to determine subcutaneous adipose tissue (SAT) and intermuscular adipose tissue (IMAT) areas based on data from a quantitative chemical shift-based water-fat separation approach. Materials and Methods Unsupervised standard k-means clustering was employed to define sets of similar features (k = 2) within the whole multi-modal image after the water-fat separation. The automated image processing chain was composed of three primary stages including tissue, muscle and bone region segmentation. The algorithm was applied on calf and thigh datasets to compute SAT and IMAT areas and was compared to a manual segmentation. Results The IMAT area using the automatic segmentation had excellent agreement with the IMAT area using the manual segmentation for all the cases in the thigh (R2: 0.96) and for cases with up to moderate IMAT area in the calf (R2: 0.92). The group with the highest grade of muscle fat infiltration in the calf had the highest error in the inner SAT contour calculation. Conclusion The proposed multi-parametric segmentation approach combined with quantitative water-fat imaging provides an accurate and reliable method for an automated calculation of the SAT and IMAT areas reducing considerably the total post-processing time. PMID:23097409

Optofluidic encapsulation and manipulation of silicon microchips using image processing based optofluidic maskless lithography and railed microfluidics.

PubMed

Chung, Su Eun; Lee, Seung Ah; Kim, Jiyun; Kwon, Sunghoon

2009-10-07

We demonstrate optofluidic encapsulation of silicon microchips using image processing based optofluidic maskless lithography and manipulation using railed microfluidics. Optofluidic maskless lithography is a dynamic photopolymerization technique of free-floating microstructures within a fluidic channel using spatial light modulator. Using optofluidic maskless lithography via computer-vision aided image processing, polymer encapsulants are fabricated for chip protection and guiding-fins for efficient chip conveying within a fluidic channel. Encapsulated silicon chips with guiding-fins are assembled using railed microfluidics, which is an efficient guiding and heterogeneous self-assembly system of microcomponents. With our technology, externally fabricated silicon microchips are encapsulated, fluidically guided and self-assembled potentially enabling low cost fluidic manipulation and assembly of integrated circuits.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2014-2016).

PubMed

Breadmore, Michael C; Wuethrich, Alain; Li, Feng; Phung, Sui Ching; Kalsoom, Umme; Cabot, Joan M; Tehranirokh, Masoomeh; Shallan, Aliaa I; Abdul Keyon, Aemi S; See, Hong Heng; Dawod, Mohamed; Quirino, Joselito P

2017-01-01

One of the most cited limitations of capillary (and microchip) electrophoresis is the poor sensitivity. This review continues to update this series of biennial reviews, first published in Electrophoresis in 2007, on developments in the field of on-line/in-line concentration methods in capillaries and microchips, covering the period July 2014-June 2016. It includes developments in the field of stacking, covering all methods from field amplified sample stacking and large volume sample stacking, through to isotachophoresis, dynamic pH junction, and sweeping. Attention is also given to on-line or in-line extraction methods that have been used for electrophoresis. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-efficiency microchip laser with self-injection seeding.

PubMed

Wang, Sha; Wang, Yan-biao; Yang, Xian-heng; Feng, Guo-ying; Zhou, Shou-huan

2015-12-10

In this paper, we use a small bandwidth 808 nm cw Ti:sapphire laser as a pump source to pump a picosecond microchip laser. Different focal length pump focus lenses have been tested to improve laser efficiency. A maximum slope efficiency of around 20% is obtained by a 30 mm focal length lens. The pump threshold is only 13 mW. In order to reduce the timing jitter, we explored the self-injection seeding method by adding a seeding cavity to the microchip laser. A reduction factor in the timing jitter of up to a factor of 23 relative to the unseeded laser is obtained. From the experiments, we also found that higher seeding pulse energy will help to reduce the jitter more.

Design and Fabrication of a PDMS Microchip Based Immunoassay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shao, Guocheng; Wang, Wanjun; Wang, Jun

2010-07-01

In this paper, we describe the design and fabrication process of a polydimethylsiloxane (PDMS) microchip for on-chip multiplex immunoassay application. The microchip consists of a PDMS microfluidic channel layer and a micro pneumatic valve control layer. By selectively pressurizing the pneumatic microvalves, immuno reagents were controlled to flow and react in certain fluidic channel sites. Cross contamination was prevented by tightly closed valves. Our design was proposed to utilize PDMS micro channel surface as the solid phase immunoassay substrate and simultaneously detect four targets antigens on chip. Experiment result shows that 20psi valve pressure is sufficient to tightly close amore » 200µm wide micro channel with flow rate up to 20µl/min.« less

High-pulse-energy passively Q-switched quasi-monolithic microchip lasers operating in the sub-100-ps pulse regime.

PubMed

Nodop, D; Limpert, J; Hohmuth, R; Richter, W; Guina, M; Tünnermann, A

2007-08-01

We present passively Q-switched microchip lasers with items bonded by spin-on-glass glue. Passive Q-switching is obtained by a semiconductor saturable absorber mirror. The laser medium is a Nd:YVO(4) crystal. These lasers generate pulse peak powers up to 20 kW at a pulse duration as short as 50 ps and pulse repetition rates of 166 kHz. At 1064 nm, a linear polarized transversal and longitudinal single-mode beam is emitted. To the best of our knowledge, these are the shortest pulses in the 1 microJ energy range ever obtained with passively Q-switched microchip lasers. The quasi-monolithic setup ensures stable and reliable performance.

A Monolithic Multisensor Microchip with Complete On-Chip RF Front-End

PubMed Central

Felini, Corrado; Della Corte, Francesco G.

2018-01-01

In this paper, a new wireless sensor, designed for a 0.35 µm CMOS technology, is presented. The microchip was designed to be placed on an object for the continuous remote monitoring of its temperature and illumination state. The temperature sensor is based on the temperature dependence of the I-V characteristics of bipolar transistors available in CMOS technology, while the illumination sensor is an integrated p-n junction photodiode. An on-chip 2.5 GHz transmitter, coupled to a mm-sized dipole radiating element fabricated on the same microchip and made in the top metal layer of the same die, sends the collected data wirelessly to a radio receiver using an On-Off Keying (OOK) modulation pattern. PMID:29301297

Dynamic 3D scanning as a markerless method to calculate multi-segment foot kinematics during stance phase: methodology and first application.

PubMed

Van den Herrewegen, Inge; Cuppens, Kris; Broeckx, Mario; Barisch-Fritz, Bettina; Vander Sloten, Jos; Leardini, Alberto; Peeraer, Louis

2014-08-22

Multi-segmental foot kinematics have been analyzed by means of optical marker-sets or by means of inertial sensors, but never by markerless dynamic 3D scanning (D3DScanning). The use of D3DScans implies a radically different approach for the construction of the multi-segment foot model: the foot anatomy is identified via the surface shape instead of distinct landmark points. We propose a 4-segment foot model consisting of the shank (Sha), calcaneus (Cal), metatarsus (Met) and hallux (Hal). These segments are manually selected on a static scan. To track the segments in the dynamic scan, the segments of the static scan are matched on each frame of the dynamic scan using the iterative closest point (ICP) fitting algorithm. Joint rotations are calculated between Sha-Cal, Cal-Met, and Met-Hal. Due to the lower quality scans at heel strike and toe off, the first and last 10% of the stance phase is excluded. The application of the method to 5 healthy subjects, 6 trials each, shows a good repeatability (intra-subject standard deviations between 1° and 2.5°) for Sha-Cal and Cal-Met joints, and inferior results for the Met-Hal joint (>3°). The repeatability seems to be subject-dependent. For the validation, a qualitative comparison with joint kinematics from a corresponding established marker-based multi-segment foot model is made. This shows very consistent patterns of rotation. The ease of subject preparation and also the effective and easy to interpret visual output, make the present technique very attractive for functional analysis of the foot, enhancing usability in clinical practice. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Automatic Segmentation of Fluorescence Lifetime Microscopy Images of Cells Using Multi-Resolution Community Detection -A First Study

PubMed Central

Hu, Dandan; Sarder, Pinaki; Ronhovde, Peter; Orthaus, Sandra; Achilefu, Samuel; Nussinov, Zohar

2014-01-01

Inspired by a multi-resolution community detection (MCD) based network segmentation method, we suggest an automatic method for segmenting fluorescence lifetime (FLT) imaging microscopy (FLIM) images of cells in a first pilot investigation on two selected images. The image processing problem is framed as identifying segments with respective average FLTs against the background in FLIM images. The proposed method segments a FLIM image for a given resolution of the network defined using image pixels as the nodes and similarity between the FLTs of the pixels as the edges. In the resulting segmentation, low network resolution leads to larger segments, and high network resolution leads to smaller segments. Further, using the proposed method, the mean-square error (MSE) in estimating the FLT segments in a FLIM image was found to consistently decrease with increasing resolution of the corresponding network. The MCD method appeared to perform better than a popular spectral clustering based method in performing FLIM image segmentation. At high resolution, the spectral segmentation method introduced noisy segments in its output, and it was unable to achieve a consistent decrease in MSE with increasing resolution. PMID:24251410

Peak capacity and peak capacity per unit time in capillary and microchip zone electrophoresis.

PubMed

Foley, Joe P; Blackney, Donna M; Ennis, Erin J

2017-11-10

The origins of the peak capacity concept are described and the important contributions to the development of that concept in chromatography and electrophoresis are reviewed. Whereas numerous quantitative expressions have been reported for one- and two-dimensional separations, most are focused on chromatographic separations and few, if any, quantitative unbiased expressions have been developed for capillary or microchip zone electrophoresis. Making the common assumption that longitudinal diffusion is the predominant source of zone broadening in capillary electrophoresis, analytical expressions for the peak capacity are derived, first in terms of migration time, diffusion coefficient, migration distance, and desired resolution, and then in terms of the remaining underlying fundamental parameters (electric field, electroosmotic and electrophoretic mobilities) that determine the migration time. The latter expressions clearly illustrate the direct square root dependence of peak capacity on electric field and migration distance and the inverse square root dependence on solute diffusion coefficient. Conditions that result in a high peak capacity will result in a low peak capacity per unit time and vice-versa. For a given symmetrical range of relative electrophoretic mobilities for co- and counter-electroosmotic species (cations and anions), the peak capacity increases with the square root of the electric field even as the temporal window narrows considerably, resulting in a significant reduction in analysis time. Over a broad relative electrophoretic mobility interval [-0.9, 0.9], an approximately two-fold greater amount of peak capacity can be generated for counter-electroosmotic species although it takes about five-fold longer to do so, consistent with the well-known bias in migration time and resolving power for co- and counter-electroosmotic species. The optimum lower bound of the relative electrophoretic mobility interval [μ r,Z , μ r,A ] that provides the maximum peak capacity per unit time is a simple function of the upper bound, but its direct application is limited to samples with analytes whose electrophoretic mobilities can be varied independently of electroosmotic flow. For samples containing both co- and counter-electroosmotic ions whose electrophoretic mobilities cannot be easily manipulated, comparable levels of peak capacity and peak capacity per unit time for all ions can be obtained by adjusting the EOF to devote the same amount of time to the separation of each class of ions; this corresponds to μ r,Z =-0.5. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of a kinetic multi-segment foot model. Part I: Model repeatability and kinematic validity.

PubMed

Bruening, Dustin A; Cooney, Kevin M; Buczek, Frank L

2012-04-01

Kinematic multi-segment foot models are still evolving, but have seen increased use in clinical and research settings. The addition of kinetics may increase knowledge of foot and ankle function as well as influence multi-segment foot model evolution; however, previous kinetic models are too complex for clinical use. In this study we present a three-segment kinetic foot model and thorough evaluation of model performance during normal gait. In this first of two companion papers, model reference frames and joint centers are analyzed for repeatability, joint translations are measured, segment rigidity characterized, and sample joint angles presented. Within-tester and between-tester repeatability were first assessed using 10 healthy pediatric participants, while kinematic parameters were subsequently measured on 17 additional healthy pediatric participants. Repeatability errors were generally low for all sagittal plane measures as well as transverse plane Hindfoot and Forefoot segments (median<3°), while the least repeatable orientations were the Hindfoot coronal plane and Hallux transverse plane. Joint translations were generally less than 2mm in any one direction, while segment rigidity analysis suggested rigid body behavior for the Shank and Hindfoot, with the Forefoot violating the rigid body assumptions in terminal stance/pre-swing. Joint excursions were consistent with previously published studies. Copyright © 2012 Elsevier B.V. All rights reserved.

SU-E-J-110: A Novel Level Set Active Contour Algorithm for Multimodality Joint Segmentation/Registration Using the Jensen-Rényi Divergence.

PubMed

Markel, D; Naqa, I El; Freeman, C; Vallières, M

2012-06-01

To present a novel joint segmentation/registration for multimodality image-guided and adaptive radiotherapy. A major challenge to this framework is the sensitivity of many segmentation or registration algorithms to noise. Presented is a level set active contour based on the Jensen-Renyi (JR) divergence to achieve improved noise robustness in a multi-modality imaging space. To present a novel joint segmentation/registration for multimodality image-guided and adaptive radiotherapy. A major challenge to this framework is the sensitivity of many segmentation or registration algorithms to noise. Presented is a level set active contour based on the Jensen-Renyi (JR) divergence to achieve improved noise robustness in a multi-modality imaging space. It was found that JR divergence when used for segmentation has an improved robustness to noise compared to using mutual information, or other entropy-based metrics. The MI metric failed at around 2/3 the noise power than the JR divergence. The JR divergence metric is useful for the task of joint segmentation/registration of multimodality images and shows improved results compared entropy based metric. The algorithm can be easily modified to incorporate non-intensity based images, which would allow applications into multi-modality and texture analysis. © 2012 American Association of Physicists in Medicine.

Method of Grassland Information Extraction Based on Multi-Level Segmentation and Cart Model

NASA Astrophysics Data System (ADS)

Qiao, Y.; Chen, T.; He, J.; Wen, Q.; Liu, F.; Wang, Z.

2018-04-01

It is difficult to extract grassland accurately by traditional classification methods, such as supervised method based on pixels or objects. This paper proposed a new method combing the multi-level segmentation with CART (classification and regression tree) model. The multi-level segmentation which combined the multi-resolution segmentation and the spectral difference segmentation could avoid the over and insufficient segmentation seen in the single segmentation mode. The CART model was established based on the spectral characteristics and texture feature which were excavated from training sample data. Xilinhaote City in Inner Mongolia Autonomous Region was chosen as the typical study area and the proposed method was verified by using visual interpretation results as approximate truth value. Meanwhile, the comparison with the nearest neighbor supervised classification method was obtained. The experimental results showed that the total precision of classification and the Kappa coefficient of the proposed method was 95 % and 0.9, respectively. However, the total precision of classification and the Kappa coefficient of the nearest neighbor supervised classification method was 80 % and 0.56, respectively. The result suggested that the accuracy of classification proposed in this paper was higher than the nearest neighbor supervised classification method. The experiment certificated that the proposed method was an effective extraction method of grassland information, which could enhance the boundary of grassland classification and avoid the restriction of grassland distribution scale. This method was also applicable to the extraction of grassland information in other regions with complicated spatial features, which could avoid the interference of woodland, arable land and water body effectively.

Classification of heavy metal ions present in multi-frequency multi-electrode potable water data using evolutionary algorithm

NASA Astrophysics Data System (ADS)

Karkra, Rashmi; Kumar, Prashant; Bansod, Baban K. S.; Bagchi, Sudeshna; Sharma, Pooja; Krishna, C. Rama

2017-11-01

Access to potable water for the common people is one of the most challenging tasks in the present era. Contamination of drinking water has become a serious problem due to various anthropogenic and geogenic events. The paper demonstrates the application of evolutionary algorithms, viz., particle swan optimization and genetic algorithm to 24 water samples containing eight different heavy metal ions (Cd, Cu, Co, Pb, Zn, Ar, Cr and Ni) for the optimal estimation of electrode and frequency to classify the heavy metal ions. The work has been carried out on multi-variate data, viz., single electrode multi-frequency, single frequency multi-electrode and multi-frequency multi-electrode water samples. The electrodes used are platinum, gold, silver nanoparticles and glassy carbon electrodes. Various hazardous metal ions present in the water samples have been optimally classified and validated by the application of Davis Bouldin index. Such studies are useful in the segregation of hazardous heavy metal ions found in water resources, thereby quantifying the degree of water quality.

Low voltage electrophoresis chip with multi-segments synchronized scanning

NASA Astrophysics Data System (ADS)

Gu, Wenwen; Wen, Zhiyu; Xu, Yi

2017-03-01

For low voltage electrophoresis chip, there is always a problem that the samples are truncated and peaks are broadened, as well as longer time for separation. In this paper, a low voltage electrophoresis separation model was established, and the separation conditions were discussed. A new driving mode was proposed for applying low voltage, which was called multi-segments synchronized scanning. By using this driving mode, the reversed electric field that existed between the multi-segments can enrich samples and shorten the sample zone. The low voltage electrophoresis experiments using multi-segments synchronized scanning were carried out by home-made silicon-PDMS-based chip. The fluorescein isothiocyanate (FITC) labeled lysine and phenylalanine mixed samples with the concentration of 10-4 mol/L were successfully separated under the optimal conditions of 10 mmol/L borax buffer (pH = 10.0), 200 V/cm separation electric field and electrode switch time of 2.5 s. The separation was completed with a resolution of 2.0, and the peak time for lysine and phenylalanine was 4 min and 6 min, respectively.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes.

PubMed

Fredlake, Christopher P; Hert, Daniel G; Kan, Cheuk-Wai; Chiesl, Thomas N; Root, Brian E; Forster, Ryan E; Barron, Annelise E

2008-01-15

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

PubMed Central

Fredlake, Christopher P.; Hert, Daniel G.; Kan, Cheuk-Wai; Chiesl, Thomas N.; Root, Brian E.; Forster, Ryan E.; Barron, Annelise E.

2008-01-01

To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require ≈70 min to deliver ≈650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered “hybrid” mechanism of DNA electromigration, in which DNA molecules alternate rapidly between reptating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs. PMID:18184818

Encapsulation of Fluidic Tubing and Microelectrodes in Microfluidic Devices: Integrating Off-Chip Process and Coupling Conventional Capillary Electrophoresis with Electrochemical Detection

PubMed Central

Becirovic, Vedada; Doonan, Steven R.; Martin, R. Scott

2013-01-01

In this paper, an approach to fabricate epoxy or polystyrene microdevices with encapsulated tubing and electrodes is described. Key features of this approach include a fixed alignment between the fluidic tubing and electrodes, the ability to polish the device when desired, and the low dead volume nature of the fluidic interconnects. It is shown that a variety of tubing can be encapsulated with this approach, including fused silica capillary, polyetheretherketone (PEEK), and perfluoroalkoxy (PFA), with the resulting tubing/microchip interface not leading to significant band broadening or plug dilution. The applicability of the devices with embedded tubing is demonstrated by integrating several off-chip analytical methods to the microchip. This includes droplet transfer, droplet desegmentation, and microchip-based flow injection analysis. Off-chip generated droplets can be transferred to the microchip with minimal coalescence, while flow injection studies showed improved peak shape and sensitivity when compared to the use of fluidic interconnects with an appreciable dead volume. Importantly, it is shown that this low dead volume approach can be extended to also enable the integration of conventional capillary electrophoresis (CE) with electrochemical detection. This is accomplished by embedding fused silica capillary along with palladium (for grounding the electrophoresis voltage) and platinum (for detection) electrodes. With this approach, up to 128,000 theoretical plates for dopamine was possible. In all cases, the tubing and electrodes are housed in a rigid base; this results in extremely robust devices that will be of interest to researchers wanting to develop microchips for use by non-experts. PMID:24159363

Encapsulation of Fluidic Tubing and Microelectrodes in Microfluidic Devices: Integrating Off-Chip Process and Coupling Conventional Capillary Electrophoresis with Electrochemical Detection.

PubMed

Becirovic, Vedada; Doonan, Steven R; Martin, R Scott

2013-08-21

In this paper, an approach to fabricate epoxy or polystyrene microdevices with encapsulated tubing and electrodes is described. Key features of this approach include a fixed alignment between the fluidic tubing and electrodes, the ability to polish the device when desired, and the low dead volume nature of the fluidic interconnects. It is shown that a variety of tubing can be encapsulated with this approach, including fused silica capillary, polyetheretherketone (PEEK), and perfluoroalkoxy (PFA), with the resulting tubing/microchip interface not leading to significant band broadening or plug dilution. The applicability of the devices with embedded tubing is demonstrated by integrating several off-chip analytical methods to the microchip. This includes droplet transfer, droplet desegmentation, and microchip-based flow injection analysis. Off-chip generated droplets can be transferred to the microchip with minimal coalescence, while flow injection studies showed improved peak shape and sensitivity when compared to the use of fluidic interconnects with an appreciable dead volume. Importantly, it is shown that this low dead volume approach can be extended to also enable the integration of conventional capillary electrophoresis (CE) with electrochemical detection. This is accomplished by embedding fused silica capillary along with palladium (for grounding the electrophoresis voltage) and platinum (for detection) electrodes. With this approach, up to 128,000 theoretical plates for dopamine was possible. In all cases, the tubing and electrodes are housed in a rigid base; this results in extremely robust devices that will be of interest to researchers wanting to develop microchips for use by non-experts.

High-efficient Nd:YAG microchip laser for optical surface scanning

NASA Astrophysics Data System (ADS)

Šulc, Jan; Jelínková, Helena; Nejezchleb, Karel; Škoda, Václav

2017-12-01

A CW operating, compact, high-power, high-efficient diode pumped 1064nm laser, based on Nd:YAG active medium, was developed for optical surface scanning and mapping applications. To enhance the output beam quality, laser stability, and compactness, a microchip configuration was used. In this arrangement the resonator mirrors were deposited directly on to the laser crystal faces. The Nd-doping concentration was 1 at.% Nd/Y. The Nd:YAG crystal was 5mm long. The laser resonator without pumping radiation recuperation was investigated {the output coupler was transparent for pumping radiation. For the generated laser radiation the output coupler reflectivity was 95%@1064 nm. The diameter of the samples was 5 mm. For the laser pumping two arrangements were investigated. Firstly, a fibre coupled laser diode operating at wavelength 808nm was used in CW mode. The 400 ¹m fiber was delivering up to 14W of pump power amplitude to the microchip laser. The maximum CW output power of 7.2W @ 1064nm in close to TEM00 beam was obtained for incident pumping power 13.7W @ 808 nm. The differential efficiency in respect to the incident pump power reached 56 %. Secondly, a single-emitter, 1W laser diode operating at 808nm was used for Nd:YAG microchip pumping. The laser pumping was directly coupled into the microchip laser using free-space lens optics. Slope efficiency up to 70% was obtained in stable, high-quality, 1064nm laser beam with CW power up to 350mW. The system was successfully used for scanning of super-Gaussian laser mirrors reflectivity profile.

Multi-Sectional Views Textural Based SVM for MS Lesion Segmentation in Multi-Channels MRIs

PubMed Central

Abdullah, Bassem A; Younis, Akmal A; John, Nigel M

2012-01-01

In this paper, a new technique is proposed for automatic segmentation of multiple sclerosis (MS) lesions from brain magnetic resonance imaging (MRI) data. The technique uses a trained support vector machine (SVM) to discriminate between the blocks in regions of MS lesions and the blocks in non-MS lesion regions mainly based on the textural features with aid of the other features. The classification is done on each of the axial, sagittal and coronal sectional brain view independently and the resultant segmentations are aggregated to provide more accurate output segmentation. The main contribution of the proposed technique described in this paper is the use of textural features to detect MS lesions in a fully automated approach that does not rely on manually delineating the MS lesions. In addition, the technique introduces the concept of the multi-sectional view segmentation to produce verified segmentation. The proposed textural-based SVM technique was evaluated using three simulated datasets and more than fifty real MRI datasets. The results were compared with state of the art methods. The obtained results indicate that the proposed method would be viable for use in clinical practice for the detection of MS lesions in MRI. PMID:22741026

Hippocampal unified multi-atlas network (HUMAN): protocol and scale validation of a novel segmentation tool.

PubMed

Amoroso, N; Errico, R; Bruno, S; Chincarini, A; Garuccio, E; Sensi, F; Tangaro, S; Tateo, A; Bellotti, R

2015-11-21

In this study we present a novel fully automated Hippocampal Unified Multi-Atlas-Networks (HUMAN) algorithm for the segmentation of the hippocampus in structural magnetic resonance imaging. In multi-atlas approaches atlas selection is of crucial importance for the accuracy of the segmentation. Here we present an optimized method based on the definition of a small peri-hippocampal region to target the atlas learning with linear and non-linear embedded manifolds. All atlases were co-registered to a data driven template resulting in a computationally efficient method that requires only one test registration. The optimal atlases identified were used to train dedicated artificial neural networks whose labels were then propagated and fused to obtain the final segmentation. To quantify data heterogeneity and protocol inherent effects, HUMAN was tested on two independent data sets provided by the Alzheimer's Disease Neuroimaging Initiative and the Open Access Series of Imaging Studies. HUMAN is accurate and achieves state-of-the-art performance (Dice[Formula: see text] and Dice[Formula: see text]). It is also a robust method that remains stable when applied to the whole hippocampus or to sub-regions (patches). HUMAN also compares favorably with a basic multi-atlas approach and a benchmark segmentation tool such as FreeSurfer.

Hippocampal unified multi-atlas network (HUMAN): protocol and scale validation of a novel segmentation tool

NASA Astrophysics Data System (ADS)

Amoroso, N.; Errico, R.; Bruno, S.; Chincarini, A.; Garuccio, E.; Sensi, F.; Tangaro, S.; Tateo, A.; Bellotti, R.; Alzheimers Disease Neuroimaging Initiative,the

2015-11-01

In this study we present a novel fully automated Hippocampal Unified Multi-Atlas-Networks (HUMAN) algorithm for the segmentation of the hippocampus in structural magnetic resonance imaging. In multi-atlas approaches atlas selection is of crucial importance for the accuracy of the segmentation. Here we present an optimized method based on the definition of a small peri-hippocampal region to target the atlas learning with linear and non-linear embedded manifolds. All atlases were co-registered to a data driven template resulting in a computationally efficient method that requires only one test registration. The optimal atlases identified were used to train dedicated artificial neural networks whose labels were then propagated and fused to obtain the final segmentation. To quantify data heterogeneity and protocol inherent effects, HUMAN was tested on two independent data sets provided by the Alzheimer’s Disease Neuroimaging Initiative and the Open Access Series of Imaging Studies. HUMAN is accurate and achieves state-of-the-art performance (Dice{{}\\text{ADNI}} =0.929+/- 0.003 and Dice{{}\\text{OASIS}} =0.869+/- 0.002 ). It is also a robust method that remains stable when applied to the whole hippocampus or to sub-regions (patches). HUMAN also compares favorably with a basic multi-atlas approach and a benchmark segmentation tool such as FreeSurfer.

Material transport method and apparatus

DOEpatents

Ramsey, J. Michael; Ramsey, Roswitha S.

2000-01-01

An electrospray apparatus uses a microchannel formed in a microchip. Fluid is pumped through the channel to an outlet orifice using either hydraulic or electrokinetic means. An electrospray is generated by establishing a sufficient potential difference between the fluid at the outlet orifice and a target electrode spaced from the outlet orifice. Electrokinetic pumping is also utilized to provide additional benefits to microchip devices.

Material transport method and apparatus

DOEpatents

Ramsey, J. Michael; Ramsey, Roswitha S.

2001-01-01

An electrospray apparatus uses a microchannel formed in a microchip. Fluid is pumped through the channel to an outlet orifice using either hydraulic or electrokinetic means. An electrospray is generated by establishing a sufficient potential difference between the fluid at the outlet orifice and a target electrode spaced from the outlet orifice. Electrokinetic pumping is also utilized to provide additional benefits to microchip devices.

From Bonding Wires to Banding Women. Proceedings of the International Consultation on Micro-Chips Technology (Manila, Philippines, October 1986).

ERIC Educational Resources Information Center

Center for Women's Resources, Quezon City (Philippines).

In October 1986, 40 women from 12 countries gathered in the Philippines for a 10-day meeting of organizers, educators, and workers affected by and confronting the international electronics industry in microchip plants and in automated offices. Participants were from Malaysia, Indonesia, Thailand, the Philippines, Hong Kong, Japan, the Netherlands,…

Particle-free microchip processing

DOEpatents

Geller, Anthony S.; Rader, Daniel J.

1996-01-01

Method and apparatus for reducing particulate contamination in microchip processing are disclosed. The method and apparatus comprise means to reduce particle velocity toward the wafer before the particles can be deposited on the wafer surface. A reactor using electric fields to reduce particle velocity and prevent particulate contamination is disclosed. A reactor using a porous showerhead to reduce particle velocities and prevent particulate contamination is disclosed.

Single-frequency Ince-Gaussian mode operations of laser-diode-pumped microchip solid-state lasers.

PubMed

Ohtomo, Takayuki; Kamikariya, Koji; Otsuka, Kenju; Chu, Shu-Chun

2007-08-20

Various single-frequency Ince-Gaussian mode oscillations have been achieved in laser-diode-pumped microchip solid-state lasers, including LiNdP(4)O(12) (LNP) and Nd:GdVO(4), by adjusting the azimuthal symmetry of the short laser resonator. Ince-Gaussian modes formed by astigmatic pumping have been reproduced by numerical simulation.

Polymer microchip capillary electrophoresis of proteins either off- or on-chip labeled with chameleon dye for simplified analysis

PubMed Central

Yu, Ming; Wang, Hsiang-Yu; Woolley, Adam

2009-01-01

Microchip capillary electrophoresis of proteins labeled either off- or on-chip with the “chameleon” CE dye 503 using poly(methyl methacrylate) microchips is presented. A simple dynamic coating using the cationic surfactant cetyltrimethyl ammonium bromide prevented nonspecific adsorption of protein and dye to the channel walls. The labeling reactions for both off- and on-chip labeling proceeded at room temperature without requiring heating steps. In off-chip labeling, a 9 ng/mL concentration detection limit for bovine serum albumin (BSA), corresponding to a ~7 fg (100 zmol) mass detection limit, was obtained. In on-chip tagging, the free dye and protein were placed in different reservoirs of the microchip, and an extra incubation step was not needed. A 1 μg/mL concentration detection limit for BSA, corresponding to a ~700 fg (10 amol) mass detection limit, was obtained from this protocol. The earlier elution time of the BSA peak in on-chip labeling resulted from fewer total labels on each protein molecule. Our on-chip labeling method is an important part of automation in miniaturized devices. PMID:19924700

Detection of Plasmodium Aldolase Using a Smartphone and Microfluidic Enzyme Linked Immunosorbent Assay

PubMed Central

2017-01-01

Background Malaria control efforts are limited in rural areas. A low-cost system to monitor response without the use of electricity is needed. Plasmodium aldolase is a malaria biomarker measured using enzyme linked immunosorbent assay (ELISA) techniques. A three-part system using ELISA was developed consisting of a microfluidic chip, hand crank centrifuge, and a smartphone. Methods A circular microfluidic chip was fabricated using clear acrylic and a CO2 laser. A series of passive valves released reagents at precise times based upon centrifugal force. Color change was measured via smartphone camera using an application programmed in Java. The microchip was compared to a standard 96-well sandwich ELISA. Results Results from standard ELISA were compared to microchip at varying concentrations (1–10 ng/mL). Over 15 different microfluidic patterns were tested, and a final prototype of the chip was created. The prototype microchip was compared to standard sandwich ELISA (n = 20) using samples of recombinant aldolase. Color readings of standard ELISA and microfluidic microchip showed similar results. Conclusion A low-cost microfluidic system could detect and follow therapeutic outcomes in rural areas and identify resistant strains. PMID:29057138

Sensitive, label-free protein assay using 1-ethyl-3-methylimidazolium tetrafluoroborate-supported microchip electrophoresis with laser-induced fluorescence detection.

PubMed

Xu, Yuanhong; Li, Jing; Wang, Erkang

2008-05-01

Based on the dimer-monomer equilibrium movement of the fluorescent dye Pyronin Y (PY), a rapid, simple, highly sensitive, label-free method for protein detection was developed by microchip electrophoresis with LIF detection. PY formed a nonfluorescent dimer induced by the premicellar aggregation of an anionic surfactant, SDS, however, the fluorescence intensity of the system increased dramatically when proteins such as BSA, bovine hemoglobin, cytochrome c, and trypsin were added to the solution due to the transition of dimer to fluorescent monomer. Furthermore, 1-ethyl-3-methylimidazolium tetrafluoroborate (EMImBF4) instead of PBS was applied as running buffers in microchip electrophoresis. Due to the excellent properties of EMImBF4, not only nonspecific protein adsorption was more efficiently suppressed, but also approximately ten-fold higher fluorescence intensity enhancement was obtained than that using PBS. Under the optimal conditions, detection limits for BSA, bovine hemoglobin, cytochrome c, and trypsin were 1.00x10(-6), 2x10(-6), 7x10(-7), and 5x10(-7) mg/mL, respectively. Thus, without covalent modification of the protein, a protein assay method with high sensitivity was achieved on microchips.

Integration of Microdialysis Sampling and Microchip Electrophoresis with Electrochemical Detection

PubMed Central

Mecker, Laura C.; Martin, R. Scott

2009-01-01

Here we describe the fabrication, optimization, and application of a microfluidic device that integrates microdialysis (MD) sampling, microchip electrophoresis (ME), and electrochemical detection (EC). The manner in which the chip is produced is reproducible and enables the fixed alignment of the MD/ME and ME/EC interfaces. Poly(dimethylsiloxane) (PDMS) -based valves were used for the discrete injection of sample from the hydrodynamic MD dialysate stream into a separation channel for analysis with ME. To enable the integration of ME with EC detection, a palladium decoupler was used to isolate the high voltages associated with electrophoresis from micron-sized carbon ink detection electrodes. Optimization of the ME/EC interface was needed to allow the use of biologically appropriate perfusate buffers containing high salt content. This optimization included changes in the fabrication procedure, increases in the decoupler surface area, and a programmed voltage shutoff. The ability of the MD/ME/EC system to sample a biological system was demonstrated by using a linear probe to monitor the stimulated release of dopamine from a confluent layer of PC 12 cells. To our knowledge, this is the first report of a microchip-based system that couples microdialysis sampling with microchip electrophoresis and electrochemical detection. PMID:19551945

Targeting as the basis for pre-test market of lithium-ion battery

NASA Astrophysics Data System (ADS)

Yuniaristanto, Zakaria, R.; Saputri, V. H. L.; Sutopo, W.; Kadir, E. A.

2017-11-01

This article discusses about market segmentation and targeting as a first step in pre-test market of a new technology. The benefits of targeting towards pre-test market are pre-test market can be conducted to focus on selected target markets so there is no bias during the pre-test market. In determining the target market then do some surveys to identify the state of market in the future, so that the marketing process is not misplaced. Lithium ion battery which is commercialized through start-up companies is the case study. This start-up companies must be able to respond the changes and bring in customers as well as maintain them so that companies can survive and evolve to achieve its objectives. The research aims to determine market segments and target market effectively. Marketing strategy (segmentation and targeting) is used to make questionnaire and cluster analysis in data processing. Respondents were selected by purposive sampling and have obtained data as many as 80 samples. As the results study, there are three segments for lithium ion battery with their own distinguished characteristics and there are two segments that can be used as the target market for the company.

A proposed framework for consensus-based lung tumour volume auto-segmentation in 4D computed tomography imaging

NASA Astrophysics Data System (ADS)

Martin, Spencer; Brophy, Mark; Palma, David; Louie, Alexander V.; Yu, Edward; Yaremko, Brian; Ahmad, Belal; Barron, John L.; Beauchemin, Steven S.; Rodrigues, George; Gaede, Stewart

2015-02-01

This work aims to propose and validate a framework for tumour volume auto-segmentation based on ground-truth estimates derived from multi-physician input contours to expedite 4D-CT based lung tumour volume delineation. 4D-CT datasets of ten non-small cell lung cancer (NSCLC) patients were manually segmented by 6 physicians. Multi-expert ground truth (GT) estimates were constructed using the STAPLE algorithm for the gross tumour volume (GTV) on all respiratory phases. Next, using a deformable model-based method, multi-expert GT on each individual phase of the 4D-CT dataset was propagated to all other phases providing auto-segmented GTVs and motion encompassing internal gross target volumes (IGTVs) based on GT estimates (STAPLE) from each respiratory phase of the 4D-CT dataset. Accuracy assessment of auto-segmentation employed graph cuts for 3D-shape reconstruction and point-set registration-based analysis yielding volumetric and distance-based measures. STAPLE-based auto-segmented GTV accuracy ranged from (81.51  ±  1.92) to (97.27  ±  0.28)% volumetric overlap of the estimated ground truth. IGTV auto-segmentation showed significantly improved accuracies with reduced variance for all patients ranging from 90.87 to 98.57% volumetric overlap of the ground truth volume. Additional metrics supported these observations with statistical significance. Accuracy of auto-segmentation was shown to be largely independent of selection of the initial propagation phase. IGTV construction based on auto-segmented GTVs within the 4D-CT dataset provided accurate and reliable target volumes compared to manual segmentation-based GT estimates. While inter-/intra-observer effects were largely mitigated, the proposed segmentation workflow is more complex than that of current clinical practice and requires further development.

A proposed framework for consensus-based lung tumour volume auto-segmentation in 4D computed tomography imaging.

PubMed

Martin, Spencer; Brophy, Mark; Palma, David; Louie, Alexander V; Yu, Edward; Yaremko, Brian; Ahmad, Belal; Barron, John L; Beauchemin, Steven S; Rodrigues, George; Gaede, Stewart

2015-02-21

This work aims to propose and validate a framework for tumour volume auto-segmentation based on ground-truth estimates derived from multi-physician input contours to expedite 4D-CT based lung tumour volume delineation. 4D-CT datasets of ten non-small cell lung cancer (NSCLC) patients were manually segmented by 6 physicians. Multi-expert ground truth (GT) estimates were constructed using the STAPLE algorithm for the gross tumour volume (GTV) on all respiratory phases. Next, using a deformable model-based method, multi-expert GT on each individual phase of the 4D-CT dataset was propagated to all other phases providing auto-segmented GTVs and motion encompassing internal gross target volumes (IGTVs) based on GT estimates (STAPLE) from each respiratory phase of the 4D-CT dataset. Accuracy assessment of auto-segmentation employed graph cuts for 3D-shape reconstruction and point-set registration-based analysis yielding volumetric and distance-based measures. STAPLE-based auto-segmented GTV accuracy ranged from (81.51  ±  1.92) to (97.27  ±  0.28)% volumetric overlap of the estimated ground truth. IGTV auto-segmentation showed significantly improved accuracies with reduced variance for all patients ranging from 90.87 to 98.57% volumetric overlap of the ground truth volume. Additional metrics supported these observations with statistical significance. Accuracy of auto-segmentation was shown to be largely independent of selection of the initial propagation phase. IGTV construction based on auto-segmented GTVs within the 4D-CT dataset provided accurate and reliable target volumes compared to manual segmentation-based GT estimates. While inter-/intra-observer effects were largely mitigated, the proposed segmentation workflow is more complex than that of current clinical practice and requires further development.

Performance of an Artificial Multi-observer Deep Neural Network for Fully Automated Segmentation of Polycystic Kidneys.

PubMed

Kline, Timothy L; Korfiatis, Panagiotis; Edwards, Marie E; Blais, Jaime D; Czerwiec, Frank S; Harris, Peter C; King, Bernard F; Torres, Vicente E; Erickson, Bradley J

2017-08-01

Deep learning techniques are being rapidly applied to medical imaging tasks-from organ and lesion segmentation to tissue and tumor classification. These techniques are becoming the leading algorithmic approaches to solve inherently difficult image processing tasks. Currently, the most critical requirement for successful implementation lies in the need for relatively large datasets that can be used for training the deep learning networks. Based on our initial studies of MR imaging examinations of the kidneys of patients affected by polycystic kidney disease (PKD), we have generated a unique database of imaging data and corresponding reference standard segmentations of polycystic kidneys. In the study of PKD, segmentation of the kidneys is needed in order to measure total kidney volume (TKV). Automated methods to segment the kidneys and measure TKV are needed to increase measurement throughput and alleviate the inherent variability of human-derived measurements. We hypothesize that deep learning techniques can be leveraged to perform fast, accurate, reproducible, and fully automated segmentation of polycystic kidneys. Here, we describe a fully automated approach for segmenting PKD kidneys within MR images that simulates a multi-observer approach in order to create an accurate and robust method for the task of segmentation and computation of TKV for PKD patients. A total of 2000 cases were used for training and validation, and 400 cases were used for testing. The multi-observer ensemble method had mean ± SD percent volume difference of 0.68 ± 2.2% compared with the reference standard segmentations. The complete framework performs fully automated segmentation at a level comparable with interobserver variability and could be considered as a replacement for the task of segmentation of PKD kidneys by a human.

Segmentation of hepatic artery in multi-phase liver CT using directional dilation and connectivity analysis

NASA Astrophysics Data System (ADS)

Wang, Lei; Schnurr, Alena-Kathrin; Zidowitz, Stephan; Georgii, Joachim; Zhao, Yue; Razavi, Mohammad; Schwier, Michael; Hahn, Horst K.; Hansen, Christian

2016-03-01

Segmentation of hepatic arteries in multi-phase computed tomography (CT) images is indispensable in liver surgery planning. During image acquisition, the hepatic artery is enhanced by the injection of contrast agent. The enhanced signals are often not stably acquired due to non-optimal contrast timing. Other vascular structure, such as hepatic vein or portal vein, can be enhanced as well in the arterial phase, which can adversely affect the segmentation results. Furthermore, the arteries might suffer from partial volume effects due to their small diameter. To overcome these difficulties, we propose a framework for robust hepatic artery segmentation requiring a minimal amount of user interaction. First, an efficient multi-scale Hessian-based vesselness filter is applied on the artery phase CT image, aiming to enhance vessel structures with specified diameter range. Second, the vesselness response is processed using a Bayesian classifier to identify the most probable vessel structures. Considering the vesselness filter normally performs not ideally on the vessel bifurcations or the segments corrupted by noise, two vessel-reconnection techniques are proposed. The first technique uses a directional morphological operator to dilate vessel segments along their centerline directions, attempting to fill the gap between broken vascular segments. The second technique analyzes the connectivity of vessel segments and reconnects disconnected segments and branches. Finally, a 3D vessel tree is reconstructed. The algorithm has been evaluated using 18 CT images of the liver. To quantitatively measure the similarities between segmented and reference vessel trees, the skeleton coverage and mean symmetric distance are calculated to quantify the agreement between reference and segmented vessel skeletons, resulting in an average of 0:55+/-0:27 and 12:7+/-7:9 mm (mean standard deviation), respectively.

Automated bone segmentation from large field of view 3D MR images of the hip joint

NASA Astrophysics Data System (ADS)

Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S.; Schwarz, Raphael; Engstrom, Craig; Crozier, Stuart

2013-10-01

Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head-neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone-cartilage interfaces for potential cartilage segmentation.

Automated bone segmentation from large field of view 3D MR images of the hip joint.

PubMed

Xia, Ying; Fripp, Jurgen; Chandra, Shekhar S; Schwarz, Raphael; Engstrom, Craig; Crozier, Stuart

2013-10-21

Accurate bone segmentation in the hip joint region from magnetic resonance (MR) images can provide quantitative data for examining pathoanatomical conditions such as femoroacetabular impingement through to varying stages of osteoarthritis to monitor bone and associated cartilage morphometry. We evaluate two state-of-the-art methods (multi-atlas and active shape model (ASM) approaches) on bilateral MR images for automatic 3D bone segmentation in the hip region (proximal femur and innominate bone). Bilateral MR images of the hip joints were acquired at 3T from 30 volunteers. Image sequences included water-excitation dual echo stead state (FOV 38.6 × 24.1 cm, matrix 576 × 360, thickness 0.61 mm) in all subjects and multi-echo data image combination (FOV 37.6 × 23.5 cm, matrix 576 × 360, thickness 0.70 mm) for a subset of eight subjects. Following manual segmentation of femoral (head-neck, proximal-shaft) and innominate (ilium+ischium+pubis) bone, automated bone segmentation proceeded via two approaches: (1) multi-atlas segmentation incorporating non-rigid registration and (2) an advanced ASM-based scheme. Mean inter- and intra-rater reliability Dice's similarity coefficients (DSC) for manual segmentation of femoral and innominate bone were (0.970, 0.963) and (0.971, 0.965). Compared with manual data, mean DSC values for femoral and innominate bone volumes using automated multi-atlas and ASM-based methods were (0.950, 0.922) and (0.946, 0.917), respectively. Both approaches delivered accurate (high DSC values) segmentation results; notably, ASM data were generated in substantially less computational time (12 min versus 10 h). Both automated algorithms provided accurate 3D bone volumetric descriptions for MR-based measures in the hip region. The highly computational efficient ASM-based approach is more likely suitable for future clinical applications such as extracting bone-cartilage interfaces for potential cartilage segmentation.

Sub-5-ps, multimegawatt peak-power pulses from a fiber-amplified and optically compressed passively Q-switched microchip laser.

PubMed

Steinmetz, A; Jansen, F; Stutzki, F; Lehneis, R; Limpert, J; Tünnermann, A

2012-07-01

We report on high-energy picosecond pulse generation from a passively Q-switched and fiber-amplified microchip laser system. Initially, the utilized microchip lasers produce pulses with durations of around 100 ps at 1064 nm central wavelength. These pulses are amplified to energies exceeding 100 μJ, simultaneously chirped and spectrally broadened by self-phase modulation using a double stage amplifier based on single-mode LMA photonic crystal fibers at repetition rates of up to 1 MHz. Subsequently, the pulse duration of chirped pulses is reduced by means of nonlinear pulse compression to durations of 2.7 ps employing a conventional grating compressor and 4.7 ps using a compact compressor based on a chirped volume Bragg grating.

Laser characteristics at 1535 nm and thermal effects of an Er:Yb phosphate glass microchip pumped by Ti:sapphire laser

NASA Astrophysics Data System (ADS)

Cai, Zhiping; Chardon, Alain; Xu, Huiying; Féron, Patrice; Michel Stéphan, Guy

2002-03-01

An Er:Yb codoped phosphate glass microchip laser has been studied under pumping with a Ti:sapphire laser ranging from 945 to 990 nm. The characteristics (threshold, slope efficiency) are first described for an optimized laser. The gain spectrum is calculated for the transition 4I13/2→ 4I15/2 around 1535 nm from fundamental spectroscopic data and from experimental results. Red-shift effect on the frequency of a single mode is experimentally observed when the pump power is increased, originating from thermal effects. Temperature inside the microchip cavity and thermal expansion coefficient were determined by employing the intensity ratio of two green upconversion emission line centered at 530 and 554 nm, respectively, which quantitatively explain this red shift.

Improvement and Extension of Shape Evaluation Criteria in Multi-Scale Image Segmentation

NASA Astrophysics Data System (ADS)

Sakamoto, M.; Honda, Y.; Kondo, A.

2016-06-01

From the last decade, the multi-scale image segmentation is getting a particular interest and practically being used for object-based image analysis. In this study, we have addressed the issues on multi-scale image segmentation, especially, in improving the performances for validity of merging and variety of derived region's shape. Firstly, we have introduced constraints on the application of spectral criterion which could suppress excessive merging between dissimilar regions. Secondly, we have extended the evaluation for smoothness criterion by modifying the definition on the extent of the object, which was brought for controlling the shape's diversity. Thirdly, we have developed new shape criterion called aspect ratio. This criterion helps to improve the reproducibility on the shape of object to be matched to the actual objectives of interest. This criterion provides constraint on the aspect ratio in the bounding box of object by keeping properties controlled with conventional shape criteria. These improvements and extensions lead to more accurate, flexible, and diverse segmentation results according to the shape characteristics of the target of interest. Furthermore, we also investigated a technique for quantitative and automatic parameterization in multi-scale image segmentation. This approach is achieved by comparing segmentation result with training area specified in advance by considering the maximization of the average area in derived objects or satisfying the evaluation index called F-measure. Thus, it has been possible to automate the parameterization that suited the objectives especially in the view point of shape's reproducibility.

Automated coronal hole identification via multi-thermal intensity segmentation

NASA Astrophysics Data System (ADS)

Garton, Tadhg M.; Gallagher, Peter T.; Murray, Sophie A.

2018-01-01

Coronal holes (CH) are regions of open magnetic fields that appear as dark areas in the solar corona due to their low density and temperature compared to the surrounding quiet corona. To date, accurate identification and segmentation of CHs has been a difficult task due to their comparable intensity to local quiet Sun regions. Current segmentation methods typically rely on the use of single Extreme Ultra-Violet passband and magnetogram images to extract CH information. Here, the coronal hole identification via multi-thermal emission recognition algorithm (CHIMERA) is described, which analyses multi-thermal images from the atmospheric image assembly (AIA) onboard the solar dynamics observatory (SDO) to segment coronal hole boundaries by their intensity ratio across three passbands (171 Å, 193 Å, and 211 Å). The algorithm allows accurate extraction of CH boundaries and many of their properties, such as area, position, latitudinal and longitudinal width, and magnetic polarity of segmented CHs. From these properties, a clear linear relationship was identified between the duration of geomagnetic storms and coronal hole areas. CHIMERA can therefore form the basis of more accurate forecasting of the start and duration of geomagnetic storms.

Kansei Biosensor and IT Society

NASA Astrophysics Data System (ADS)

Toko, Kiyoshi

A taste sensor with global selectivity is composed of several kinds of lipid/polymer membranes for transforming information of taste substances into electric signal. The sensor output shows different patterns for chemical substances which have different taste qualities such as saltiness and sourness. Taste interactions such as suppression effect, which occurs between bitterness and sweetness, can be detected and quantified using the taste sensor. The taste and also smell of foodstuffs such as beer, coffee, mineral water, soup and milk can be discussed quantitatively. The taste sensor provides the objective scale for the human sensory expression. Multi-modal communication becomes possible using a taste/smell recognition microchip, which produces virtual taste. We are now standing at the beginning of a new age of communication using digitized taste.

Poly-Pattern Compressive Segmentation of ASTER Data for GIS

NASA Technical Reports Server (NTRS)

Myers, Wayne; Warner, Eric; Tutwiler, Richard

2007-01-01

Pattern-based segmentation of multi-band image data, such as ASTER, produces one-byte and two-byte approximate compressions. This is a dual segmentation consisting of nested coarser and finer level pattern mappings called poly-patterns. The coarser A-level version is structured for direct incorporation into geographic information systems in the manner of a raster map. GIs renderings of this A-level approximation are called pattern pictures which have the appearance of color enhanced images. The two-byte version consisting of thousands of B-level segments provides a capability for approximate restoration of the multi-band data in selected areas or entire scenes. Poly-patterns are especially useful for purposes of change detection and landscape analysis at multiple scales. The primary author has implemented the segmentation methodology in a public domain software suite.

Multi-segmental movement patterns reflect juggling complexity and skill level.

PubMed

Zago, Matteo; Pacifici, Ilaria; Lovecchio, Nicola; Galli, Manuela; Federolf, Peter Andreas; Sforza, Chiarella

2017-08-01

The juggling action of six experts and six intermediates jugglers was recorded with a motion capture system and decomposed into its fundamental components through Principal Component Analysis. The aim was to quantify trends in movement dimensionality, multi-segmental patterns and rhythmicity as a function of proficiency level and task complexity. Dimensionality was quantified in terms of Residual Variance, while the Relative Amplitude was introduced to account for individual differences in movement components. We observed that: experience-related modifications in multi-segmental actions exist, such as the progressive reduction of error-correction movements, especially in complex task condition. The systematic identification of motor patterns sensitive to the acquisition of specific experience could accelerate the learning process. Copyright © 2017 Elsevier B.V. All rights reserved.

Structure and mechanisms underlying ion transport in ternary polymer electrolytes containing ionic liquids

NASA Astrophysics Data System (ADS)

Mogurampelly, Santosh; Ganesan, Venkat

2017-02-01

We use all atom molecular dynamics simulations to investigate the influence of 1-butyl-3-methylimidazolium hexafluorophosphate (BMIMPF6) ionic liquid on the structure and transport properties of poly(ethylene oxide) (PEO) polymer electrolytes doped with LiPF6 salt. We observe enhanced diffusivities of the Li+, PF6-, and BMIM+ ions with increasing loading of the ionic liquid. Interplay between the different ion-ion and ion-polymer interactions is seen to lead to a destabilization of the Li-PF6 coordination and increase in the strength of association between the Li+ cations and the polymer backbone. As a consequence, the polymer segmental relaxation times are shown to be only moderately affected by the addition of ionic liquids. The ionic-liquid induced changes in the mobilities of Li+ ions are seen to be correlated to polymer segmental relaxation times. However, the mobilities of BMIM+ ions are seen to be more strongly correlated to the BMIM-PF6 ion-pair relaxation times.

Three-dimensional Model of Tissue and Heavy Ions Effects

NASA Technical Reports Server (NTRS)

Ponomarev, Artem L.; Sundaresan, Alamelu; Huff, Janice L.; Cucinotta, Francis A.

2007-01-01

A three-dimensional tissue model was incorporated into a new Monte Carlo algorithm that simulates passage of heavy ions in a tissue box . The tissue box was given as a realistic model of tissue based on confocal microscopy images. The action of heavy ions on the cellular matrix for 2- or 3-dimensional cases was simulated. Cells were modeled as a cell culture monolayer in one example, where the data were taken directly from microscopy (2-d cell matrix), and as a multi-layer obtained from confocal microscopy (3-d case). Image segmentation was used to identify cells with precise areas/volumes in an irradiated cell culture monolayer, and slices of tissue with many cell layers. The cells were then inserted into the model box of the simulated physical space pixel by pixel. In the case of modeled tissues (3-d), the tissue box had periodic boundary conditions imposed, which extrapolates the technique to macroscopic volumes of tissue. For the real tissue (3-d), specific spatial patterns for cell apoptosis and necrosis are expected. The cell patterns were modeled based on action cross sections for apoptosis and necrosis estimated from current experimental data. A spatial correlation function indicating a higher spatial concentration of damaged cells from heavy ions relative to the low-LET radiation cell damage pattern is presented. The spatial correlation effects among necrotic cells can help studying microlesions in organs, and probable effects of directionality of heavy ion radiation on epithelium and endothelium.

Algorithmic structural segmentation of defective particle systems: a lithium-ion battery study.

PubMed

Westhoff, D; Finegan, D P; Shearing, P R; Schmidt, V

2018-04-01

We describe a segmentation algorithm that is able to identify defects (cracks, holes and breakages) in particle systems. This information is used to segment image data into individual particles, where each particle and its defects are identified accordingly. We apply the method to particle systems that appear in Li-ion battery electrodes. First, the algorithm is validated using simulated data from a stochastic 3D microstructure model, where we have full information about defects. This allows us to quantify the accuracy of the segmentation result. Then we show that the algorithm can successfully be applied to tomographic image data from real battery anodes and cathodes, which are composed of particle systems with very different morpohological properties. Finally, we show how the results of the segmentation algorithm can be used for structural analysis. © 2017 The Authors Journal of Microscopy © 2017 Royal Microscopical Society.

Particle-free microchip processing

DOEpatents

Geller, A.S.; Rader, D.J.

1996-06-04

Method and apparatus for reducing particulate contamination in microchip processing are disclosed. The method and apparatus comprise means to reduce particle velocity toward the wafer before the particles can be deposited on the wafer surface. A reactor using electric fields to reduce particle velocity and prevent particulate contamination is disclosed. A reactor using a porous showerhead to reduce particle velocities and prevent particulate contamination is disclosed. 5 figs.

International Consultation on Micro-Chip Technology: Its Impact on the Lives of Women Workers. Summary of Proceedings (Manila, Philippines, October 5-15, 1986).

ERIC Educational Resources Information Center

Participatory Research Group, Toronto (Ontario).

An international consultation was attended by 40 women workers, educators, and organizers who work directly with women affected by the new "global assembly line" that has developed as a part of the microchip technology industry. The women, who represented 12 countries, shared information and organizing experiences and worked to…

Additive manufacturing and analysis of high frequency interconnects for microwave devices

NASA Astrophysics Data System (ADS)

Harper, Elicia K.

Wire bond interconnects have been the main approach to interconnecting microelectronic devices within a package. Conventional wirebonding however offers little control of the impedance of the interconnect and also introduces parasitic inductance that can degrade performance at microwave frequencies. The size and compactness of microchips is often an issue when it comes to attaching wirebonds to the microchip or other components within a microwave module. This work demonstrates the use of additive manufacturing for printing interconnects directly between bare die microchips and other components within a microwave module. A test structure was developed consisting of a GaAs microchip sandwiched between two alumina blocks patterned with coplanar waveguides (CPW). A printed dielectric ink is used to fill the gap between the alumina CPW blocks and the GaAs chip. Conductive interconnects are printed on top of the dielectric bridge material to connect the CPW traces to the bonding pads on the GaAs microchip. Simulations of these structures were modeled in the electromagnetics simulation tool by ANSYS, high frequency structure simulation (HFSS), to optimize the printed interconnects at 1-40 GHz (ANSYS Inc., Canonsburg, PA). The dielectric constant and loss tangent of the simulated dielectric was varied along with the dimensions of the conductive interconnects. The best combination of dielectric properties and interconnect dimensions was chosen for impedance matching by analyzing the insertion losses and return losses. A dielectric ink, which was chosen based on the simulated results, was experimentally printed between the two CPW blocks and the GaAs chip and subsequently cured. The conductive interconnects were then printed with an aerosol jet printer, connecting the CPW traces to the bonding pads on the GaAs microchip. The experimental prototype was then measured with a network analyzer and the measured data were compared to simulations. Results show good agreement between the simulated and measured S-parameters. This work demonstrates the potential for using additive manufacturing technology to create impedance- matched interconnects between high frequency ICs and other module components such as high frequency CPW transmission lines.

Novel active contour model based on multi-variate local Gaussian distribution for local segmentation of MR brain images

NASA Astrophysics Data System (ADS)

Zheng, Qiang; Li, Honglun; Fan, Baode; Wu, Shuanhu; Xu, Jindong

2017-12-01

Active contour model (ACM) has been one of the most widely utilized methods in magnetic resonance (MR) brain image segmentation because of its ability of capturing topology changes. However, most of the existing ACMs only consider single-slice information in MR brain image data, i.e., the information used in ACMs based segmentation method is extracted only from one slice of MR brain image, which cannot take full advantage of the adjacent slice images' information, and cannot satisfy the local segmentation of MR brain images. In this paper, a novel ACM is proposed to solve the problem discussed above, which is based on multi-variate local Gaussian distribution and combines the adjacent slice images' information in MR brain image data to satisfy segmentation. The segmentation is finally achieved through maximizing the likelihood estimation. Experiments demonstrate the advantages of the proposed ACM over the single-slice ACM in local segmentation of MR brain image series.

Integration of Sparse Multi-modality Representation and Anatomical Constraint for Isointense Infant Brain MR Image Segmentation

PubMed Central

Wang, Li; Shi, Feng; Gao, Yaozong; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

2014-01-01

Segmentation of infant brain MR images is challenging due to poor spatial resolution, severe partial volume effect, and the ongoing maturation and myelination process. During the first year of life, the brain image contrast between white and gray matters undergoes dramatic changes. In particular, the image contrast inverses around 6–8 months of age, where the white and gray matter tissues are isointense in T1 and T2 weighted images and hence exhibit the extremely low tissue contrast, posing significant challenges for automated segmentation. In this paper, we propose a general framework that adopts sparse representation to fuse the multi-modality image information and further incorporate the anatomical constraints for brain tissue segmentation. Specifically, we first derive an initial segmentation from a library of aligned images with ground-truth segmentations by using sparse representation in a patch-based fashion for the multi-modality T1, T2 and FA images. The segmentation result is further iteratively refined by integration of the anatomical constraint. The proposed method was evaluated on 22 infant brain MR images acquired at around 6 months of age by using a leave-one-out cross-validation, as well as other 10 unseen testing subjects. Our method achieved a high accuracy for the Dice ratios that measure the volume overlap between automated and manual segmentations, i.e., 0.889±0.008 for white matter and 0.870±0.006 for gray matter. PMID:24291615

An automatic brain tumor segmentation tool.

PubMed

Diaz, Idanis; Boulanger, Pierre; Greiner, Russell; Hoehn, Bret; Rowe, Lindsay; Murtha, Albert

2013-01-01

This paper introduces an automatic brain tumor segmentation method (ABTS) for segmenting multiple components of brain tumor using four magnetic resonance image modalities. ABTS's four stages involve automatic histogram multi-thresholding and morphological operations including geodesic dilation. Our empirical results, on 16 real tumors, show that ABTS works very effectively, achieving a Dice accuracy compared to expert segmentation of 81% in segmenting edema and 85% in segmenting gross tumor volume (GTV).

Deep Convolutional Neural Networks for Multi-Modality Isointense Infant Brain Image Segmentation

PubMed Central

Zhang, Wenlu; Li, Rongjian; Deng, Houtao; Wang, Li; Lin, Weili; Ji, Shuiwang; Shen, Dinggang

2015-01-01

The segmentation of infant brain tissue images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) plays an important role in studying early brain development in health and disease. In the isointense stage (approximately 6–8 months of age), WM and GM exhibit similar levels of intensity in both T1 and T2 MR images, making the tissue segmentation very challenging. Only a small number of existing methods have been designed for tissue segmentation in this isointense stage; however, they only used a single T1 or T2 images, or the combination of T1 and T2 images. In this paper, we propose to use deep convolutional neural networks (CNNs) for segmenting isointense stage brain tissues using multi-modality MR images. CNNs are a type of deep models in which trainable filters and local neighborhood pooling operations are applied alternatingly on the raw input images, resulting in a hierarchy of increasingly complex features. Specifically, we used multimodality information from T1, T2, and fractional anisotropy (FA) images as inputs and then generated the segmentation maps as outputs. The multiple intermediate layers applied convolution, pooling, normalization, and other operations to capture the highly nonlinear mappings between inputs and outputs. We compared the performance of our approach with that of the commonly used segmentation methods on a set of manually segmented isointense stage brain images. Results showed that our proposed model significantly outperformed prior methods on infant brain tissue segmentation. In addition, our results indicated that integration of multi-modality images led to significant performance improvement. PMID:25562829

Automatic 3D kidney segmentation based on shape constrained GC-OAAM

NASA Astrophysics Data System (ADS)

Chen, Xinjian; Summers, Ronald M.; Yao, Jianhua

2011-03-01

The kidney can be classified into three main tissue types: renal cortex, renal medulla and renal pelvis (or collecting system). Dysfunction of different renal tissue types may cause different kidney diseases. Therefore, accurate and efficient segmentation of kidney into different tissue types plays a very important role in clinical research. In this paper, we propose an automatic 3D kidney segmentation method which segments the kidney into the three different tissue types: renal cortex, medulla and pelvis. The proposed method synergistically combines active appearance model (AAM), live wire (LW) and graph cut (GC) methods, GC-OAAM for short. Our method consists of two main steps. First, a pseudo 3D segmentation method is employed for kidney initialization in which the segmentation is performed slice-by-slice via a multi-object oriented active appearance model (OAAM) method. An improved iterative model refinement algorithm is proposed for the AAM optimization, which synergistically combines the AAM and LW method. Multi-object strategy is applied to help the object initialization. The 3D model constraints are applied to the initialization result. Second, the object shape information generated from the initialization step is integrated into the GC cost computation. A multi-label GC method is used to segment the kidney into cortex, medulla and pelvis. The proposed method was tested on 19 clinical arterial phase CT data sets. The preliminary results showed the feasibility and efficiency of the proposed method.

Pathophysiology of avian intestinal ion transport.

PubMed

Nighot, Meghali; Nighot, Prashant

2018-06-01

The gut has great importance for the commercial success of poultry production. Numerous ion transporters, exchangers, and channels are present on both the apical and the basolateral membrane of intestinal epithelial cells, and their differential expression along the crypt-villus axis within the various intestinal segments ensures efficient intestinal absorption and effective barrier function. Recent studies have shown that intensive production systems, microbial exposure, and nutritional management significantly affect intestinal physiology and intestinal ion transport. Dysregulation of normal intestinal ion transport is manifested as diarrhoea, malabsorption, and intestinal inflammation resulting into poor production efficiency. This review discusses the basic mechanisms involved in avian intestinal ion transport and the impact of development during growth, nutritional and environmental alterations, and intestinal microbial infections on it. The effect of intestinal microbial infections on avian intestinal ion transport depends on factors such as host immunity, pathogen virulence, and the mucosal organisation of the particular intestinal segment.

Discriminative confidence estimation for probabilistic multi-atlas label fusion.

PubMed

Benkarim, Oualid M; Piella, Gemma; González Ballester, Miguel Angel; Sanroma, Gerard

2017-12-01

Quantitative neuroimaging analyses often rely on the accurate segmentation of anatomical brain structures. In contrast to manual segmentation, automatic methods offer reproducible outputs and provide scalability to study large databases. Among existing approaches, multi-atlas segmentation has recently shown to yield state-of-the-art performance in automatic segmentation of brain images. It consists in propagating the labelmaps from a set of atlases to the anatomy of a target image using image registration, and then fusing these multiple warped labelmaps into a consensus segmentation on the target image. Accurately estimating the contribution of each atlas labelmap to the final segmentation is a critical step for the success of multi-atlas segmentation. Common approaches to label fusion either rely on local patch similarity, probabilistic statistical frameworks or a combination of both. In this work, we propose a probabilistic label fusion framework based on atlas label confidences computed at each voxel of the structure of interest. Maximum likelihood atlas confidences are estimated using a supervised approach, explicitly modeling the relationship between local image appearances and segmentation errors produced by each of the atlases. We evaluate different spatial pooling strategies for modeling local segmentation errors. We also present a novel type of label-dependent appearance features based on atlas labelmaps that are used during confidence estimation to increase the accuracy of our label fusion. Our approach is evaluated on the segmentation of seven subcortical brain structures from the MICCAI 2013 SATA Challenge dataset and the hippocampi from the ADNI dataset. Overall, our results indicate that the proposed label fusion framework achieves superior performance to state-of-the-art approaches in the majority of the evaluated brain structures and shows more robustness to registration errors. Copyright © 2017 Elsevier B.V. All rights reserved.

Multiple ion beam irradiation for the study of radiation damage in materials

NASA Astrophysics Data System (ADS)

Taller, Stephen; Woodley, David; Getto, Elizabeth; Monterrosa, Anthony M.; Jiao, Zhijie; Toader, Ovidiu; Naab, Fabian; Kubley, Thomas; Dwaraknath, Shyam; Was, Gary S.

2017-12-01

The effects of transmutation produced helium and hydrogen must be included in ion irradiation experiments to emulate the microstructure of reactor irradiated materials. Descriptions of the criteria and systems necessary for multiple ion beam irradiation are presented and validated experimentally. A calculation methodology was developed to quantify the spatial distribution, implantation depth and amount of energy-degraded and implanted light ions when using a thin foil rotating energy degrader during multi-ion beam irradiation. A dual ion implantation using 1.34 MeV Fe+ ions and energy-degraded D+ ions was conducted on single crystal silicon to benchmark the dosimetry used for multi-ion beam irradiations. Secondary Ion Mass Spectroscopy (SIMS) analysis showed good agreement with calculations of the peak implantation depth and the total amount of iron and deuterium implanted. The results establish the capability to quantify the ion fluence from both heavy ion beams and energy-degraded light ion beams for the purpose of using multi-ion beam irradiations to emulate reactor irradiated microstructures.

Integration of continuous-flow sampling with microchip electrophoresis using poly(dimethylsiloxane)-based valves in a reversibly sealed device.

PubMed

Li, Michelle W; Martin, R Scott

2007-07-01

Here we describe a reversibly sealed microchip device that incorporates poly(dimethylsiloxane) (PDMS)-based valves for the rapid injection of analytes from a continuously flowing stream into a channel network for analysis with microchip electrophoresis. The microchip was reversibly sealed to a PDMS-coated glass substrate and microbore tubing was used for the introduction of gas and fluids to the microchip device. Two pneumatic valves were incorporated into the design and actuated on the order of hundreds of milliseconds, allowing analyte from a continuously flowing sampling stream to be injected into an electrophoresis separation channel. The device was characterized in terms of the valve actuation time and pushback voltage. It was also found that the addition of sodium dodecyl sulfate (SDS) to the buffer system greatly increased the reproducibility of the injection scheme and enabled the analysis of amino acids derivatized with naphthalene-2,3-dicarboxaldehyde/cyanide. Results from continuous injections of a 0.39 nL fluorescein plug into the optimized system showed that the injection process was reproducible (RSD of 0.7%, n = 10). Studies also showed that the device was capable of monitoring off-chip changes in concentration with a device lag time of 90 s. Finally, the ability of the device to rapidly monitor on-chip concentration changes was demonstrated by continually sampling from an analyte plug that was derivatized upstream from the electrophoresis/continuous flow interface. A reversibly sealed device of this type will be useful for the continuous monitoring and analysis of processes that occur either off-chip (such as microdialysis sampling) or on-chip from other integrated functions.

Capillary electrophoresis hyphenated with UV-native-laser induced fluorescence detection (CE/UV-native-LIF).

PubMed

Couderc, François; Ong-Meang, Varravaddheay; Poinsot, Véréna

2017-01-01

Native laser-induced fluorescence using UV lasers associated to CE offers now a large related literature, for now 30 years. The main works have been performed using very expensive Ar-ion lasers emitting at 257 and 275 nm. They are not affordable for routine analyses, but have numerous applications such as protein, catecholamine, and indolamine analysis. Some other lasers such as HeCd 325 nm have been used but only for few applications. Diode lasers, emitting at 266 nm, cheaper, are extensively used for the same topics, even if the obtained sensitivity is lower than the one observed using the costly UV-Ar-ion lasers. This review presents various CE or microchips applications and different UV lasers used for the excitation of native fluorescence. We showed that CE/Native UV laser induced fluorescence detection is very sensitive for detection as well as small aromatic biomolecules than proteins containing Trp and Tyr amino acids. Moreover, it is a simple way to analyze biomolecules without derivatization. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discriminative dictionary learning for abdominal multi-organ segmentation.

PubMed

Tong, Tong; Wolz, Robin; Wang, Zehan; Gao, Qinquan; Misawa, Kazunari; Fujiwara, Michitaka; Mori, Kensaku; Hajnal, Joseph V; Rueckert, Daniel

2015-07-01

An automated segmentation method is presented for multi-organ segmentation in abdominal CT images. Dictionary learning and sparse coding techniques are used in the proposed method to generate target specific priors for segmentation. The method simultaneously learns dictionaries which have reconstructive power and classifiers which have discriminative ability from a set of selected atlases. Based on the learnt dictionaries and classifiers, probabilistic atlases are then generated to provide priors for the segmentation of unseen target images. The final segmentation is obtained by applying a post-processing step based on a graph-cuts method. In addition, this paper proposes a voxel-wise local atlas selection strategy to deal with high inter-subject variation in abdominal CT images. The segmentation performance of the proposed method with different atlas selection strategies are also compared. Our proposed method has been evaluated on a database of 150 abdominal CT images and achieves a promising segmentation performance with Dice overlap values of 94.9%, 93.6%, 71.1%, and 92.5% for liver, kidneys, pancreas, and spleen, respectively. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Automatic Cell Segmentation in Fluorescence Images of Confluent Cell Monolayers Using Multi-object Geometric Deformable Model.

PubMed

Yang, Zhen; Bogovic, John A; Carass, Aaron; Ye, Mao; Searson, Peter C; Prince, Jerry L

2013-03-13

With the rapid development of microscopy for cell imaging, there is a strong and growing demand for image analysis software to quantitatively study cell morphology. Automatic cell segmentation is an important step in image analysis. Despite substantial progress, there is still a need to improve the accuracy, efficiency, and adaptability to different cell morphologies. In this paper, we propose a fully automatic method for segmenting cells in fluorescence images of confluent cell monolayers. This method addresses several challenges through a combination of ideas. 1) It realizes a fully automatic segmentation process by first detecting the cell nuclei as initial seeds and then using a multi-object geometric deformable model (MGDM) for final segmentation. 2) To deal with different defects in the fluorescence images, the cell junctions are enhanced by applying an order-statistic filter and principal curvature based image operator. 3) The final segmentation using MGDM promotes robust and accurate segmentation results, and guarantees no overlaps and gaps between neighboring cells. The automatic segmentation results are compared with manually delineated cells, and the average Dice coefficient over all distinguishable cells is 0.88.

Multi-segment foot kinematics after total ankle replacement and ankle arthrodesis during relatively long-distance gait.

PubMed

Rouhani, H; Favre, J; Aminian, K; Crevoisier, X

2012-07-01

This study aimed to investigate the influence of ankle osteoarthritis (AOA) treatments, i.e., ankle arthrodesis (AA) and total ankle replacement (TAR), on the kinematics of multi-segment foot and ankle complex during relatively long-distance gait. Forty-five subjects in four groups (AOA, AA, TAR, and control) were equipped with a wearable system consisting of inertial sensors installed on the tibia, calcaneus, and medial metatarsals. The subjects walked 50-m twice while the system measured the kinematic parameters of their multi-segment foot: the range of motion of joints between tibia, calcaneus, and medial metatarsals in three anatomical planes, and the peaks of angular velocity of these segments in the sagittal plane. These parameters were then compared among the four groups. It was observed that the range of motion and peak of angular velocities generally improved after TAR and were similar to the control subjects. However, unlike AOA and TAR, AA imposed impairments in the range of motion in the coronal plane for both the tibia-calcaneus and tibia-metatarsals joints. In general, the kinematic parameters showed significant correlation with established clinical scales (FFI and AOFAS), which shows their convergent validity. Based on the kinematic parameters of multi-segment foot during 50-m gait, this study showed significant improvements in foot mobility after TAR, but several significant impairments remained after AA. Copyright © 2012 Elsevier B.V. All rights reserved.

A multi-scale tensor voting approach for small retinal vessel segmentation in high resolution fundus images.

PubMed

Christodoulidis, Argyrios; Hurtut, Thomas; Tahar, Houssem Ben; Cheriet, Farida

2016-09-01

Segmenting the retinal vessels from fundus images is a prerequisite for many CAD systems for the automatic detection of diabetic retinopathy lesions. So far, research efforts have concentrated mainly on the accurate localization of the large to medium diameter vessels. However, failure to detect the smallest vessels at the segmentation step can lead to false positive lesion detection counts in a subsequent lesion analysis stage. In this study, a new hybrid method for the segmentation of the smallest vessels is proposed. Line detection and perceptual organization techniques are combined in a multi-scale scheme. Small vessels are reconstructed from the perceptual-based approach via tracking and pixel painting. The segmentation was validated in a high resolution fundus image database including healthy and diabetic subjects using pixel-based as well as perceptual-based measures. The proposed method achieves 85.06% sensitivity rate, while the original multi-scale line detection method achieves 81.06% sensitivity rate for the corresponding images (p<0.05). The improvement in the sensitivity rate for the database is 6.47% when only the smallest vessels are considered (p<0.05). For the perceptual-based measure, the proposed method improves the detection of the vasculature by 7.8% against the original multi-scale line detection method (p<0.05). Copyright © 2016 Elsevier Ltd. All rights reserved.

The evaluation of single-view and multi-view fusion 3D echocardiography using image-driven segmentation and tracking.

PubMed

Rajpoot, Kashif; Grau, Vicente; Noble, J Alison; Becher, Harald; Szmigielski, Cezary

2011-08-01

Real-time 3D echocardiography (RT3DE) promises a more objective and complete cardiac functional analysis by dynamic 3D image acquisition. Despite several efforts towards automation of left ventricle (LV) segmentation and tracking, these remain challenging research problems due to the poor-quality nature of acquired images usually containing missing anatomical information, speckle noise, and limited field-of-view (FOV). Recently, multi-view fusion 3D echocardiography has been introduced as acquiring multiple conventional single-view RT3DE images with small probe movements and fusing them together after alignment. This concept of multi-view fusion helps to improve image quality and anatomical information and extends the FOV. We now take this work further by comparing single-view and multi-view fused images in a systematic study. In order to better illustrate the differences, this work evaluates image quality and information content of single-view and multi-view fused images using image-driven LV endocardial segmentation and tracking. The image-driven methods were utilized to fully exploit image quality and anatomical information present in the image, thus purposely not including any high-level constraints like prior shape or motion knowledge in the analysis approaches. Experiments show that multi-view fused images are better suited for LV segmentation and tracking, while relatively more failures and errors were observed on single-view images. Copyright © 2011 Elsevier B.V. All rights reserved.

Monodisperse microdroplet generation and stopping without coalescence

DOEpatents

Beer, Neil Reginald

2015-04-21

A system for monodispersed microdroplet generation and trapping including providing a flow channel in a microchip; producing microdroplets in the flow channel, the microdroplets movable in the flow channel; providing carrier fluid in the flow channel using a pump or pressure source; controlling movement of the microdroplets in the flow channel and trapping the microdroplets in a desired location in the flow channel. The system includes a microchip; a flow channel in the microchip; a droplet maker that generates microdroplets, the droplet maker connected to the flow channel; a carrier fluid in the flow channel, the carrier fluid introduced to the flow channel by a source of carrier fluid, the source of carrier fluid including a pump or pressure source; a valve connected to the carrier fluid that controls flow of the carrier fluid and enables trapping of the microdroplets.

Monodisperse microdroplet generation and stopping without coalescence

DOEpatents

Beer, Neil Reginald

2016-02-23

A system for monodispersed microdroplet generation and trapping including providing a flow channel in a microchip; producing microdroplets in the flow channel, the microdroplets movable in the flow channel; providing carrier fluid in the flow channel using a pump or pressure source; controlling movement of the microdroplets in the flow channel and trapping the microdroplets in a desired location in the flow channel. The system includes a microchip; a flow channel in the microchip; a droplet maker that generates microdroplets, the droplet maker connected to the flow channel; a carrier fluid in the flow channel, the carrier fluid introduced to the flow channel by a source of carrier fluid, the source of carrier fluid including a pump or pressure source; a valve connected to the carrier fluid that controls flow of the carrier fluid and enables trapping of the microdroplets.

Single-longitudinal-mode Er:GGG microchip laser operating at 2.7  μm.

PubMed

You, Zhenyu; Wang, Yan; Xu, Jinlong; Zhu, Zhaojie; Li, Jianfu; Wang, Hongyan; Tu, Chaoyang

2015-08-15

We reported on a diode-end-pumped single-longitudinal-mode microchip laser using a 600-μm-thick Er:GGG crystal at ∼2.7  μm, generating a maximum output power of 50.8 mW and the maximum pulsed energy of 0.306 mJ, with repetition rates of pumping light of 300, 200, and 100 Hz, respectively. The maximum slope efficiency of the laser was 20.1%. The laser was operated in a single-longitudinal mode centered at about 2704 nm with a FWHM of 0.42 nm. The laser had a fundamental beam profile and the beam quality parameter M(2) was measured as 1.46. These results indicate that the Er:GGG microchip laser is a potential compact mid-infrared laser source.

Separation of large DNA molecules by applying pulsed electric field to size exclusion chromatography-based microchip

NASA Astrophysics Data System (ADS)

Azuma, Naoki; Itoh, Shintaro; Fukuzawa, Kenji; Zhang, Hedong

2018-02-01

Through electrophoresis driven by a pulsed electric field, we succeeded in separating large DNA molecules with an electrophoretic microchip based on size exclusion chromatography (SEC), which was proposed in our previous study. The conditions of the pulsed electric field required to achieve the separation were determined by numerical analyses using our originally proposed separation model. From the numerical results, we succeeded in separating large DNA molecules (λ DNA and T4 DNA) within 1600 s, which was approximately half of that achieved under a direct electric field in our previous study. Our SEC-based electrophoresis microchip will be one of the effective tools to meet the growing demand of faster and more convenient separation of large DNA molecules, especially in the field of epidemiological research of infectious diseases.

1.6 μm microchip laser

NASA Astrophysics Data System (ADS)

Šulc, J.; Jelínková, H.; Ryba-Romanowski, W.; Lukasiewicz, T.

2009-03-01

Properties of new pulsed-diode-pumped Er:YVO4 and Er:YVO4+CaO microchip lasers working in an ``eye-safe'' spectral region were investigated. As a pumping source, a fiber coupled (core diameter-200 μm) laser diode emitting radiation at wavelength 976 nm was used. The laser diode was operating in pulsed regime with 3 ms pulse width, and 20 Hz repetition rate. The result obtained was 175 mW and 152 mW output peak power for the Er:YVO4 and Er:YVO4+CaO lasers, respectively. The maximal efficiency with respect to the absorbed power was ~ 5%. The laser emission for Er:YVO4 microchip was observed in detail in the range 1593 nm to 1604 nm with respect to pumping. However, for Er:YVO4+CaO crystal only 1604 nm was generated.

Barcoded microchips for biomolecular assays.

PubMed

Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu

2015-01-20

Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

Multi-font printed Mongolian document recognition system

NASA Astrophysics Data System (ADS)

Peng, Liangrui; Liu, Changsong; Ding, Xiaoqing; Wang, Hua; Jin, Jianming

2009-01-01

Mongolian is one of the major ethnic languages in China. Large amount of Mongolian printed documents need to be digitized in digital library and various applications. Traditional Mongolian script has unique writing style and multi-font-type variations, which bring challenges to Mongolian OCR research. As traditional Mongolian script has some characteristics, for example, one character may be part of another character, we define the character set for recognition according to the segmented components, and the components are combined into characters by rule-based post-processing module. For character recognition, a method based on visual directional feature and multi-level classifiers is presented. For character segmentation, a scheme is used to find the segmentation point by analyzing the properties of projection and connected components. As Mongolian has different font-types which are categorized into two major groups, the parameter of segmentation is adjusted for each group. A font-type classification method for the two font-type group is introduced. For recognition of Mongolian text mixed with Chinese and English, language identification and relevant character recognition kernels are integrated. Experiments show that the presented methods are effective. The text recognition rate is 96.9% on the test samples from practical documents with multi-font-types and mixed scripts.

Multi-tissue and multi-scale approach for nuclei segmentation in H&E stained images.

PubMed

Salvi, Massimo; Molinari, Filippo

2018-06-20

Accurate nuclei detection and segmentation in histological images is essential for many clinical purposes. While manual annotations are time-consuming and operator-dependent, full automated segmentation remains a challenging task due to the high variability of cells intensity, size and morphology. Most of the proposed algorithms for the automated segmentation of nuclei were designed for specific organ or tissues. The aim of this study was to develop and validate a fully multiscale method, named MANA (Multiscale Adaptive Nuclei Analysis), for nuclei segmentation in different tissues and magnifications. MANA was tested on a dataset of H&E stained tissue images with more than 59,000 annotated nuclei, taken from six organs (colon, liver, bone, prostate, adrenal gland and thyroid) and three magnifications (10×, 20×, 40×). Automatic results were compared with manual segmentations and three open-source software designed for nuclei detection. For each organ, MANA obtained always an F1-score higher than 0.91, with an average F1 of 0.9305 ± 0.0161. The average computational time was about 20 s independently of the number of nuclei to be detected (anyway, higher than 1000), indicating the efficiency of the proposed technique. To the best of our knowledge, MANA is the first fully automated multi-scale and multi-tissue algorithm for nuclei detection. Overall, the robustness and versatility of MANA allowed to achieve, on different organs and magnifications, performances in line or better than those of state-of-art algorithms optimized for single tissues.

Efficient diode-pumped Tm:KYW 1.9-μm microchip laser with 1 W cw output power.

PubMed

Gaponenko, Maxim; Kuleshov, Nikolay; Südmeyer, Thomas

2014-05-19

We report on a diode-pumped Tm:KYW microchip laser generating 1 W continuous-wave output power. The laser operates at a wavelength of 1.94 μm in the fundamental TEM(00) mode with 71% slope efficiency relative to the absorbed pump radiation and 59% slope efficiency relative to the incident pump radiation. The optical-to-optical laser efficiency is 43%.

High-gain mid-infrared optical-parametric generation pumped by microchip laser.

PubMed

Ishizuki, Hideki; Taira, Takunori

2016-01-25

High-gain mid-infrared optical-parametric generation was demonstrated by simple single-pass configuration using PPMgLN devices pumped by giant-pulse microchip laser. Effective mid-infrared wavelength conversion with 1 mJ output energy from 2.4 mJ pumping using conventional PPMgLN could be realized. Broadband optical-parametric generation from 1.7 to 2.6 µm could be also measured using chirped PPMgLN.

Segmentation and pulse shape discrimination techniques for rejecting background in germanium detectors

NASA Technical Reports Server (NTRS)

Roth, J.; Primbsch, J. H.; Lin, R. P.

1984-01-01

The possibility of rejecting the internal beta-decay background in coaxial germanium detectors by distinguishing between the multi-site energy losses characteristic of photons and the single-site energy losses of electrons in the range 0.2 - 2 MeV is examined. The photon transport was modeled with a Monte Carlo routine. Background rejection by both multiple segmentation and pulse shape discrimination techniques is investigated. The efficiency of a six 1 cm-thick segment coaxial detector operating in coincidence mode alone is compared to that of a two-segment (1 cm and 5 cm) detector employing both front-rear coincidence and PSD in the rear segment to isolate photon events. Both techniques can provide at least 95 percent rejection of single-site events while accepting at least 80 percent of the multi-site events above 500 keV.

Multi-camera sensor system for 3D segmentation and localization of multiple mobile robots.

PubMed

Losada, Cristina; Mazo, Manuel; Palazuelos, Sira; Pizarro, Daniel; Marrón, Marta

2010-01-01

This paper presents a method for obtaining the motion segmentation and 3D localization of multiple mobile robots in an intelligent space using a multi-camera sensor system. The set of calibrated and synchronized cameras are placed in fixed positions within the environment (intelligent space). The proposed algorithm for motion segmentation and 3D localization is based on the minimization of an objective function. This function includes information from all the cameras, and it does not rely on previous knowledge or invasive landmarks on board the robots. The proposed objective function depends on three groups of variables: the segmentation boundaries, the motion parameters and the depth. For the objective function minimization, we use a greedy iterative algorithm with three steps that, after initialization of segmentation boundaries and depth, are repeated until convergence.

Robust segmentation of trabecular bone for in vivo CT imaging using anisotropic diffusion and multi-scale morphological reconstruction

NASA Astrophysics Data System (ADS)

Chen, Cheng; Jin, Dakai; Zhang, Xiaoliu; Levy, Steven M.; Saha, Punam K.

2017-03-01

Osteoporosis is associated with an increased risk of low-trauma fractures. Segmentation of trabecular bone (TB) is essential to assess TB microstructure, which is a key determinant of bone strength and fracture risk. Here, we present a new method for TB segmentation for in vivo CT imaging. The method uses Hessian matrix-guided anisotropic diffusion to improve local separability of trabecular structures, followed by a new multi-scale morphological reconstruction algorithm for TB segmentation. High sensitivity (0.93), specificity (0.93), and accuracy (0.92) were observed for the new method based on regional manual thresholding on in vivo CT images. Mechanical tests have shown that TB segmentation using the new method improved the ability of derived TB spacing measure for predicting actual bone strength (R2=0.83).

A Study on Segmented Multiple-Step Forming of Doubly Curved Thick Plate by Reconfigurable Multi-Punch Dies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ko, Young Ho; Han, Myoung Soo; Han, Jong Man

2007-05-17

Doubly curved thick plate forming in shipbuilding industries is currently performed by a thermal forming process, called as Line Heating by using gas flame torches. Due to the empirical manual work of it, the industries are eager for an alternative way to manufacture curved thick plates for ships. It was envisaged in this study to manufacture doubly curved thick plates by the multi-punch die forming. Experiments and finite element analyses were conducted to evaluate the feasibility of the reconfigurable discrete die forming to the thick plates. Single and segmented multiple step forming procedures were considered from both forming efficiency andmore » accuracy. Configuration of the multi-punch dies suitable for the segmented multiple step forming was also explored. As a result, Segmented multiple step forming with matched dies had a limited formability when the objective shapes become complicate, while a unmatched die configuration provided better possibility to manufacture large curved plates for ships.« less

Colorimetric Nucleic Acid Detection on Paper Microchip Using Loop Mediated Isothermal Amplification and Crystal Violet Dye.

PubMed

Roy, Sharmili; Mohd-Naim, Noor Faizah; Safavieh, Mohammadali; Ahmed, Minhaz Uddin

2017-11-22

Nucleic acid detection is of paramount importance in monitoring of microbial pathogens in food safety and infectious disease diagnostic applications. To address these challenges, a rapid, cost-effective label-free technique for nucleic acid detection with minimal instrumentations is highly desired. Here, we present paper microchip to detect and quantify nucleic acid using colorimetric sensing modality. The extracted DNA from food samples of meat as well as microbial pathogens was amplified utilizing loop-mediated isothermal amplification (LAMP). LAMP amplicon was then detected and quantified on a paper microchip fabricated in a cellulose paper and a small wax chamber utilizing crystal violet dye. The affinity of crystal violet dye toward dsDNA and positive signal were identified by changing the color from colorless to purple. Using this method, detection of Sus scrofa (porcine) and Bacillus subtilis (bacteria) DNA was possible at concentrations as low as 1 pg/μL (3.43 × 10 -1 copies/μL) and 10 pg/μL (2.2 × 10 3 copies/μL), respectively. This strategy can be adapted for detection of other DNA samples, with potential for development of a new breed of simple and inexpensive paper microchip at the point-of-need.

Linearly polarized pumped passively Q-switched Nd:YVO4 microchip laser for Ince-Gaussian laser modes with controllable orientations

NASA Astrophysics Data System (ADS)

He, Hong-Sen; Zhang, Ming-Ming; Dong, Jun; Ueda, Ken-Ichi

2016-12-01

A tilted, linearly polarized laser diode end-pumped Cr4+:YAG passively Q-switched a-cut Nd:YVO4 microchip laser for generating numerous Ince-Gaussian (IG) laser modes with controllable orientations has been demonstrated by selecting the crystalline orientation of an a-cut Nd:YVO4 crystal. The same IG laser mode with different orientations has been achieved with the same absorbed pump power in a passively Q-switched Nd:YVO4 microchip laser under linearly polarized pumping when the incident pump power and the crystalline orientation of an a-cut Nd:YVO4 crystal are both properly selected. The significant improvement of pulsed laser performance of controllable IG modes has been achieved by selecting the crystalline orientation of an a-cut Nd:YVO4 crystal. The maximum pulse energy is obtained along the a-axis of an a-cut Nd:YVO4 crystal and the highest peak power is achieved along the c-axis of an a-cut Nd:YVO4 crystal, respectively, which has potential applications on quantum computation and optical manipulation. The generation of controllable IG laser modes in microchip lasers under linearly polarized pumping provides a convenient and universal way to control IG laser mode numbers with anisotropic crystal as a gain medium.

Integration of Microchip Electrophoresis with Electrochemical Detection Using an Epoxy-Based Molding Method to Embed Multiple Electrode Materials

PubMed Central

Johnson, Alicia S.; Selimovic, Asmira; Martin, R. Scott

2012-01-01

This paper describes the use of epoxy-encapsulated electrodes to integrate microchip-based electrophoresis with electrochemical detection. Devices with various electrode combinations can easily be developed. This includes a palladium decoupler with a downstream working electrode material of either gold, mercury/gold, platinum, glassy carbon, or a carbon fiber bundle. Additional device components such as the platinum wires for the electrophoresis separation and the counter electrode for detection can also be integrated into the epoxy base. The effect of the decoupler configuration was studied in terms of the separation performance, detector noise, and the ability to analyze samples of a high ionic strength. The ability of both glassy carbon and carbon fiber bundle electrodes to analyze a complex mixture was demonstrated. It was also shown that a PDMS-based valving microchip can be used along with the epoxy embedded electrodes to integrate microdialysis sampling with microchip electrophoresis and electrochemical detection, with the microdialysis tubing also being embedded in the epoxy substrate. This approach enables one to vary the detection electrode material as desired in a manner where the electrodes can be polished and modified in a similar fashion to electrochemical flow cells used in liquid chromatography. PMID:22038707

Automatic segmentation of the prostate on CT images using deep learning and multi-atlas fusion

NASA Astrophysics Data System (ADS)

Ma, Ling; Guo, Rongrong; Zhang, Guoyi; Tade, Funmilayo; Schuster, David M.; Nieh, Peter; Master, Viraj; Fei, Baowei

2017-02-01

Automatic segmentation of the prostate on CT images has many applications in prostate cancer diagnosis and therapy. However, prostate CT image segmentation is challenging because of the low contrast of soft tissue on CT images. In this paper, we propose an automatic segmentation method by combining a deep learning method and multi-atlas refinement. First, instead of segmenting the whole image, we extract the region of interesting (ROI) to delete irrelevant regions. Then, we use the convolutional neural networks (CNN) to learn the deep features for distinguishing the prostate pixels from the non-prostate pixels in order to obtain the preliminary segmentation results. CNN can automatically learn the deep features adapting to the data, which are different from some handcrafted features. Finally, we select some similar atlases to refine the initial segmentation results. The proposed method has been evaluated on a dataset of 92 prostate CT images. Experimental results show that our method achieved a Dice similarity coefficient of 86.80% as compared to the manual segmentation. The deep learning based method can provide a useful tool for automatic segmentation of the prostate on CT images and thus can have a variety of clinical applications.

Application of Polypyrrole Multi-Walled Carbon Nanotube Composite Layer for Detection of Mercury, Lead and Iron Ions Using Surface Plasmon Resonance Technique

PubMed Central

Sadrolhosseini, Amir Reza; Noor, A. S. M.; Bahrami, Afarin; Lim, H. N.; Talib, Zainal Abidin; Mahdi, Mohd. Adzir

2014-01-01

Polypyrrole multi-walled carbon nanotube composite layers were used to modify the gold layer to measure heavy metal ions using the surface plasmon resonance technique. The new sensor was fabricated to detect trace amounts of mercury (Hg), lead (Pb), and iron (Fe) ions. In the present research, the sensitivity of a polypyrrole multi-walled carbon nanotube composite layer and a polypyrrole layer were compared. The application of polypyrrole multi-walled carbon nanotubes enhanced the sensitivity and accuracy of the sensor for detecting ions in an aqueous solution due to the binding of mercury, lead, and iron ions to the sensing layer. The Hg ion bonded to the sensing layer more strongly than did the Pb and Fe ions. The limitation of the sensor was calculated to be about 0.1 ppm, which produced an angle shift in the region of 0.3° to 0.6°. PMID:24733263

Ionization source utilizing a multi-capillary inlet and method of operation

DOEpatents

Smith, Richard D.; Kim, Taeman; Udseth, Harold R.

2004-10-12

A multi-capillary inlet to focus ions and other charged particles generated at or near atmospheric pressure into a relatively low pressure region, which allows increased conductance of ions and other charged particles. The multi-capillary inlet is juxtaposed between an ion source and the interior of an instrument maintained at near atmospheric pressure, it finds particular advantages when deployed to improve the ion transmission between an electrospray ionization source and the first vacuum stage of a mass spectrometer, and finds its greatest advantages when deployed in conjunction with an electrodynamic (RF) ion funnel deployed within the interior of the mass spectrometer, particularly an ion funnel equipped with a jet disturber.

Photon-Counting Laser Altimeters: Aircraft Demonstration and Future Application to Globally Contiguous Spaceborne Topographic Mapping

NASA Astrophysics Data System (ADS)

Degnan, J. J.

2002-05-01

We have recently demonstrated a scanning, photon-counting, laser altimeter, which is capable of daylight operations from aircraft cruise altitudes. The instrument measures the times-of-flight of individual photons to deduce the distances between the instrument reference and points on the underlying terrain from which the arriving photons were reflected. By imaging the terrain onto a highly pixellated detector followed by a multi-channel timing receiver, one can make multiple spatially-resolved measurements to the surface within a single laser pulse. The horizontal spatial resolution is limited by the optical projection of a single pixel onto the surface. In short, a 3D image of the terrain within the laser ground spot is obtained on each laser fire, assuming at least one signal photon is recorded by each pixel.. In test flights, a prototype airborne system has successfully recorded few kHz rate, single photon returns from clouds, soils, man-made objects, vegetation, and water surfaces at mid-day under conditions of maximum solar illumination. The system has also demonstrated a capability to resolve volumetrically distributed targets, such as tree canopies, and has performed wave height measurements and shallow water bathymetry over the Chesapeake Bay and Atlantic Ocean. The signal photons were reliably extracted from the solar noise background using an optimized Post-Detection Poisson Filter. The passively Q-switched microchip Nd:YAG laser transmitter measures only 2.25 mm in length and is pumped by a single 1.2 Watt laser diode. The output is frequency-doubled to take advantage of higher detector counting efficiencies and narrower spectral filters available at 532 nm. The transmitter produces a few microjoules of green energy in a subnanosecond pulse at several kilohertz rates. The illuminated ground area is imaged by a 14 cm diameter, diffraction-limited, off-axis telescope onto a segmented anode photomultiplier with up to 16 pixels (4 x4). Each anode segment is input to one channel of "fine" range receiver (5 cm detector-limited resolution), which records the times-of-flight of the individual photons. A parallel "coarse" receiver provides a lower resolution (>75 cm) histogram of atmospheric scatterers between the aircraft and ground and centers the "fine" receiver gate on the last set of returns, permitting the fine receiver to lock onto ground features with no a priori range knowledge. Many scientists have expressed a desire for globally contiguous maps of planetary bodies with few meter horizontal spatial resolutions and decimeter vertical resolutions. By sequentially overcoming various technical hurdles to globally contiguous mapping from space, we are led to a conceptual point design for a spaceborne, 3D imaging lidar, which utilizes low energy, high repetition rate lasers, photon-counting detector arrays, multi-channel timing receivers, and a unique optical scanner.

Automated Multi-Atlas Segmentation of Hippocampal and Extrahippocampal Subregions in Alzheimer's Disease at 3T and 7T: What Atlas Composition Works Best?

PubMed

Xie, Long; Shinohara, Russell T; Ittyerah, Ranjit; Kuijf, Hugo J; Pluta, John B; Blom, Kim; Kooistra, Minke; Reijmer, Yael D; Koek, Huiberdina L; Zwanenburg, Jaco J M; Wang, Hongzhi; Luijten, Peter R; Geerlings, Mirjam I; Das, Sandhitsu R; Biessels, Geert Jan; Wolk, David A; Yushkevich, Paul A; Wisse, Laura E M

2018-01-01

Multi-atlas segmentation, a popular technique implemented in the Automated Segmentation of Hippocampal Subfields (ASHS) software, utilizes multiple expert-labelled images ("atlases") to delineate medial temporal lobe substructures. This multi-atlas method is increasingly being employed in early Alzheimer's disease (AD) research, it is therefore becoming important to know how the construction of the atlas set in terms of proportions of controls and patients with mild cognitive impairment (MCI) and/or AD affects segmentation accuracy. To evaluate whether the proportion of controls in the training sets affects the segmentation accuracy of both controls and patients with MCI and/or early AD at 3T and 7T. We performed cross-validation experiments varying the proportion of control subjects in the training set, ranging from a patient-only to a control-only set. Segmentation accuracy of the test set was evaluated by the Dice similarity coeffiecient (DSC). A two-stage statistical analysis was applied to determine whether atlas composition is linked to segmentation accuracy in control subjects and patients, for 3T and 7T. The different atlas compositions did not significantly affect segmentation accuracy at 3T and for patients at 7T. For controls at 7T, including more control subjects in the training set significantly improves the segmentation accuracy, but only marginally, with the maximum of 0.0003 DSC improvement per percent increment of control subject in the training set. ASHS is robust in this study, and the results indicate that future studies investigating hippocampal subfields in early AD populations can be flexible in the selection of their atlas compositions.

A Systematic Study on the Generation of Multimetallic Lanthanide Fullerene ions by Laser Ablation Mass Spectrometry.

PubMed

Wang, Yiyun; Ma, LiFu; Mu, Lei; Ren, Juan; Kong, Xianglei

2018-06-01

Laser ablation masss spectromety has been previously proved to be a powerful tool for studying endohedro metallofullerene (EMF) ions. Our previous study showed the possiblity of forming multi-metallofullerene ions containg more than six metal atoms for La, Y and Lu. Thus, it is important to conduct a systematic study on the generation of multi-metallofullerenes and their distribuitons for all lanthanide elements. Experiments were performed on a 7.0 T Fourier transform ion cyclotron resonance (FT ICR) mass spectrometer. Laser ablation mass spectra were obtained by laser irradiation on mixtures of graphene and MCl 3 on a stainless steel plate, applying a 355 nm Nd: YAG laser with a typical energy of 2.5 mJ/pulse. Reaction test experiments were performed by introducing O 2 into the FT ICR cell with a pulse valve. Multi-metallofullerene ions Ce2-4C2m+, Pr2-4C2m+, Gd2-4C2m+, Nd3C2m+, Dy2-3C2m+, Tb2-7C2m+, Ho2-6C2m+ were observed in the mass spectra. For metal Sm and Eu, no multi-metallofullerene ion was observed. No reaction with O 2 was observed in the reaction experiments, verifying that these species had endohedral structures. For the observed series of multi-metallofullerene ions, tri-metallofullerene ions dominated their mass spectra. The results were further compared with previously generated EMF ions for La, Er, Tm, Yb and Lu. Endohedral lanthanide metallofullerene ions were generated by laser ablation of graphene and the corresponding metal salts MCl 3 (M = Ce, Pr, Nd, Gd, Tb, Dy and Ho) and studied with a FT ICR mass spectrometer. Typically, multi-metallofullerene ions of TbnC2m+2≤n≤780≤2m≤176, Ho6C2m+2≤n≤674≤2m≤162 were observed. The results show that the formation of multi-EMF ions containing lanthanides that have +3 and +4 oxidation states is easier than those containing +2 oxidation states in the process of laser ablation. This article is protected by copyright. All rights reserved.

Dual Segment Glocal Model Based Capacitive Level Sensor (CLS) for Adhesive Material and Level Detection

NASA Astrophysics Data System (ADS)

Khan, F. A.; Yousaf, A.; Reindl, L. M.

2018-04-01

This paper presents a multi segment capacitive level monitoring sensor based on distributed E-fields approach Glocal. This approach has an advantage to analyze build-up problem by the local E-fields as well the fluid level monitoring by the global E-fields. The multi segment capacitive approach presented within this work addresses the main problem of unwanted parasitic capacitance generated from Copper (Cu) strips by applying active shielding concept. Polyvinyl chloride (PVC) is used for isolation and parafilm is used for creating artificial build-up on a CLS.

Dual-threshold segmentation using Arimoto entropy based on chaotic bee colony optimization

NASA Astrophysics Data System (ADS)

Li, Li

2018-03-01

In order to extract target from complex background more quickly and accurately, and to further improve the detection effect of defects, a method of dual-threshold segmentation using Arimoto entropy based on chaotic bee colony optimization was proposed. Firstly, the method of single-threshold selection based on Arimoto entropy was extended to dual-threshold selection in order to separate the target from the background more accurately. Then intermediate variables in formulae of Arimoto entropy dual-threshold selection was calculated by recursion to eliminate redundant computation effectively and to reduce the amount of calculation. Finally, the local search phase of artificial bee colony algorithm was improved by chaotic sequence based on tent mapping. The fast search for two optimal thresholds was achieved using the improved bee colony optimization algorithm, thus the search could be accelerated obviously. A large number of experimental results show that, compared with the existing segmentation methods such as multi-threshold segmentation method using maximum Shannon entropy, two-dimensional Shannon entropy segmentation method, two-dimensional Tsallis gray entropy segmentation method and multi-threshold segmentation method using reciprocal gray entropy, the proposed method can segment target more quickly and accurately with superior segmentation effect. It proves to be an instant and effective method for image segmentation.

Resource atlases for multi-atlas brain segmentations with multiple ontology levels based on T1-weighted MRI.

PubMed

Wu, Dan; Ma, Ting; Ceritoglu, Can; Li, Yue; Chotiyanonta, Jill; Hou, Zhipeng; Hsu, John; Xu, Xin; Brown, Timothy; Miller, Michael I; Mori, Susumu

2016-01-15

Technologies for multi-atlas brain segmentation of T1-weighted MRI images have rapidly progressed in recent years, with highly promising results. This approach, however, relies on a large number of atlases with accurate and consistent structural identifications. Here, we introduce our atlas inventories (n=90), which cover ages 4-82years with unique hierarchical structural definitions (286 structures at the finest level). This multi-atlas library resource provides the flexibility to choose appropriate atlases for various studies with different age ranges and structure-definition criteria. In this paper, we describe the details of the atlas resources and demonstrate the improved accuracy achievable with a dynamic age-matching approach, in which atlases that most closely match the subject's age are dynamically selected. The advanced atlas creation strategy, together with atlas pre-selection principles, is expected to support the further development of multi-atlas image segmentation. Copyright © 2015 Elsevier Inc. All rights reserved.

Balancing the Role of Priors in Multi-Observer Segmentation Evaluation

PubMed Central

Huang, Xiaolei; Wang, Wei; Lopresti, Daniel; Long, Rodney; Antani, Sameer; Xue, Zhiyun; Thoma, George

2009-01-01

Comparison of a group of multiple observer segmentations is known to be a challenging problem. A good segmentation evaluation method would allow different segmentations not only to be compared, but to be combined to generate a “true” segmentation with higher consensus. Numerous multi-observer segmentation evaluation approaches have been proposed in the literature, and STAPLE in particular probabilistically estimates the true segmentation by optimal combination of observed segmentations and a prior model of the truth. An Expectation–Maximization (EM) algorithm, STAPLE’S convergence to the desired local minima depends on good initializations for the truth prior and the observer-performance prior. However, accurate modeling of the initial truth prior is nontrivial. Moreover, among the two priors, the truth prior always dominates so that in certain scenarios when meaningful observer-performance priors are available, STAPLE can not take advantage of that information. In this paper, we propose a Bayesian decision formulation of the problem that permits the two types of prior knowledge to be integrated in a complementary manner in four cases with differing application purposes: (1) with known truth prior; (2) with observer prior; (3) with neither truth prior nor observer prior; and (4) with both truth prior and observer prior. The third and fourth cases are not discussed (or effectively ignored) by STAPLE, and in our research we propose a new method to combine multiple-observer segmentations based on the maximum a posterior (MAP) principle, which respects the observer prior regardless of the availability of the truth prior. Based on the four scenarios, we have developed a web-based software application that implements the flexible segmentation evaluation framework for digitized uterine cervix images. Experiment results show that our framework has flexibility in effectively integrating different priors for multi-observer segmentation evaluation and it also generates results comparing favorably to those by the STAPLE algorithm and the Majority Vote Rule. PMID:20523759

Linearly Polarized Single-Frequency Oscillations of Laser-Diode-Pumped Microchip Ceramic Nd:YAG Lasers with Forced Ince-Gaussian Mode Operations

NASA Astrophysics Data System (ADS)

Otsuka, Kenju; Nemoto, Kana; Kamikariya, Koji; Miyasaka, Yoshihiko; Chu, Shu-Chun

2007-09-01

Detailed oscillation spectra and polarization properties have been examined in laser-diode-pumped (LD-pumped) microchip ceramic (i.e., polycrystalline) Nd:YAG lasers and the inherent segregation of lasing patterns into local modes possessing different polarization states was observed. Single-frequency linearly-polarized stable oscillations were realized by forcing the laser to Ince-Gaussian mode operations by adjusting azimuthal cavity symmetry.

Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

DOEpatents

Bavykin, Sergei G.; Mirzabekova, legal representative, Natalia V.; Mirzabekov, deceased, Andrei D.

2007-12-04

The present invention relates to methods and compositions for using nucleotide sequence variations of 16S and 23S rRNA within the B. cereus group to discriminate a highly infectious bacterium B. anthracis from closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations and discriminate B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed samples, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

Microchannel-electrode alignment and separation parameters comparison in microchip capillary electrophoresis by scanning electrochemical microscopy.

PubMed

Wang, Kang; Xia, Xing-Hua

2006-03-31

The end of separation channel in a microchip was electrochemically mapped using the feedback imaging mode of scanning electrochemical microscopy (SECM). This method provides a convenient way for microchannel-electrode alignment in microchip capillary electrophoresis. Influence of electrode-to-channel positions on separation parameters in this capillary electrophoresis-electrochemical detection (CE-ED) was then investigated. For the trapezoid shaped microchannel, detection in the central area resulted in the best apparent separation efficiency and peak shape. In the electrode-to-channel distance ranging from 65 to 15mum, the limiting peak currents of dopamine increased with the decrease of the detection distance due to the limited diffusion and convection of the sample band. Results showed that radial position and axial distance of the detection electrode to microchannel was important for the improvement of separation parameters in CE amperometric detection.

Capillary electrochromatography and preconcentration of neutral compounds on poly(dimethylsiloxane) microchips.

PubMed

Ro, Kyung Won; Chang, Woo-Jin; Kim, Ho; Koo, Yoon-Mo; Hahn, Jong Hoon

2003-09-01

Capillary electrochromatography (CEC) and preconcentration of neutral compounds have been realized on poly(dimethylsiloxane) (PDMS) microchips. The channels are coated with polyelectrolyte multilayers to avoid absorption of hydrophobic analytes into PDMS. The structures of a microchip include an injector and a bead chamber with integrated frits, where the particles of the stationary phase are completely retained. Dimensions of the frit structures are 25 micro mx20 micro m, and the space between the structures is 3 micro m. A neutral compound, BODIPY, that is strongly absorbed into native PDMS, is successfully and selectively retained on octadecylsilane-coated silica beads in the bead chamber with a concentration enhancement of up to 100 times and eluted with elution buffer solution containing 70% acetonitrile. Preconcentrations and CEC separations of coumarins have been conducted with the same device and achieved complete separations in less than 50 s.

Fundamentals and practice for ultrasensitive laser-induced fluorescence detection in microanalytical systems.

PubMed

Johnson, Mitchell E; Landers, James P

2004-11-01

Laser-induced fluorescence is an extremely sensitive method for detection in chemical separations. In addition, it is well-suited to detection in small volumes, and as such is widely used for capillary electrophoresis and microchip-based separations. This review explores the detailed instrumental conditions required for sub-zeptomole, sub-picomolar detection limits. The key to achieving the best sensitivity is to use an excitation and emission volume that is matched to the separation system and that, simultaneously, will keep scattering and luminescence background to a minimum. We discuss how this is accomplished with confocal detection, 90 degrees on-capillary detection, and sheath-flow detection. It is shown that each of these methods have their advantages and disadvantages, but that all can be used to produce extremely sensitive detectors for capillary- or microchip-based separations. Analysis of these capabilities allows prediction of the optimal means of achieving ultrasensitive detection on microchips.

Diode-pumped 1.5-1.6 μm laser operation in Er³⁺ doped YbAl₃(BO₃)₄ microchip.

PubMed

Chen, Yujin; Lin, Yanfu; Zou, Yuqi; Huang, Jianhua; Gong, Xinghong; Luo, Zundu; Huang, Yidong

2014-06-02

Er3+ doped YbAl3(BO3)4 crystal with large absorption coefficient of 184 cm(-1) at pump wavelength of 976 nm is a promising microchip gain medium of 1.5-1.6 μm laser. End-pumped by a 976 nm diode laser, 1.5-1.6 μm continuous-wave laser with maximum output power of 220 mW and slope efficiency of 8.1% was obtained at incident pump power of 4.54 W in a c-cut 200-μm-thick Er:YbAl3(BO3)4 microchip. When a Co2+:Mg0.4Al2.4O4 crystal was used as the saturable absorber, 1521 nm passively Q-switched pulse laser with about 0.19 μJ energy, 265 ns duration, and 96 kHz repetition rate was realized.

Trace analysis of D-tyrosine in biological samples by microchip electrophoresis with laser induced fluorescence detection.

PubMed

Huang, Yong; Shi, Ming; Zhao, Shulin; Liang, Hong

2011-11-01

A rapid and sensitive microchip electrophoresis (MCE) method with laser induced fluorescence (LIF) detection has been developed for the quantification of D-tyrosine (Tyr) in biological samples. The assay was performed using a MCE-LIF system with glass/poly(dimethylsiloxane) (PDMS) hybrid microchip after pre-column derivatization of amino acids with fluorescein isothiocyanate (FITC). Chiral separation of the derivatives was achieved by cyclodextrin-modified micellar electrokinetic chromatography (CD-MEKC) using γ-CD as chiral selector in the running buffer. D/L-Tyr enantiomer was well separated in less than 140s. The limit of detection (S/N=3) was 3.3 × 10(-8) M. Using the present method, D-Tyr level in human plasma was found to vary significantly from normal humans to patients suffering from renal failure. Copyright © 2011 Elsevier B.V. All rights reserved.

Diode-pumped microchip Tm:KLu(WO₄)₂ laser with more than 3 W of output power.

PubMed

Serres, Josep Maria; Mateos, Xavier; Loiko, Pavel; Yumashev, Konstantin; Kuleshov, Nikolai; Petrov, Valentin; Griebner, Uwe; Aguiló, Magdalena; Díaz, Francesc

2014-07-15

A diode-pumped microchip laser containing a quasi-monolithic plano-plano cavity is realized on the basis of a Tm:KLu(WO₄)₂ crystal. The maximum CW output power is 3.2 W (at an absorbed pump power of 6.8 W) and the slope efficiency as high as 50.4%. The laser is operating at 1946 nm in the TEM₀₀ mode with a M²<1.05. Microchip operation with Tm:KLu(WO₄)₂ is, in principle, due to a special crystal cut along the N(g) optical indicatrix axis. This crystal cut possesses positive near-spherical thermal lens that provides the required mode stabilization in the plano-plano cavity. Sensitivity factors of the thermal lens, "generalized" thermo-optic coefficients and constants describing the photoelastic effect are determined for the monolithic Tm:KLu(WO₄)₂ crystal.

Single-longitudinal mode Nd:YVO4 microchip laser with orthogonal-polarization bidirectional traveling-waves mode.

PubMed

Ma, Yingjun; Wu, Li; Wu, Hehui; Chen, Weimin; Wang, Yanli; Gu, Shijie

2008-11-10

We present a single longitudinal mode, diode pumped Nd:YVO(4) microchip laser where a pair of quarter-wave plates (QWPs) sandwich Nd:YVO(4) and the principle axes of QWPs are oriented at 45 degrees to the c-axis of Nd:YVO(4). Three pieces of crystals were optically bonded together as a microchip without adhesive. Owing to large birefringence of Nd:YVO(4), two standing waves with orthogonal polarizations compensate their hole-burning effects with each other, which diminish total spatial hole-burning effects in Nd:YVO(4). The maximum pump power of greater than 25 times the threshold for single longitudinal mode operation has been theoretically shown and experimentally demonstrated. The power of output, slope efficiencies and temperature range of single longitudinal mode operation are greater than 730 mw (at 1.25 W pump), 60% and 30 degrees C, respectively.

Fast analysis of domoic acid using microchip electrophoresis with laser-induced fluorescence detection.

PubMed

Cheng, Yongqiang; Guo, Cuilian; Zhao, Bin; Yang, Li

2017-04-01

A fast and effective method was developed to detect domoic acid based upon microchip electrophoresis combined with laser-induced fluorescence detection. Through study of the gated injection process on the cross channel of the microchip, the low-voltage mode with relatively longer sample loading time was adopted to reduce the sample discrimination and improve the signal sensitivity. Fluorescein isothiocyanate was used as the derivatizing reagent for domoic acid. Under the optimized conditions, domoic acid was completely separated in 60 s with separation efficiency of 1.35 × 10 5  m -1 . The calibration curve was obtained in the range of 1.0 × 10 -9 to 1.0 × 10 -7  mol/L, and the detection limit reached 2.8 × 10 -10  mol/L. This developed method was successfully applied to analyze domoic acid in real samples. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discrimination of Bacillus anthracis from closely related microorganisms by analysis of 16S and 23S rRNA with oligonucleotide microchips

DOEpatents

Bavykin, Sergei G.; Mirzabekov, Andrei D.

2007-10-30

The present invention is directed to a novel method of discriminating a highly infectious bacterium Bacillus anthracis from a group of closely related microorganisms. Sequence variations in the 16S and 23S rRNA of the B. cereus subgroup including B. anthracis are utilized to construct an array that can detect these sequence variations through selective hybridizations. The identification and analysis of these sequence variations enables positive discrimination of isolates of the B. cereus group that includes B. anthracis. Discrimination of single base differences in rRNA was achieved with a microchip during analysis of B. cereus group isolates from both single and in mixed probes, as well as identification of polymorphic sites. Successful use of a microchip to determine the appropriate subgroup classification using eight reference microorganisms from the B. cereus group as a study set, was demonstrated.

Carotid stenosis assessment with multi-detector CT angiography: comparison between manual and automatic segmentation methods.

PubMed

Zhu, Chengcheng; Patterson, Andrew J; Thomas, Owen M; Sadat, Umar; Graves, Martin J; Gillard, Jonathan H

2013-04-01

Luminal stenosis is used for selecting the optimal management strategy for patients with carotid artery disease. The aim of this study is to evaluate the reproducibility of carotid stenosis quantification using manual and automated segmentation methods using submillimeter through-plane resolution Multi-Detector CT angiography (MDCTA). 35 patients having carotid artery disease with >30 % luminal stenosis as identified by carotid duplex imaging underwent contrast enhanced MDCTA. Two experienced CT readers quantified carotid stenosis from axial source images, reconstructed maximum intensity projection (MIP) and 3D-carotid geometry which was automatically segmented by an open-source toolkit (Vascular Modelling Toolkit, VMTK) using NASCET criteria. Good agreement among the measurement using axial images, MIP and automatic segmentation was observed. Automatic segmentation methods show better inter-observer agreement between the readers (intra-class correlation coefficient (ICC): 0.99 for diameter stenosis measurement) than manual measurement of axial (ICC = 0.82) and MIP (ICC = 0.86) images. Carotid stenosis quantification using an automatic segmentation method has higher reproducibility compared with manual methods.

Application of pulsed multi-ion irradiations in radiation damage research: A stochastic cluster dynamics simulation study

NASA Astrophysics Data System (ADS)

Hoang, Tuan L.; Nazarov, Roman; Kang, Changwoo; Fan, Jiangyuan

2018-07-01

Under the multi-ion irradiation conditions present in accelerated material-testing facilities or fission/fusion nuclear reactors, the combined effects of atomic displacements with radiation products may induce complex synergies in the structural materials. However, limited access to multi-ion irradiation facilities and the lack of computational models capable of simulating the evolution of complex defects and their synergies make it difficult to understand the actual physical processes taking place in the materials under these extreme conditions. In this paper, we propose the application of pulsed single/dual-beam irradiation as replacements for the expensive steady triple-beam irradiation to study radiation damages in materials under multi-ion irradiation.

Volume measurements of individual muscles in human quadriceps femoris using atlas-based segmentation approaches.

PubMed

Le Troter, Arnaud; Fouré, Alexandre; Guye, Maxime; Confort-Gouny, Sylviane; Mattei, Jean-Pierre; Gondin, Julien; Salort-Campana, Emmanuelle; Bendahan, David

2016-04-01

Atlas-based segmentation is a powerful method for automatic structural segmentation of several sub-structures in many organs. However, such an approach has been very scarcely used in the context of muscle segmentation, and so far no study has assessed such a method for the automatic delineation of individual muscles of the quadriceps femoris (QF). In the present study, we have evaluated a fully automated multi-atlas method and a semi-automated single-atlas method for the segmentation and volume quantification of the four muscles of the QF and for the QF as a whole. The study was conducted in 32 young healthy males, using high-resolution magnetic resonance images (MRI) of the thigh. The multi-atlas-based segmentation method was conducted in 25 subjects. Different non-linear registration approaches based on free-form deformable (FFD) and symmetric diffeomorphic normalization algorithms (SyN) were assessed. Optimal parameters of two fusion methods, i.e., STAPLE and STEPS, were determined on the basis of the highest Dice similarity index (DSI) considering manual segmentation (MSeg) as the ground truth. Validation and reproducibility of this pipeline were determined using another MRI dataset recorded in seven healthy male subjects on the basis of additional metrics such as the muscle volume similarity values, intraclass coefficient, and coefficient of variation. Both non-linear registration methods (FFD and SyN) were also evaluated as part of a single-atlas strategy in order to assess longitudinal muscle volume measurements. The multi- and the single-atlas approaches were compared for the segmentation and the volume quantification of the four muscles of the QF and for the QF as a whole. Considering each muscle of the QF, the DSI of the multi-atlas-based approach was high 0.87 ± 0.11 and the best results were obtained with the combination of two deformation fields resulting from the SyN registration method and the STEPS fusion algorithm. The optimal variables for FFD and SyN registration methods were four templates and a kernel standard deviation ranging between 5 and 8. The segmentation process using a single-atlas-based method was more robust with DSI values higher than 0.9. From the vantage of muscle volume measurements, the multi-atlas-based strategy provided acceptable results regarding the QF muscle as a whole but highly variable results regarding individual muscle. On the contrary, the performance of the single-atlas-based pipeline for individual muscles was highly comparable to the MSeg, thereby indicating that this method would be adequate for longitudinal tracking of muscle volume changes in healthy subjects. In the present study, we demonstrated that both multi-atlas and single-atlas approaches were relevant for the segmentation of individual muscles of the QF in healthy subjects. Considering muscle volume measurements, the single-atlas method provided promising perspectives regarding longitudinal quantification of individual muscle volumes.

Automatic coronary artery segmentation based on multi-domains remapping and quantile regression in angiographies.

PubMed

Li, Zhixun; Zhang, Yingtao; Gong, Huiling; Li, Weimin; Tang, Xianglong

2016-12-01

Coronary artery disease has become the most dangerous diseases to human life. And coronary artery segmentation is the basis of computer aided diagnosis and analysis. Existing segmentation methods are difficult to handle the complex vascular texture due to the projective nature in conventional coronary angiography. Due to large amount of data and complex vascular shapes, any manual annotation has become increasingly unrealistic. A fully automatic segmentation method is necessary in clinic practice. In this work, we study a method based on reliable boundaries via multi-domains remapping and robust discrepancy correction via distance balance and quantile regression for automatic coronary artery segmentation of angiography images. The proposed method can not only segment overlapping vascular structures robustly, but also achieve good performance in low contrast regions. The effectiveness of our approach is demonstrated on a variety of coronary blood vessels compared with the existing methods. The overall segmentation performances si, fnvf, fvpf and tpvf were 95.135%, 3.733%, 6.113%, 96.268%, respectively. Copyright © 2016 Elsevier Ltd. All rights reserved.

MS lesion segmentation using a multi-channel patch-based approach with spatial consistency

NASA Astrophysics Data System (ADS)

Mechrez, Roey; Goldberger, Jacob; Greenspan, Hayit

2015-03-01

This paper presents an automatic method for segmentation of Multiple Sclerosis (MS) in Magnetic Resonance Images (MRI) of the brain. The approach is based on similarities between multi-channel patches (T1, T2 and FLAIR). An MS lesion patch database is built using training images for which the label maps are known. For each patch in the testing image, k similar patches are retrieved from the database. The matching labels for these k patches are then combined to produce an initial segmentation map for the test case. Finally a novel iterative patch-based label refinement process based on the initial segmentation map is performed to ensure spatial consistency of the detected lesions. A leave-one-out evaluation is done for each testing image in the MS lesion segmentation challenge of MICCAI 2008. Results are shown to compete with the state-of-the-art methods on the MICCAI 2008 challenge.

Ionization based multi-directional flow sensor

DOEpatents

Chorpening, Benjamin T [Morgantown, WV; Casleton, Kent H [Morgantown, WV

2009-04-28

A method, system, and apparatus for conducting real-time monitoring of flow (airflow for example) in a system (a hybrid power generation system for example) is disclosed. The method, system and apparatus measure at least flow direction and velocity with minimal pressure drop and fast response. The apparatus comprises an ion source and a multi-directional collection device proximate the ion source. The ion source is configured to generate charged species (electrons and ions for example). The multi-directional collection source is configured to determine the direction and velocity of the flow in real-time.

Photometric flow injection determination of phosphate on a PDMS microchip using an optical detection system assembled with an organic light emitting diode and an organic photodiode.

PubMed

Liu, Rong; Ishimatsu, Ryoichi; Yahiro, Masayuki; Adachi, Chihaya; Nakano, Koji; Imato, Toshihiko

2015-01-01

A compact photometric detector was constructed from an organic light emitting diode (OLED) based on a europium complex, europium(diben-zoylmethanato)3(bathophenanthroline) (Eu(DBM)3bath), as the light source and an organic photodiode (OPD) fabricated from a hetero-junction of two layers of copper phthalocyanine (CuPc)/fullerene (C60) as the photo-detector on a microchip prepared from poly(dimethylsiloxan) (PDMS) and was applied to the determination of phosphate. The OLED and the OPD were fabricated by a vapor deposition method on an indium tin oxide (ITO) coated glass substrate with the following layered structure; Glass (0.7 mm)/ITO (110 nm)/4,4'-bis[N-(1-naphthyl)-N-phenyl amino]-biphenyl (α-NPD) (30 nm)/4,4'-di(N-carbazolyl)biphenyl (CBP): Eu(3+) (8 wt%, 30 nm)/bathocuproine (BCP) (30 nm)/aluminum tris(8-hydroxyquinoline) (Alq3) (25 nm)/magnesium and silver (MgAg) (100 nm)/Ag (10nm) and Glass (0.7 mm)/ITO (110 nm)/CuPc (35 nm)/C60 (50 nm)/BCP (10 nm)/Ag (50 nm), respectively. The OLED based on the europium complex emitted a sharp light at the wavelength of 612 nm with a full width at half maximum (FWHM) of 8 nm. The performance of the photometric detector assembled was evaluated based on measurements of the absorbance of different concentrations of malachite green (MG) solutions for a batch system with 1cm long path length. The molar absorptive coefficient of the MG solution, calculated from the photocurrent of the OPD, was in good agreement with the value reported in the literature. A microchip with two inlets and one outlet U-shaped channel was prepared by a conventional photolithograph method. The OLED and the OPD were configured so as to face each other through the PDMS microchip in parallel in order to align the light axis of the OLED and the OPD with the flow cell (optical path length of 5mm), which was located at the end of outlet. For the determination of phosphate, an ion-association reaction between MG and a molybdenum-phosphate complex was utilized and a good linear relationship between the concentration and absorbance was observed in the concentration range 0-0.2 ppm, with a detection limit (S/N=3) of 0.02 ppm. The assembled photometric detector was also applied to the determination of phosphate by the flow injection of river water samples using the reagent solution containing MG and molybdenum ammonium in sulfuric acid. A good recovery (97-99%) for the river water samples, which had been spiked with the standard 0.08 ppm, with an RSD of ca 5% (n=5) was obtained using the constructed system. Copyright © 2014 Elsevier B.V. All rights reserved.

Broadband Dielectric Spectroscopy and Quasi-Elastic Neutron Scattering on Single-Ion Polymer Conductors

NASA Astrophysics Data System (ADS)

Soles, Christopher; Peng, Hua-Gen; Page, Kirt; Snyder, Chad; Pandy, Ashoutosh; Jeong, Youmi; Runt, James; NIST Collaboration; Pennsylvania Collaboration

2011-03-01

The application of solid polymer electrolytes in rechargeable batteries has not been fully realized after decades of research due to its low conductivity. Dramatic increases of the ion conductivity are needed and this progress requires the understanding of conduction mechanism. We address this topic in two fronts, namely, the effect of plasticizer additives and geometric confinement on the charge transfer mechanism. To this end, we combine broadband dielectric spectroscopy (BDS) to characterize the ion mobility and quasi-elastic neutron scattering (QENS) to quantify segmental motion on a single-ion model polymer electrolyte. Deuterated small molecules were used as plasticizers so that the segmental motion of the polymer electrolyte could be monitored by QENS to understand the mechanism behind the increased conductivity. Anodic aluminum oxide (AAO) membranes with well defined channel sizes are used as the matrix to study the transport of ions solvated in a 1D polymer electrolyte.

Cell Motility Dynamics: A Novel Segmentation Algorithm to Quantify Multi-Cellular Bright Field Microscopy Images

PubMed Central

Zaritsky, Assaf; Natan, Sari; Horev, Judith; Hecht, Inbal; Wolf, Lior; Ben-Jacob, Eshel; Tsarfaty, Ilan

2011-01-01

Confocal microscopy analysis of fluorescence and morphology is becoming the standard tool in cell biology and molecular imaging. Accurate quantification algorithms are required to enhance the understanding of different biological phenomena. We present a novel approach based on image-segmentation of multi-cellular regions in bright field images demonstrating enhanced quantitative analyses and better understanding of cell motility. We present MultiCellSeg, a segmentation algorithm to separate between multi-cellular and background regions for bright field images, which is based on classification of local patches within an image: a cascade of Support Vector Machines (SVMs) is applied using basic image features. Post processing includes additional classification and graph-cut segmentation to reclassify erroneous regions and refine the segmentation. This approach leads to a parameter-free and robust algorithm. Comparison to an alternative algorithm on wound healing assay images demonstrates its superiority. The proposed approach was used to evaluate common cell migration models such as wound healing and scatter assay. It was applied to quantify the acceleration effect of Hepatocyte growth factor/scatter factor (HGF/SF) on healing rate in a time lapse confocal microscopy wound healing assay and demonstrated that the healing rate is linear in both treated and untreated cells, and that HGF/SF accelerates the healing rate by approximately two-fold. A novel fully automated, accurate, zero-parameters method to classify and score scatter-assay images was developed and demonstrated that multi-cellular texture is an excellent descriptor to measure HGF/SF-induced cell scattering. We show that exploitation of textural information from differential interference contrast (DIC) images on the multi-cellular level can prove beneficial for the analyses of wound healing and scatter assays. The proposed approach is generic and can be used alone or alongside traditional fluorescence single-cell processing to perform objective, accurate quantitative analyses for various biological applications. PMID:22096600

Cell motility dynamics: a novel segmentation algorithm to quantify multi-cellular bright field microscopy images.

PubMed

Zaritsky, Assaf; Natan, Sari; Horev, Judith; Hecht, Inbal; Wolf, Lior; Ben-Jacob, Eshel; Tsarfaty, Ilan

2011-01-01

Confocal microscopy analysis of fluorescence and morphology is becoming the standard tool in cell biology and molecular imaging. Accurate quantification algorithms are required to enhance the understanding of different biological phenomena. We present a novel approach based on image-segmentation of multi-cellular regions in bright field images demonstrating enhanced quantitative analyses and better understanding of cell motility. We present MultiCellSeg, a segmentation algorithm to separate between multi-cellular and background regions for bright field images, which is based on classification of local patches within an image: a cascade of Support Vector Machines (SVMs) is applied using basic image features. Post processing includes additional classification and graph-cut segmentation to reclassify erroneous regions and refine the segmentation. This approach leads to a parameter-free and robust algorithm. Comparison to an alternative algorithm on wound healing assay images demonstrates its superiority. The proposed approach was used to evaluate common cell migration models such as wound healing and scatter assay. It was applied to quantify the acceleration effect of Hepatocyte growth factor/scatter factor (HGF/SF) on healing rate in a time lapse confocal microscopy wound healing assay and demonstrated that the healing rate is linear in both treated and untreated cells, and that HGF/SF accelerates the healing rate by approximately two-fold. A novel fully automated, accurate, zero-parameters method to classify and score scatter-assay images was developed and demonstrated that multi-cellular texture is an excellent descriptor to measure HGF/SF-induced cell scattering. We show that exploitation of textural information from differential interference contrast (DIC) images on the multi-cellular level can prove beneficial for the analyses of wound healing and scatter assays. The proposed approach is generic and can be used alone or alongside traditional fluorescence single-cell processing to perform objective, accurate quantitative analyses for various biological applications.

A fuzzy feature fusion method for auto-segmentation of gliomas with multi-modality diffusion and perfusion magnetic resonance images in radiotherapy.

PubMed

Guo, Lu; Wang, Ping; Sun, Ranran; Yang, Chengwen; Zhang, Ning; Guo, Yu; Feng, Yuanming

2018-02-19

The diffusion and perfusion magnetic resonance (MR) images can provide functional information about tumour and enable more sensitive detection of the tumour extent. We aimed to develop a fuzzy feature fusion method for auto-segmentation of gliomas in radiotherapy planning using multi-parametric functional MR images including apparent diffusion coefficient (ADC), fractional anisotropy (FA) and relative cerebral blood volume (rCBV). For each functional modality, one histogram-based fuzzy model was created to transform image volume into a fuzzy feature space. Based on the fuzzy fusion result of the three fuzzy feature spaces, regions with high possibility belonging to tumour were generated automatically. The auto-segmentations of tumour in structural MR images were added in final auto-segmented gross tumour volume (GTV). For evaluation, one radiation oncologist delineated GTVs for nine patients with all modalities. Comparisons between manually delineated and auto-segmented GTVs showed that, the mean volume difference was 8.69% (±5.62%); the mean Dice's similarity coefficient (DSC) was 0.88 (±0.02); the mean sensitivity and specificity of auto-segmentation was 0.87 (±0.04) and 0.98 (±0.01) respectively. High accuracy and efficiency can be achieved with the new method, which shows potential of utilizing functional multi-parametric MR images for target definition in precision radiation treatment planning for patients with gliomas.

Multi-Atlas Based Segmentation of Brainstem Nuclei from MR Images by Deep Hyper-Graph Learning.

PubMed

Dong, Pei; Guo, Yangrong; Gao, Yue; Liang, Peipeng; Shi, Yonghong; Wang, Qian; Shen, Dinggang; Wu, Guorong

2016-10-01

Accurate segmentation of brainstem nuclei (red nucleus and substantia nigra) is very important in various neuroimaging applications such as deep brain stimulation and the investigation of imaging biomarkers for Parkinson's disease (PD). Due to iron deposition during aging, image contrast in the brainstem is very low in Magnetic Resonance (MR) images. Hence, the ambiguity of patch-wise similarity makes the recently successful multi-atlas patch-based label fusion methods have difficulty to perform as competitive as segmenting cortical and sub-cortical regions from MR images. To address this challenge, we propose a novel multi-atlas brainstem nuclei segmentation method using deep hyper-graph learning. Specifically, we achieve this goal in three-fold. First , we employ hyper-graph to combine the advantage of maintaining spatial coherence from graph-based segmentation approaches and the benefit of harnessing population priors from multi-atlas based framework. Second , besides using low-level image appearance, we also extract high-level context features to measure the complex patch-wise relationship. Since the context features are calculated on a tentatively estimated label probability map, we eventually turn our hyper-graph learning based label propagation into a deep and self-refining model. Third , since anatomical labels on some voxels (usually located in uniform regions) can be identified much more reliably than other voxels (usually located at the boundary between two regions), we allow these reliable voxels to propagate their labels to the nearby difficult-to-label voxels. Such hierarchical strategy makes our proposed label fusion method deep and dynamic. We evaluate our proposed label fusion method in segmenting substantia nigra (SN) and red nucleus (RN) from 3.0 T MR images, where our proposed method achieves significant improvement over the state-of-the-art label fusion methods.

Novel approach for identification of influenza virus host range and zoonotic transmissible sequences by determination of host-related associative positions in viral genome segments.

PubMed

Kargarfard, Fatemeh; Sami, Ashkan; Mohammadi-Dehcheshmeh, Manijeh; Ebrahimie, Esmaeil

2016-11-16

Recent (2013 and 2009) zoonotic transmission of avian or porcine influenza to humans highlights an increase in host range by evading species barriers. Gene reassortment or antigenic shift between viruses from two or more hosts can generate a new life-threatening virus when the new shuffled virus is no longer recognized by antibodies existing within human populations. There is no large scale study to help understand the underlying mechanisms of host transmission. Furthermore, there is no clear understanding of how different segments of the influenza genome contribute in the final determination of host range. To obtain insight into the rules underpinning host range determination, various supervised machine learning algorithms were employed to mine reassortment changes in different viral segments in a range of hosts. Our multi-host dataset contained whole segments of 674 influenza strains organized into three host categories: avian, human, and swine. Some of the sequences were assigned to multiple hosts. In point of fact, the datasets are a form of multi-labeled dataset and we utilized a multi-label learning method to identify discriminative sequence sites. Then algorithms such as CBA, Ripper, and decision tree were applied to extract informative and descriptive association rules for each viral protein segment. We found informative rules in all segments that are common within the same host class but varied between different hosts. For example, for infection of an avian host, HA14V and NS1230S were the most important discriminative and combinatorial positions. Host range identification is facilitated by high support combined rules in this study. Our major goal was to detect discriminative genomic positions that were able to identify multi host viruses, because such viruses are likely to cause pandemic or disastrous epidemics.

Controllability in Multi-Stage Laser Ion Acceleration

NASA Astrophysics Data System (ADS)

Kawata, S.; Kamiyama, D.; Ohtake, Y.; Barada, D.; Ma, Y. Y.; Kong, Q.; Wang, P. X.; Gu, Y. J.; Li, X. F.; Yu, Q.

2015-11-01

The present paper shows a concept for a future laser ion accelerator, which should have an ion source, ion collimators, ion beam bunchers and ion post acceleration devices. Based on the laser ion accelerator components, the ion particle energy and the ion energy spectrum are controlled, and a future compact laser ion accelerator would be designed for ion cancer therapy or for ion material treatment. In this study each component is designed to control the ion beam quality. The energy efficiency from the laser to ions is improved by using a solid target with a fine sub-wavelength structure or a near-critical density gas plasma. The ion beam collimation is performed by holes behind the solid target or a multi-layered solid target. The control of the ion energy spectrum and the ion particle energy, and the ion beam bunching are successfully realized by a multi-stage laser-target interaction. A combination of each component provides a high controllability of the ion beam quality to meet variable requirements in various purposes in the laser ion accelerator. The work was partly supported by MEXT, JSPS, ASHULA project/ ILE, Osaka University, CORE (Center for Optical Research and Education, Utsunomiya University, Japan), Fudan University and CDI (Creative Dept. for Innovation) in CCRD, Utsunomiya University.

International Microgravity Plasma Facility IMPF: A Multi-User Modular Research Facility for Complex Plasma Research on ISS

NASA Astrophysics Data System (ADS)

Seurig, R.; Burfeindt, J.; Castegini, R.; Griethe, W.; Hofmann, P.

2002-01-01

On March 03, 2001, the PKE-Nefedov plasma experiment was successfully put into operation on board ISS. This complex plasma experiment is the predecessor for the semi-autonomous multi-user facility IMPF (International Microgravity Plasma Facility) to be flown in 2006 with an expected operational lifetime of 10 years. IMPF is envisioned to be an international research facility for investigators in the field of multi-component plasmas containing ions, electrons, and charged microparticles. This research filed is often referred to as "complex plasmas". The actual location of IMPF on ISS is not decided yet; potential infrastructure under consideration are EXPRESS Rack, Standard Interface Rack SIR, European Drawer Rack EDR, or a to be designed custom rack infrastructure on the Russian Segment. The actual development status of the DLR funded Pre-phase B Study for IMPF will be presented. For this phase, IMPF was assumed to be integrated in an EXPRESS Rack requiring four middeck lockers with two 4-PU ISIS drawers for accommodation. Technical and operational challenges, like a 240 Mbytes/sec continuous experimental data stream for 60 minutes, will be addressed. The project was funded by the German Space Agency (DLR) and was performed in close cooperation with scientists from the Max-Planck-Institute for Extraterrestical Physics in Munich, Germany.

Kinetic theory and Vlasov simulation of nonlinear ion-acoustic waves in multi-ion species plasmas.

PubMed

Chapman, T; Berger, R L; Brunner, S; Williams, E A

2013-05-10

The theory of damping and nonlinear frequency shifts from particles resonant with ion-acoustic waves (IAWs) is presented for multi-ion species plasma and compared to driven wave Vlasov simulations. Two distinct IAW modes may be supported in multi-ion species plasmas, broadly classified as fast and slow by their phase velocity relative to the constituent ion thermal velocities. In current fusion-relevant long pulse experiments, the ion to electron temperature ratio, T(i)/T(e), is expected to reach a level such that the least damped and thus more readily driven mode is the slow mode, with both linear and nonlinear properties that are shown to differ significantly from the fast mode. The lighter ion species of the slow mode is found to make no significant contribution to the IAW frequency shift despite typically being the dominant contributor to the Landau damping.

Mineral Ion Contents and Cell Transmembrane Electropotentials of Pea and Oat Seedling Tissue 1

PubMed Central

Higinbotham, N.; Etherton, Bud; Foster, R. J.

1967-01-01

The relationships of concentration gradients to electropotential gradients resulting from passive diffusion processes, after equilibration, are described by the Nernst equation. The primary criterion for the hypothesis that any given ion is actively transported is to establish that it is not diffusing passively. A test was made of how closely the Nernst equation describes the electrochemical equilibrium in seedling tissues. Segments of roots and epicotyl internodes of pea (Pisum sativum var. Alaska) and of roots and coleoptiles of oat (Avena sativa var. Victory) seedlings were immersed and shaken in defined nutrient solutions containing eight major nutrients (K+, Na+, Ca2+, Mg2+, Cl−, NO3−, H2PO4− and SO42−) at 1-fold and 10-fold concentrations. The tissue content of each ion was assayed at 0, 8, 24, and 48 hours. A near-equilibrium condition was approached by roots for most ions; however, the segments of shoot tissue generally continued to show a net accumulation of some ions, mainly K+ and NO3−. Only K+ approached a reasonable fit to the Nernst equation and this was true for the 1-fold concentration but not the 10-fold. The data suggest that for Na+, Mg2+, and Ca2+ the electrochemical gradient is from the external solution to the cell interior; thus passive diffusion should be in an inward direction. Consequently, some mechanism must exist in plant tissue either to exclude these cations or to extrude them (e.g., by an active efflux pump). For each of the anions the electrochemical gradient is from the tissue to the solution; thus an active influx pump for anions seems required. Root segments approach ionic equilibrium with the solution concentration in which the seedlings were grown. Segments of shoot tissue, however, are far removed from such equilibration. Thus in the intact seedling the extracellular (wall space) fluid must be very different from that of the nutrient solution bathing the segments; it would appear that the root is the site of regulation of ion uptake in the intact plant although other correlative mechanisms may be involved. PMID:16656483

Investigations of Nuclear Structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sarantites, Demetrios; Reviol, W.

The proposal addresses studies of nuclear structure at low-energies and development of instrumentation for that purpose. The structure studies deal with features of neutron-rich nuclei with unexplored shapes (football- or pear-shaped nuclei). The regions of interest are: neutron rich nuclei like 132-138Sn, or 48-54Ca, and the Zr, Mo, and Ru isotopes. The tools used can be grouped as follows: either Gammasphere or Gretina multi-gamma detector arrays and auxiliary detectors (Microball, Neutron Shell, and the newly completed Phoswich Wall).The neutron-rich nuclei are accessed by radioactive-beam binary reactions or by 252Cf spontaneous fission. The experiments with heavy radioactive beams aim at excitingmore » the beam nuclei by pick-up or transfer a neutron or a proton from a light target like 13C, 9Be, 11B or 14N .For these binary-reaction studies the Phoswich Wall detector system is essential. It is based on four multi-anode photomultiplier tubes on which CsI and thin fast-timing plastic scintillators are attached. Their signals are digitized with a high density microchip system.« less

A multi-segment soft actuator for biomedical applications based on IPMCs

NASA Astrophysics Data System (ADS)

Zhao, Dongxu; Wang, Yanjie; Liu, Jiayu; Luo, Meng; Li, Dichen; Chen, Hualing

2015-04-01

With rapid progress of biomedical devices towards miniaturization, flexibility, multifunction and low cost, the restrictions of traditional mechanical structures become particularly apparent, while soft materials become research focus in broad fields. As one of the most attractive soft materials, Ionic Polymer-Metal Composite (IPMC) is widely used as artificial muscles and actuators, with the advantages of low driving-voltage, high efficiency of electromechanical transduction and functional stabilization. In this paper, a new intuitive control method was presented to achieve the omnidirectional bending movements and was applied on a representative actuation structure of a multi-degree-offreedom soft actuator composed of two segments bar-shaped IPMC with a square cross section. Firstly, the bar-shaped IPMCs were fabricated by the solution casting method, reducing plating, autocatalytic plating method and cut into shapes successively. The connectors of the multi-segment IPMC actuator were fabricated by 3D printing. Then, a new control method was introduced to realize the intuitive mapping relationship between the actuator and the joystick manipulator. The control circuit was designed and tested. Finally, the multi-degree-of-freedom actuator of 2 segments bar-shaped IPMCs was implemented and omnidirectional bending movements were achieved, which could be a promising actuator for biomedical applications, such as endoscope, catheterism, laparoscopy and the surgical resection of tumors.

Termination Shock Transition in Multi-ion Multi-fluid MHD Models of the Heliosphere

NASA Astrophysics Data System (ADS)

Zieger, B.; Opher, M.; Toth, G.

2013-12-01

As evidenced by Voyager 2 observations, pickup ions (PUIs) play a significant role in the termination shock (TS) transition of the solar wind [Richardson et al., Nature, 2008]. Recent kinetic simulations [Ariad and Gedalin, JGR, 2013] came to the conclusion that the contribution of the high energy tail of PUIs is negligible at the shock transition. The Rankine-Hugoniot (R-H) relations are determined by the low energy body of PUIs. Particle-in-cell simulations by Wu et al. [JGR, 2010] have shown that the sum of the thermal solar wind and non-thermal PUI distributions downstream of the TS can be approximated with a 2-Maxwellian distribution. It is important to note that this 2-Maxwellian distribution neglects the suprathermal tail population that has a characteristic power-law distribution. These results justify the fluid description of PUIs in our large-scale multi-ion multi-fluid MHD simulations of the heliospheric interface [Prested et al., JGR, 2013; Zieger et al., GRL, 2013]. The closure of the multi-ion MHD equations could be implemented with separate momentum and energy equations for the different ion species (thermal solar wind and PUIs) where the transfer rate of momentum and energy between the two ion species are considered as source terms, like in Glocer et al. [JGR, 2009]. Another option is to solve for the total energy equation with an additional equation for the PUI pressure, as suggested by Fahr and Chalov [A&A, 2008]. In this paper, we validate the energy conservation and the R-H relations across the TS in different numerical implementations of our latest multi-ion multi-fluid MHD model. We assume an instantaneous pickup process, where the convection velocity of the two ion fluids are the same, and the so-called strong scattering approximation, where newly born PUIs attain their spherical shell distribution within a short distance on fluid scales (spatial scales much larger than the respective ion gyroradius).

Complexity and performance of on-chip biochemical assays

NASA Astrophysics Data System (ADS)

Kopf-Sill, Anne R.; Nikiforov, Theo; Bousse, Luc J.; Nagle, Rob; Parce, J. W.

1997-03-01

The use of microchips for performing biochemical processes has the potential to reduce reagent use and thus assay costs, increase throughput, and automate complex processes. We are building a multifunctional platform that provides sensing and actuation functions for a variety of microchip- based biochemical and analytical processes. Here we describe recent experiments that include on-chip dilution, reagent mixing, reaction, separation, and detection for important classes of biochemical assays. Issues in chip design and control are discussed.

Continuous two-wave lasing in microchip Nd : YAG lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ievlev, Ivan V; Koryukin, Igor' V; Lebedeva, Yu S

2011-08-31

Simultaneous two-wave lasing was obtained in microchip end-pumped Nd:YAG lasers at the wavelengths of 1061.5 and 1064.17 nm at room temperature. Laser wave intensities were studied as functions of crystal temperature and pump power. The ranges of parameters were determined in which the two-wave lasing occurs and the reasons for such lasing were established. A model is suggested, which adequately describes the experimental results obtained. (control of radiation parameters)

Miniaturization of flight deflection measurement system

NASA Technical Reports Server (NTRS)

Fodale, Robert (Inventor); Hampton, Herbert R. (Inventor)

1990-01-01

A flight deflection measurement system is disclosed including a hybrid microchip of a receiver/decoder. The hybrid microchip decoder is mounted piggy back on the miniaturized receiver and forms an integral unit therewith. The flight deflection measurement system employing the miniaturized receiver/decoder can be used in a wind tunnel. In particular, the miniaturized receiver/decoder can be employed in a spin measurement system due to its small size and can retain already established control surface actuation functions.

On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization

PubMed Central

Gooneratne, Chinthaka P.; Kodzius, Rimantas; Li, Fuquan; Foulds, Ian G.; Kosel, Jürgen

2016-01-01

The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA) for the manipulation of superparamagnetic beads (SPBs), and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads® demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead® SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads® travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device. PMID:27571084

On-Chip Magnetic Bead Manipulation and Detection Using a Magnetoresistive Sensor-Based Micro-Chip: Design Considerations and Experimental Characterization.

PubMed

Gooneratne, Chinthaka P; Kodzius, Rimantas; Li, Fuquan; Foulds, Ian G; Kosel, Jürgen

2016-08-26

The remarkable advantages micro-chip platforms offer over cumbersome, time-consuming equipment currently in use for bio-analysis are well documented. In this research, a micro-chip that includes a unique magnetic actuator (MA) for the manipulation of superparamagnetic beads (SPBs), and a magnetoresistive sensor for the detection of SPBs is presented. A design methodology, which takes into account the magnetic volume of SPBs, diffusion and heat transfer phenomena, is presented with the aid of numerical analysis to optimize the parameters of the MA. The MA was employed as a magnetic flux generator and experimental analysis with commercially available COMPEL™ and Dynabeads(®) demonstrated the ability of the MA to precisely transport a small number of SPBs over long distances and concentrate SPBs to a sensing site for detection. Moreover, the velocities of COMPEL™ and Dynabead(®) SPBs were correlated to their magnetic volumes and were in good agreement with numerical model predictions. We found that 2.8 μm Dynabeads(®) travel faster, and can be attracted to a magnetic source from a longer distance, than 6.2 μm COMPEL™ beads at magnetic flux magnitudes of less than 10 mT. The micro-chip system could easily be integrated with electronic circuitry and microfluidic functions, paving the way for an on-chip biomolecule quantification device.

Microchip integrating magnetic nanoparticles for allergy diagnosis.

PubMed

Teste, Bruno; Malloggi, Florent; Siaugue, Jean-Michel; Varenne, Anne; Kanoufi, Frederic; Descroix, Stéphanie

2011-12-21

We report on the development of a simple and easy to use microchip dedicated to allergy diagnosis. This microchip combines both the advantages of homogeneous immunoassays i.e. species diffusion and heterogeneous immunoassays i.e. easy separation and preconcentration steps. In vitro allergy diagnosis is based on specific Immunoglobulin E (IgE) quantitation, in that way we have developed and integrated magnetic core-shell nanoparticles (MCSNPs) as an IgE capture nanoplatform in a microdevice taking benefit from both their magnetic and colloidal properties. Integrating such immunosupport allows to perform the target analyte (IgE) capture in the colloidal phase thus increasing the analyte capture kinetics since both immunological partners are diffusing during the immune reaction. This colloidal approach improves 1000 times the analyte capture kinetics compared to conventional methods. Moreover, based on the MCSNPs' magnetic properties and on the magnetic chamber we have previously developed the MCSNPs and therefore the target can be confined and preconcentrated within the microdevice prior to the detection step. The MCSNPs preconcentration factor achieved was about 35,000 and allows to reach high sensitivity thus avoiding catalytic amplification during the detection step. The developed microchip offers many advantages: the analytical procedure was fully integrated on-chip, analyses were performed in short assay time (20 min), the sample and reagents consumption was reduced to few microlitres (5 μL) while a low limit of detection can be achieved (about 1 ng mL(-1)).

Capillary Electrophoresis Chips for Fingerprinting Endotoxin Chemotypes and Subclasses.

PubMed

Kocsis, Béla; Makszin, Lilla; Kilár, Anikó; Péterfi, Zoltán; Kilár, Ferenc

2017-01-01

Endotoxins (lipopolysaccharides, LPS; lipooligosaccharides, LOS) are components of the envelope of Gram-negative bacteria. These molecules, responsible for both advantageous and harmful biological activity of these microorganisms, are highly immunogenic and directly involved in numerous bacterial diseases in humans, such as Gram-negative sepsis. The characterization of endotoxins is of importance, since their physiological and pathophysiological effects depend on their chemical structure. The differences among the LPS from different bacterial serotypes and their mutants include variations mainly within the composition and length or missing of their O-polysaccharide chains. Microchip electrophoretic methodology enables the structural characterization of LPS molecules from several bacteria and the quantitative evaluation of components of endotoxin extracts. The improved microchip electrophoretic method is based on the direct labeling of endotoxins by covalent binding of a fluorescent dye. The classification of the S-type LPSs can be done according to their electrophoretic profiles, which are characteristics of the respective bacterial strains. According to the number, distribution, and the relative amounts of components in an endotoxin extract, it is possible to differentiate between the S-type endotoxins from different Gram-negative bacterial strains. The microchip electrophoresis affords high-resolution separation of pure and partially purified (e.g., obtained from whole-cell lysate) S and R endotoxins. This microchip technique provides a new, standardizable, fast, and sensitive method for the detection of endotoxins and for the quantitative evaluation of components of an endotoxin extract.

Multi scales based sparse matrix spectral clustering image segmentation

NASA Astrophysics Data System (ADS)

Liu, Zhongmin; Chen, Zhicai; Li, Zhanming; Hu, Wenjin

2018-04-01

In image segmentation, spectral clustering algorithms have to adopt the appropriate scaling parameter to calculate the similarity matrix between the pixels, which may have a great impact on the clustering result. Moreover, when the number of data instance is large, computational complexity and memory use of the algorithm will greatly increase. To solve these two problems, we proposed a new spectral clustering image segmentation algorithm based on multi scales and sparse matrix. We devised a new feature extraction method at first, then extracted the features of image on different scales, at last, using the feature information to construct sparse similarity matrix which can improve the operation efficiency. Compared with traditional spectral clustering algorithm, image segmentation experimental results show our algorithm have better degree of accuracy and robustness.

Ischemic stroke lesion segmentation in multi-spectral MR images with support vector machine classifiers

NASA Astrophysics Data System (ADS)

Maier, Oskar; Wilms, Matthias; von der Gablentz, Janina; Krämer, Ulrike; Handels, Heinz

2014-03-01

Automatic segmentation of ischemic stroke lesions in magnetic resonance (MR) images is important in clinical practice and for neuroscientific trials. The key problem is to detect largely inhomogeneous regions of varying sizes, shapes and locations. We present a stroke lesion segmentation method based on local features extracted from multi-spectral MR data that are selected to model a human observer's discrimination criteria. A support vector machine classifier is trained on expert-segmented examples and then used to classify formerly unseen images. Leave-one-out cross validation on eight datasets with lesions of varying appearances is performed, showing our method to compare favourably with other published approaches in terms of accuracy and robustness. Furthermore, we compare a number of feature selectors and closely examine each feature's and MR sequence's contribution.

Active Contours Driven by Multi-Feature Gaussian Distribution Fitting Energy with Application to Vessel Segmentation.

PubMed

Wang, Lei; Zhang, Huimao; He, Kan; Chang, Yan; Yang, Xiaodong

2015-01-01

Active contour models are of great importance for image segmentation and can extract smooth and closed boundary contours of the desired objects with promising results. However, they cannot work well in the presence of intensity inhomogeneity. Hence, a novel region-based active contour model is proposed by taking image intensities and 'vesselness values' from local phase-based vesselness enhancement into account simultaneously to define a novel multi-feature Gaussian distribution fitting energy in this paper. This energy is then incorporated into a level set formulation with a regularization term for accurate segmentations. Experimental results based on publicly available STructured Analysis of the Retina (STARE) demonstrate our model is more accurate than some existing typical methods and can successfully segment most small vessels with varying width.

Conditional, Time-Dependent Probabilities for Segmented Type-A Faults in the WGCEP UCERF 2

USGS Publications Warehouse

Field, Edward H.; Gupta, Vipin

2008-01-01

This appendix presents elastic-rebound-theory (ERT) motivated time-dependent probabilities, conditioned on the date of last earthquake, for the segmented type-A fault models of the 2007 Working Group on California Earthquake Probabilities (WGCEP). These probabilities are included as one option in the WGCEP?s Uniform California Earthquake Rupture Forecast 2 (UCERF 2), with the other options being time-independent Poisson probabilities and an ?Empirical? model based on observed seismicity rate changes. A more general discussion of the pros and cons of all methods for computing time-dependent probabilities, as well as the justification of those chosen for UCERF 2, are given in the main body of this report (and the 'Empirical' model is also discussed in Appendix M). What this appendix addresses is the computation of conditional, time-dependent probabilities when both single- and multi-segment ruptures are included in the model. Computing conditional probabilities is relatively straightforward when a fault is assumed to obey strict segmentation in the sense that no multi-segment ruptures occur (e.g., WGCEP (1988, 1990) or see Field (2007) for a review of all previous WGCEPs; from here we assume basic familiarity with conditional probability calculations). However, and as we?ll see below, the calculation is not straightforward when multi-segment ruptures are included, in essence because we are attempting to apply a point-process model to a non point process. The next section gives a review and evaluation of the single- and multi-segment rupture probability-calculation methods used in the most recent statewide forecast for California (WGCEP UCERF 1; Petersen et al., 2007). We then present results for the methodology adopted here for UCERF 2. We finish with a discussion of issues and possible alternative approaches that could be explored and perhaps applied in the future. A fault-by-fault comparison of UCERF 2 probabilities with those of previous studies is given in the main part of this report.

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters

PubMed Central

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme. PMID:27362762

Information Extraction of High Resolution Remote Sensing Images Based on the Calculation of Optimal Segmentation Parameters.

PubMed

Zhu, Hongchun; Cai, Lijie; Liu, Haiying; Huang, Wei

2016-01-01

Multi-scale image segmentation and the selection of optimal segmentation parameters are the key processes in the object-oriented information extraction of high-resolution remote sensing images. The accuracy of remote sensing special subject information depends on this extraction. On the basis of WorldView-2 high-resolution data, the optimal segmentation parameters methodof object-oriented image segmentation and high-resolution image information extraction, the following processes were conducted in this study. Firstly, the best combination of the bands and weights was determined for the information extraction of high-resolution remote sensing image. An improved weighted mean-variance method was proposed andused to calculatethe optimal segmentation scale. Thereafter, the best shape factor parameter and compact factor parameters were computed with the use of the control variables and the combination of the heterogeneity and homogeneity indexes. Different types of image segmentation parameters were obtained according to the surface features. The high-resolution remote sensing images were multi-scale segmented with the optimal segmentation parameters. Ahierarchical network structure was established by setting the information extraction rules to achieve object-oriented information extraction. This study presents an effective and practical method that can explain expert input judgment by reproducible quantitative measurements. Furthermore the results of this procedure may be incorporated into a classification scheme.

Extracellular Bio-imaging of Acetylcholine-stimulated PC12 Cells Using a Calcium and Potassium Multi-ion Image Sensor.

PubMed

Matsuba, Sota; Kato, Ryo; Okumura, Koichi; Sawada, Kazuaki; Hattori, Toshiaki

2018-01-01

In biochemistry, Ca 2+ and K + play essential roles to control signal transduction. Much interest has been focused on ion-imaging, which facilitates understanding of their ion flux dynamics. In this paper, we report a calcium and potassium multi-ion image sensor and its application to living cells (PC12). The multi-ion sensor had two selective plasticized poly(vinyl chloride) membranes containing ionophores. Each region on the sensor responded to only the corresponding ion. The multi-ion sensor has many advantages including not only label-free and real-time measurement but also simultaneous detection of Ca 2+ and K + . Cultured PC12 cells treated with nerve growth factor were prepared, and a practical observation for the cells was conducted with the sensor. After the PC12 cells were stimulated by acetylcholine, only the extracellular Ca 2+ concentration increased while there was no increase in the extracellular K + concentration. Through the practical observation, we demonstrated that the sensor was helpful for analyzing the cell events with changing Ca 2+ and/or K + concentration.

Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in the small wave number region

NASA Astrophysics Data System (ADS)

Feng, Q. S.; Xiao, C. Z.; Wang, Q.; Zheng, C. Y.; Liu, Z. J.; Cao, L. H.; He, X. T.

2016-08-01

The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given, and the results of Vlasov simulation are consistent with the theoretical result of multi-ion species plasmas. When the wave number k λD e is small, such as k λD e=0.1 , the fluid NFS dominates in the total NFS and will reach as large as nearly 15 % when the wave amplitude |e ϕ / Te|˜0.1 , which indicates that in the condition of small k λD e , the fluid NFS dominates in the saturation of stimulated Brillouin scattering, especially when the nonlinear IAW amplitude is large.

Fluid nonlinear frequency shift of nonlinear ion acoustic waves in multi-ion species plasmas in the small wave number region.

PubMed

Feng, Q S; Xiao, C Z; Wang, Q; Zheng, C Y; Liu, Z J; Cao, L H; He, X T

2016-08-01

The properties of the nonlinear frequency shift (NFS), especially the fluid NFS from the harmonic generation of the ion-acoustic wave (IAW) in multi-ion species plasmas, have been researched by Vlasov simulation. Pictures of the nonlinear frequency shift from harmonic generation and particle trapping are shown to explain the mechanism of NFS qualitatively. The theoretical model of the fluid NFS from harmonic generation in multi-ion species plasmas is given, and the results of Vlasov simulation are consistent with the theoretical result of multi-ion species plasmas. When the wave number kλ_{De} is small, such as kλ_{De}=0.1, the fluid NFS dominates in the total NFS and will reach as large as nearly 15% when the wave amplitude |eϕ/T_{e}|∼0.1, which indicates that in the condition of small kλ_{De}, the fluid NFS dominates in the saturation of stimulated Brillouin scattering, especially when the nonlinear IAW amplitude is large.

Multifractal modeling, segmentation, prediction, and statistical validation of posterior fossa tumors

NASA Astrophysics Data System (ADS)

Islam, Atiq; Iftekharuddin, Khan M.; Ogg, Robert J.; Laningham, Fred H.; Sivakumar, Bhuvaneswari

2008-03-01

In this paper, we characterize the tumor texture in pediatric brain magnetic resonance images (MRIs) and exploit these features for automatic segmentation of posterior fossa (PF) tumors. We focus on PF tumor because of the prevalence of such tumor in pediatric patients. Due to varying appearance in MRI, we propose to model the tumor texture with a multi-fractal process, such as a multi-fractional Brownian motion (mBm). In mBm, the time-varying Holder exponent provides flexibility in modeling irregular tumor texture. We develop a detailed mathematical framework for mBm in two-dimension and propose a novel algorithm to estimate the multi-fractal structure of tissue texture in brain MRI based on wavelet coefficients. This wavelet based multi-fractal feature along with MR image intensity and a regular fractal feature obtained using our existing piecewise-triangular-prism-surface-area (PTPSA) method, are fused in segmenting PF tumor and non-tumor regions in brain T1, T2, and FLAIR MR images respectively. We also demonstrate a non-patient-specific automated tumor prediction scheme based on these image features. We experimentally show the tumor discriminating power of our novel multi-fractal texture along with intensity and fractal features in automated tumor segmentation and statistical prediction. To evaluate the performance of our tumor prediction scheme, we obtain ROCs and demonstrate how sharply the curves reach the specificity of 1.0 sacrificing minimal sensitivity. Experimental results show the effectiveness of our proposed techniques in automatic detection of PF tumors in pediatric MRIs.

A tree canopy height delineation method based on Morphological Reconstruction—Open Crown Decomposition

NASA Astrophysics Data System (ADS)

Liu, Q.; Jing, L.; Li, Y.; Tang, Y.; Li, H.; Lin, Q.

2016-04-01

For the purpose of forest management, high resolution LIDAR and optical remote sensing imageries are used for treetop detection, tree crown delineation, and classification. The purpose of this study is to develop a self-adjusted dominant scales calculation method and a new crown horizontal cutting method of tree canopy height model (CHM) to detect and delineate tree crowns from LIDAR, under the hypothesis that a treetop is radiometric or altitudinal maximum and tree crowns consist of multi-scale branches. The major concept of the method is to develop an automatic selecting strategy of feature scale on CHM, and a multi-scale morphological reconstruction-open crown decomposition (MRCD) to get morphological multi-scale features of CHM by: cutting CHM from treetop to the ground; analysing and refining the dominant multiple scales with differential horizontal profiles to get treetops; segmenting LiDAR CHM using watershed a segmentation approach marked with MRCD treetops. This method has solved the problems of false detection of CHM side-surface extracted by the traditional morphological opening canopy segment (MOCS) method. The novel MRCD delineates more accurate and quantitative multi-scale features of CHM, and enables more accurate detection and segmentation of treetops and crown. Besides, the MRCD method can also be extended to high optical remote sensing tree crown extraction. In an experiment on aerial LiDAR CHM of a forest of multi-scale tree crowns, the proposed method yielded high-quality tree crown maps.

The evaluation of multi-structure, multi-atlas pelvic anatomy features in a prostate MR lymphography CAD system

NASA Astrophysics Data System (ADS)

Meijs, M.; Debats, O.; Huisman, H.

2015-03-01

In prostate cancer, the detection of metastatic lymph nodes indicates progression from localized disease to metastasized cancer. The detection of positive lymph nodes is, however, a complex and time consuming task for experienced radiologists. Assistance of a two-stage Computer-Aided Detection (CAD) system in MR Lymphography (MRL) is not yet feasible due to the large number of false positives in the first stage of the system. By introducing a multi-structure, multi-atlas segmentation, using an affine transformation followed by a B-spline transformation for registration, the organ location is given by a mean density probability map. The atlas segmentation is semi-automatically drawn with ITK-SNAP, using Active Contour Segmentation. Each anatomic structure is identified by a label number. Registration is performed using Elastix, using Mutual Information and an Adaptive Stochastic Gradient optimization. The dataset consists of the MRL scans of ten patients, with lymph nodes manually annotated in consensus by two expert readers. The feature map of the CAD system consists of the Multi-Atlas and various other features (e.g. Normalized Intensity and multi-scale Blobness). The voxel-based Gentleboost classifier is evaluated using ROC analysis with cross validation. We show in a set of 10 studies that adding multi-structure, multi-atlas anatomical structure likelihood features improves the quality of the lymph node voxel likelihood map. Multiple structure anatomy maps may thus make MRL CAD more feasible.

A Learning-Based Wrapper Method to Correct Systematic Errors in Automatic Image Segmentation: Consistently Improved Performance in Hippocampus, Cortex and Brain Segmentation

PubMed Central

Wang, Hongzhi; Das, Sandhitsu R.; Suh, Jung Wook; Altinay, Murat; Pluta, John; Craige, Caryne; Avants, Brian; Yushkevich, Paul A.

2011-01-01

We propose a simple but generally applicable approach to improving the accuracy of automatic image segmentation algorithms relative to manual segmentations. The approach is based on the hypothesis that a large fraction of the errors produced by automatic segmentation are systematic, i.e., occur consistently from subject to subject, and serves as a wrapper method around a given host segmentation method. The wrapper method attempts to learn the intensity, spatial and contextual patterns associated with systematic segmentation errors produced by the host method on training data for which manual segmentations are available. The method then attempts to correct such errors in segmentations produced by the host method on new images. One practical use of the proposed wrapper method is to adapt existing segmentation tools, without explicit modification, to imaging data and segmentation protocols that are different from those on which the tools were trained and tuned. An open-source implementation of the proposed wrapper method is provided, and can be applied to a wide range of image segmentation problems. The wrapper method is evaluated with four host brain MRI segmentation methods: hippocampus segmentation using FreeSurfer (Fischl et al., 2002); hippocampus segmentation using multi-atlas label fusion (Artaechevarria et al., 2009); brain extraction using BET (Smith, 2002); and brain tissue segmentation using FAST (Zhang et al., 2001). The wrapper method generates 72%, 14%, 29% and 21% fewer erroneously segmented voxels than the respective host segmentation methods. In the hippocampus segmentation experiment with multi-atlas label fusion as the host method, the average Dice overlap between reference segmentations and segmentations produced by the wrapper method is 0.908 for normal controls and 0.893 for patients with mild cognitive impairment. Average Dice overlaps of 0.964, 0.905 and 0.951 are obtained for brain extraction, white matter segmentation and gray matter segmentation, respectively. PMID:21237273

Delayed bunching for multi-reflection time-of-flight mass separation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rosenbusch, M.; Marx, G.; Schweikhard, L.

2015-06-29

Many experiments are handicapped when the ion sources do not only deliver the ions of interest but also contaminations, i.e., unwanted ions of similar mass. In the recent years, multi-reflection time-of-flight mass separation has become a promising method to isolate the ions of interest from the contaminants, in particular for measurements with low-energy short-lived nuclides. To further improve the performance of multi-reflection mass separators with respect to the limitations by space-charge effects, the simultaneously trapped ions are spatially widely distributed in the apparatus. Thus, the ions can propagate with reduced Coulomb interactions until, finally, they are bunched by a changemore » in the trapping conditions for high-resolution mass separation. Proof-of-principle measurements are presented.« less

An analytic expression for the sheath criterion in magnetized plasmas with multi-charged ion species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hatami, M. M., E-mail: m-hatami@kntu.ac.ir

2015-04-15

The generalized Bohm criterion in magnetized multi-component plasmas consisting of multi-charged positive and negative ion species and electrons is analytically investigated by using the hydrodynamic model. It is assumed that the electrons and negative ion density distributions are the Boltzmann distribution with different temperatures and the positive ions enter into the sheath region obliquely. Our results show that the positive and negative ion temperatures, the orientation of the applied magnetic field and the charge number of positive and negative ions strongly affect the Bohm criterion in these multi-component plasmas. To determine the validity of our derived generalized Bohm criterion, itmore » reduced to some familiar physical condition and it is shown that monotonically reduction of the positive ion density distribution leading to the sheath formation occurs only when entrance velocity of ion into the sheath satisfies the obtained Bohm criterion. Also, as a practical application of the obtained Bohm criterion, effects of the ionic temperature and concentration as well as magnetic field on the behavior of the charged particle density distributions and so the sheath thickness of a magnetized plasma consisting of electrons and singly charged positive and negative ion species are studied numerically.« less

Statistical label fusion with hierarchical performance models

PubMed Central

Asman, Andrew J.; Dagley, Alexander S.; Landman, Bennett A.

2014-01-01

Label fusion is a critical step in many image segmentation frameworks (e.g., multi-atlas segmentation) as it provides a mechanism for generalizing a collection of labeled examples into a single estimate of the underlying segmentation. In the multi-label case, typical label fusion algorithms treat all labels equally – fully neglecting the known, yet complex, anatomical relationships exhibited in the data. To address this problem, we propose a generalized statistical fusion framework using hierarchical models of rater performance. Building on the seminal work in statistical fusion, we reformulate the traditional rater performance model from a multi-tiered hierarchical perspective. This new approach provides a natural framework for leveraging known anatomical relationships and accurately modeling the types of errors that raters (or atlases) make within a hierarchically consistent formulation. Herein, we describe several contributions. First, we derive a theoretical advancement to the statistical fusion framework that enables the simultaneous estimation of multiple (hierarchical) performance models within the statistical fusion context. Second, we demonstrate that the proposed hierarchical formulation is highly amenable to the state-of-the-art advancements that have been made to the statistical fusion framework. Lastly, in an empirical whole-brain segmentation task we demonstrate substantial qualitative and significant quantitative improvement in overall segmentation accuracy. PMID:24817809

Segmenting the Femoral Head and Acetabulum in the Hip Joint Automatically Using a Multi-Step Scheme

NASA Astrophysics Data System (ADS)

Wang, Ji; Cheng, Yuanzhi; Fu, Yili; Zhou, Shengjun; Tamura, Shinichi

We describe a multi-step approach for automatic segmentation of the femoral head and the acetabulum in the hip joint from three dimensional (3D) CT images. Our segmentation method consists of the following steps: 1) construction of the valley-emphasized image by subtracting valleys from the original images; 2) initial segmentation of the bone regions by using conventional techniques including the initial threshold and binary morphological operations from the valley-emphasized image; 3) further segmentation of the bone regions by using the iterative adaptive classification with the initial segmentation result; 4) detection of the rough bone boundaries based on the segmented bone regions; 5) 3D reconstruction of the bone surface using the rough bone boundaries obtained in step 4) by a network of triangles; 6) correction of all vertices of the 3D bone surface based on the normal direction of vertices; 7) adjustment of the bone surface based on the corrected vertices. We evaluated our approach on 35 CT patient data sets. Our experimental results show that our segmentation algorithm is more accurate and robust against noise than other conventional approaches for automatic segmentation of the femoral head and the acetabulum. Average root-mean-square (RMS) distance from manual reference segmentations created by experienced users was approximately 0.68mm (in-plane resolution of the CT data).

Electro-optically tunable microwave source based on composite-cavity microchip laser.

PubMed

Qiao, Yunfei; Zheng, Shilie; Chi, Hao; Jin, Xiaofeng; Zhang, Xianmin

2012-12-17

A compact and electric tuning microwave source based on a diode-pumped composite Nd:YAG-LiNbO(3) cavity microchip laser is demonstrated. The electro-optical element introduces an electric tuning intra-cavity birefringence which causes a tunable frequency difference between two spilt orthogonal polarization states of a longitude mode. Thus a continuously tunable microwave signal with frequency up to 14.12 GHz can be easily generated by beating the two polarization modes on a high speed photodetector.

Tm:KLu(WO(4))(2) microchip laser Q-switched by a graphene-based saturable absorber.

PubMed

Serres, Josep Maria; Loiko, Pavel; Mateos, Xavier; Yumashev, Konstantin; Griebner, Uwe; Petrov, Valentin; Aguiló, Magdalena; Díaz, Francesc

2015-06-01

We report on the first Tm-doped double tungstate microchip laser Q-switched with graphene using a Tm:KLu(WO₄)₂ crystal cut along the N_g dielectric axis. This laser generates a maximum average output power of 310 mW with a slope efficiency of 13%. At a repetition rate of 190 kHz the shortest pulses with 285 ns duration and 1.6 µJ energy are achieved.

Pulse laser head with monolithic thermally bonded microchip operating at 1.5 μm wavelength

NASA Astrophysics Data System (ADS)

Młyńczak, Jarosław; Kopczyński, Krzysztof; Belghachem, Nabil; Kisielewski, Jarosław; Stepień, Ryszard; Wychowaniec, Marek; Galas, Jacek; Litwin, Dariusz; CzyŻewski, Adam

2016-12-01

On the basis of thermally bonded Er,Yb:glass/Co:MALO microchip a laser head pumped by fiber coupled laser diode was designed. The performance of the laser head were investigated and the main output parameters were determined. The energy over 40 μJ in 3.8 ns pulse with repetition rate of 0.735 kHz was achieved. The laser head characterized by such parameters can successfully be used in tele-detection applications.

Generation of Hermite-Gaussian modes and vortex arrays based on two-dimensional gain distribution controlled microchip laser.

PubMed

Kong, Weipeng; Sugita, Atsushi; Taira, Takunori

2012-07-01

We have demonstrated high-order Hermite-Gaussian (HG) mode generation based on 2D gain distribution control edge-pumped, composite all-ceramic Yb:YAG/YAG microchip lasers using a V-type cavity. Several hundred milliwatts to several watts HG(mn) modes are achieved. We also generated different kinds of vortex arrays directly from the oscillator with the same power level. In addition, a more than 7 W doughnut-shape mode can be generated in the same cavity.

Kinetic Alfven wave with density variation and loss-cone distribution function of multi-ions in PSBL region

NASA Astrophysics Data System (ADS)

Tamrakar, Radha; Varma, P.; Tiwari, M. S.

2018-05-01

Kinetic Alfven wave (KAW) generation due to variation of loss-cone index J and density of multi-ions (H+, He+ and O+) in the plasma sheet boundary layer region (PSBL) is investigated. Kinetic approach is used to derive dispersion relation of wave using Vlasov equation. Variation of frequency with respect to wide range of k⊥ρi (where k⊥ is wave vector across the magnetic field, ρi is gyroradius of ions and i denotes H+, He+ and O+ ions) is analyzed. It is found that each ion gyroradius and number density shows different effect on wave generation with varying width of loss-cone. KAW is generated with multi-ions (H+, He+ and O+) over wide regime for J=1 and shows dissimilar effect for J=2. Frequency is reduced with increasing density of gyrating He+ and O+ ions. Wave frequency is obtained within the reported range which strongly supports generation of kinetic Alfven waves. A sudden drop of frequency is also observed for H+ and He+ ion which may be due to heavy penetration of these ions through the loss-cone. The parameters of PSBL region are used for numerical calculation. The application of these results are in understanding the effect of gyrating multi-ions in transfer of energy and Poynting flux losses from PSBL region towards ionosphere and also describing the generation of aurora.

Erratum: “Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment” [Rev. Sci. Instrum. 83, 10D516 (2012)

DOE PAGES

Burke, Marcus G.; Fonck, Raymond J.; Bongard, Michael W.; ...

2016-07-18

This article corrects an error in M.G. Burke et al., 'Multi-point, high-speed passive ion velocity distribution diagnostic on the Pegasus Toroidal Experiment,' Rev. Sci. Instrum. 83, 10D516 (2012) pertaining to ion temperature. The conclusions of this paper are not altered by the revised ion temperature measurements.

[Surgical treatment of degenerative lumbar scoliosis with multi-segment lumbar spinal stenosis].

PubMed

Lan, Jiaping; Tang, Xun; Xu, Yongqing; Zhou, Tianhua; Shi, Jian; Cui, Yi; Xiang, Qili; Cai, Zhijun; Zhao, Qingkai; Yang, Xiaoyong; Zhao, Caihua

2014-08-01

To explore the surgical indications, decompression and fusion method, and fusion level selection of degenerative lumbar scoliosis (DLS) and multi-segment lumbar spinal stenosis. Between April 2000 and November 2011, 46 cases of DLS and multi-segment lumbar spinal stenosis were treated with multi-level decompression by fenestration and crept enlargement plus internal fixation by interbody and posterior-lateral bone graft fusion (5 segments or above). Of 46 cases, 25 were male and 21 were female, with a mean age of 70.2 years (range, 65-81 years) and with a mean disease duration of 6.4 years (range, 4 years and 6 months to 13 years). X-ray films showed that the lumbar Cobb angle was (26.7 ± 10.0) degrees, and the lumbar lordotic angle was (20.3 ± 8.8)degrees. The lumbar CT and MRI images showed three-segment stenosis in 24 cases, four-segment stenosis in 17 cases, and five-segment stenosis in 5 cases. A total of 165 stenosed segments included 12 L1,2, 34 L2,3, 43 L3,4, 45 L4,5, and 31 L5 and S1. Visual analogue scale (VAS) score, Oswestry disability index (ODI), and Japanese Orthopedic Association (JOA) score (29 points) were employed to evaluate effectiveness. Thirteen patients had leakage of cerebrospinal fluid during operation, and no infection was found after corresponding treatment; pulmonary infection and urinary system infection occurred in 4 and 2 patients respectively, who relieved after received antibiotic therapy; 8 patients with poor wound healing received dressing change, adequate drainage, debridement and suture. No death, paralysis, central nervous system infection, or other complication was observed in these patients. Forty-six cases were followed up 12-72 months (mean, 36.2 months). Lumbago and backache and intermittent claudication of lower extremity were obviously improved. During follow-up, no screw incising, loosening and broken screws, or pseudarthrosis was noted under X-ray film and CT scanning. At last follow-up, the lumbar Cobb angle was reduced to (9.8 ± 3.6) degrees, while the lumbar lordotic angle was increased to (34.1 ± 9.4) degrees, which were significantly improved when compared with preoperative ones (t = 16.935, P = 0.000; t = 15.233, P = 0.000). At last follow-up, VAS, ODI, and JOA scores were 3.2 ± 1.2, 35.5% ± 14.0%, and 26.6 ± 5.7 respectively, showing significant differences when compared with preoperative scores (8.0 ± 2.2, 60.8% ± 13.3%, and 12.9 ± 3.4) (t = 19.857, P = 0.000; t = 16.642, P = 0.000; t = 15.922, P = 0.000). Multi-segment decompression by fenestration and crept enlargement plus internal fixation by interbody and posterior-lateral bone graft fusion is helpful to relieve nerve compression symptoms, rebuild spinal balance, and improve the life quality of the patients. It is a very effective way to treat DLS and multi-segment lumbar spinal stenosis.

Enhancing MPLS Protection Method with Adaptive Segment Repair

NASA Astrophysics Data System (ADS)

Chen, Chin-Ling

We propose a novel adaptive segment repair mechanism to improve traditional MPLS (Multi-Protocol Label Switching) failure recovery. The proposed mechanism protects one or more contiguous high failure probability links by dynamic setup of segment protection. Simulations demonstrate that the proposed mechanism reduces failure recovery time while also increasing network resource utilization.

Do Online Learning Patterns Exhibit Regional and Demographic Differences?

ERIC Educational Resources Information Center

Hsieh, Tsui-Chuan; Yang, Chyan

2012-01-01

This paper used a multi-level latent class model to evaluate whether online learning patterns exhibit regional differences and demographics. This study discovered that the Internet learning pattern consists of five segments, and the region of Taiwan is divided into two segments and further found that both the user and the regional segments are…

Comparison of unsupervised classification methods for brain tumor segmentation using multi-parametric MRI.

PubMed

Sauwen, N; Acou, M; Van Cauter, S; Sima, D M; Veraart, J; Maes, F; Himmelreich, U; Achten, E; Van Huffel, S

2016-01-01

Tumor segmentation is a particularly challenging task in high-grade gliomas (HGGs), as they are among the most heterogeneous tumors in oncology. An accurate delineation of the lesion and its main subcomponents contributes to optimal treatment planning, prognosis and follow-up. Conventional MRI (cMRI) is the imaging modality of choice for manual segmentation, and is also considered in the vast majority of automated segmentation studies. Advanced MRI modalities such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have already shown their added value in tumor tissue characterization, hence there have been recent suggestions of combining different MRI modalities into a multi-parametric MRI (MP-MRI) approach for brain tumor segmentation. In this paper, we compare the performance of several unsupervised classification methods for HGG segmentation based on MP-MRI data including cMRI, DWI, MRSI and PWI. Two independent MP-MRI datasets with a different acquisition protocol were available from different hospitals. We demonstrate that a hierarchical non-negative matrix factorization variant which was previously introduced for MP-MRI tumor segmentation gives the best performance in terms of mean Dice-scores for the pathologic tissue classes on both datasets.

Integration of Sparse Multi-modality Representation and Geometrical Constraint for Isointense Infant Brain Segmentation

PubMed Central

Wang, Li; Shi, Feng; Li, Gang; Lin, Weili; Gilmore, John H.; Shen, Dinggang

2014-01-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination process. During the first year of life, the signal contrast between white matter (WM) and gray matter (GM) in MR images undergoes inverse changes. In particular, the inversion of WM/GM signal contrast appears around 6–8 months of age, where brain tissues appear isointense and hence exhibit extremely low tissue contrast, posing significant challenges for automated segmentation. In this paper, we propose a novel segmentation method to address the above-mentioned challenge based on the sparse representation of the complementary tissue distribution information from T1, T2 and diffusion-weighted images. Specifically, we first derive an initial segmentation from a library of aligned multi-modality images with ground-truth segmentations by using sparse representation in a patch-based fashion. The segmentation is further refined by the integration of the geometrical constraint information. The proposed method was evaluated on 22 6-month-old training subjects using leave-one-out cross-validation, as well as 10 additional infant testing subjects, showing superior results in comparison to other state-of-the-art methods. PMID:24505729

Integration of sparse multi-modality representation and geometrical constraint for isointense infant brain segmentation.

PubMed

Wang, Li; Shi, Feng; Li, Gang; Lin, Weili; Gilmore, John H; Shen, Dinggang

2013-01-01

Segmentation of infant brain MR images is challenging due to insufficient image quality, severe partial volume effect, and ongoing maturation and myelination process. During the first year of life, the signal contrast between white matter (WM) and gray matter (GM) in MR images undergoes inverse changes. In particular, the inversion of WM/GM signal contrast appears around 6-8 months of age, where brain tissues appear isointense and hence exhibit extremely low tissue contrast, posing significant challenges for automated segmentation. In this paper, we propose a novel segmentation method to address the above-mentioned challenge based on the sparse representation of the complementary tissue distribution information from T1, T2 and diffusion-weighted images. Specifically, we first derive an initial segmentation from a library of aligned multi-modality images with ground-truth segmentations by using sparse representation in a patch-based fashion. The segmentation is further refined by the integration of the geometrical constraint information. The proposed method was evaluated on 22 6-month-old training subjects using leave-one-out cross-validation, as well as 10 additional infant testing subjects, showing superior results in comparison to other state-of-the-art methods.

Surface-region context in optimal multi-object graph-based segmentation: robust delineation of pulmonary tumors.

PubMed

Song, Qi; Chen, Mingqing; Bai, Junjie; Sonka, Milan; Wu, Xiaodong

2011-01-01

Multi-object segmentation with mutual interaction is a challenging task in medical image analysis. We report a novel solution to a segmentation problem, in which target objects of arbitrary shape mutually interact with terrain-like surfaces, which widely exists in the medical imaging field. The approach incorporates context information used during simultaneous segmentation of multiple objects. The object-surface interaction information is encoded by adding weighted inter-graph arcs to our graph model. A globally optimal solution is achieved by solving a single maximum flow problem in a low-order polynomial time. The performance of the method was evaluated in robust delineation of lung tumors in megavoltage cone-beam CT images in comparison with an expert-defined independent standard. The evaluation showed that our method generated highly accurate tumor segmentations. Compared with the conventional graph-cut method, our new approach provided significantly better results (p < 0.001). The Dice coefficient obtained by the conventional graph-cut approach (0.76 +/- 0.10) was improved to 0.84 +/- 0.05 when employing our new method for pulmonary tumor segmentation.

A discriminative model-constrained graph cuts approach to fully automated pediatric brain tumor segmentation in 3-D MRI.

PubMed

Wels, Michael; Carneiro, Gustavo; Aplas, Alexander; Huber, Martin; Hornegger, Joachim; Comaniciu, Dorin

2008-01-01

In this paper we present a fully automated approach to the segmentation of pediatric brain tumors in multi-spectral 3-D magnetic resonance images. It is a top-down segmentation approach based on a Markov random field (MRF) model that combines probabilistic boosting trees (PBT) and lower-level segmentation via graph cuts. The PBT algorithm provides a strong discriminative observation model that classifies tumor appearance while a spatial prior takes into account the pair-wise homogeneity in terms of classification labels and multi-spectral voxel intensities. The discriminative model relies not only on observed local intensities but also on surrounding context for detecting candidate regions for pathology. A mathematically sound formulation for integrating the two approaches into a unified statistical framework is given. The proposed method is applied to the challenging task of detection and delineation of pediatric brain tumors. This segmentation task is characterized by a high non-uniformity of both the pathology and the surrounding non-pathologic brain tissue. A quantitative evaluation illustrates the robustness of the proposed method. Despite dealing with more complicated cases of pediatric brain tumors the results obtained are mostly better than those reported for current state-of-the-art approaches to 3-D MR brain tumor segmentation in adult patients. The entire processing of one multi-spectral data set does not require any user interaction, and takes less time than previously proposed methods.

Multi-atlas segmentation for abdominal organs with Gaussian mixture models

NASA Astrophysics Data System (ADS)

Burke, Ryan P.; Xu, Zhoubing; Lee, Christopher P.; Baucom, Rebeccah B.; Poulose, Benjamin K.; Abramson, Richard G.; Landman, Bennett A.

2015-03-01

Abdominal organ segmentation with clinically acquired computed tomography (CT) is drawing increasing interest in the medical imaging community. Gaussian mixture models (GMM) have been extensively used through medical segmentation, most notably in the brain for cerebrospinal fluid / gray matter / white matter differentiation. Because abdominal CT exhibit strong localized intensity characteristics, GMM have recently been incorporated in multi-stage abdominal segmentation algorithms. In the context of variable abdominal anatomy and rich algorithms, it is difficult to assess the marginal contribution of GMM. Herein, we characterize the efficacy of an a posteriori framework that integrates GMM of organ-wise intensity likelihood with spatial priors from multiple target-specific registered labels. In our study, we first manually labeled 100 CT images. Then, we assigned 40 images to use as training data for constructing target-specific spatial priors and intensity likelihoods. The remaining 60 images were evaluated as test targets for segmenting 12 abdominal organs. The overlap between the true and the automatic segmentations was measured by Dice similarity coefficient (DSC). A median improvement of 145% was achieved by integrating the GMM intensity likelihood against the specific spatial prior. The proposed framework opens the opportunities for abdominal organ segmentation by efficiently using both the spatial and appearance information from the atlases, and creates a benchmark for large-scale automatic abdominal segmentation.

Determination of trace amount of cyanobacterial toxin in water by microchip based enzyme-linked immunosorbent assay.

PubMed

Pyo, Dongjin; Hahn, Jong Hoon

2009-01-01

Routine monitoring of microcystin in natural waters is difficult because the concentration of the toxin is usually lower than the detection limits. As a more sensitive detection method for microcystin, we developed a microchip based enzyme-linked immunosorbent assay (ELISA) based on monoclonal antibodies. New monoclonal antibodies against the microcystin leucine-arginine variant (MCLR), a cyclic peptide toxin of the freshwater cyanobacterium Microcystis aeruginosa, were prepared from cloned hybridoma cell lines. We used keyhole limpet hemocyanin(KLH)-conjugated MCLR as an immunogen for the production of mouse monoclonal antibody. The immunization, cell fusion, and screening of hybridoma cells producing anti-MCLR antibody were conducted. Since the ELISA test was highly sensitive, the newly developed microchip based ELISA can be suitable for the trace analysis of cyanobacterial hepatotoxins, microcystins in water. The linear responses of monoclonal antibodies with different concentrations of microcystin LR were established between 0.025 and 0.3 ng/mL.

When microchip implants do more than drug delivery: blending, blurring, and bundling of protected health information and patient monitoring.

PubMed

Bramstedt, Katrina A

2005-01-01

Although currently in the research stage, scientists argue that drug-releasing microchip implants are on the horizon for future patients. This paper presents ethical reflection on these implants and identifies specific areas of concern; namely, patient monitoring and tracking, and patient privacy and confidentiality. It is foreseeable that drug delivery chips could be multifunctional with the overt or covert addition of sensors that monitor more than just the bloodstream concentrations of prescribed drugs (e.g., cotinine and alcohol in non-compliant patients, patient location via radio frequency or global positioning satellite). Similarly, it is foreseeable that these chips could be embedded with a patient's protected health information that could potentially be accessed and used by unauthorized persons. While drug delivery microchips are theoretically convenient and accurate for dosing, and might offer faster drug delivery with fewer side effects, ethical issues loom and should be contemplated now, while the technology is still under development.

Electrospray micromixer chip for on-line derivatization and kinetic studies.

PubMed

Abonnenc, Mélanie; Dayon, Loïc; Perruche, Brice; Lion, Niels; Girault, Hubert H

2008-05-01

An electrospray microchip for mass spectrometry comprising an integrated passive mixer to carry out on-chip chemical derivatizations is described. The microchip fabricated using UV-photoablation is composed of two microchannels linked together by a liquid junction. Downstream of this liquid junction, a mixing unit made of parallel oblique grooves is integrated to the microchannel in order to create flow perturbations. Several mixer designs are evaluated. The mixer efficiency is investigated both by fluorescence study and mass spectrometric monitoring of the tagging reaction of cysteinyl peptides with 1,4-benzoquinone. The comparisons with a microchip without a mixing unit and a kinetic model are used to assess the efficiency of the mixer showing tagging kinetics close to that of bulk reactions in an ideally mixed reactor. As an ultimate application, the electrospray micromixer is implemented in a LC-MS workflow. On-line derivatization of albumin tryptic peptides after a reversed-phase separation and counting of their cysteines drastically enhance the protein identification.

Analysis of anabolic steroids in urine by gas chromatography-microchip atmospheric pressure photoionization-mass spectrometry with chlorobenzene as dopant.

PubMed

Hintikka, Laura; Haapala, Markus; Kuuranne, Tiia; Leinonen, Antti; Kostiainen, Risto

2013-10-18

A gas chromatography-microchip atmospheric pressure photoionization-tandem mass spectrometry (GC-μAPPI-MS/MS) method was developed for the analysis of anabolic androgenic steroids in urine as their trimethylsilyl derivatives. The method utilizes a heated nebulizer microchip in atmospheric pressure photoionization mode (μAPPI) with chlorobenzene as dopant, which provides high ionization efficiency by producing abundant radical cations with minimal fragmentation. The performance of GC-μAPPI-MS/MS was evaluated with respect to repeatability, linearity, linear range, and limit of detection (LOD). The results confirmed the potential of the method for doping control analysis of anabolic steroids. Repeatability (RSD<10%), linearity (R(2)≥0.996) and sensitivity (LODs 0.05-0.1ng/mL) were acceptable. Quantitative performance of the method was tested and compared with that of conventional GC-electron ionization-MS, and the results were in good agreement. Copyright © 2013 Elsevier B.V. All rights reserved.

A micro surface tension pump (MISPU) in a glass microchip.

PubMed

Peng, Xing Yue Larry

2011-01-07

A non-membrane micro surface tension pump (MISPU) was fabricated on a glass microchip by one-step glass etching. It needs no material other than glass and is driven by digital gas pressure. The MISPU can be seen working like a piston pump inside the glass microchip under a microscope. The design of the valves (MISVA) and pistons (MISTON) was based on the surface tension theory of the micro surface tension alveolus (MISTA). The digital gas pressure controls the moving gas-liquid interface to open or close the input and output MISVAs to refill or drive the MISTON for pumping a liquid. Without any moving parts, a MISPU is a kind of long-lasting micro pump for micro chips that does not lose its water pumping efficiency over a 20-day period. The volumetric pump output varied from 0 to 10 nl s(-1) when the pump cycle time decreased from 5 min to 15 s. The pump head pressure was 1 kPa.

Fully packed capillary electrochromatographic microchip with self-assembly colloidal silica beads.

PubMed

Park, Jongman; Lee, Dami; Kim, Won; Horiike, Shigeyoshi; Nishimoto, Takahiro; Lee, Se Hwan; Ahn, Chong H

2007-04-15

A fully packed capillary electrochromatographic (CEC) microchip showing improved solution and chip handling was developed. Microchannels for the CEC microchip were patterned on a cyclic olefin copolymer substrate by injection molding and packed fully with 0.8-microm monodisperse colloidal silica beads utilizing a self-assembly packing technique. The silica packed chip substrate was covered and thermally press-bonded. After fabrication, the chip was filled with buffer solution by self-priming capillary action. The self-assembly packing at each channel served as a built-in nanofilter allowing quick loading of samples and running buffer solution without filtration. Because of a large surface area-to-volume ratio of the silica packing, reproducible control of electroosmotic flow was possible without leveling of the solutions in the reservoirs resulting 1.3% rsd in migration rate. The capillary electrophoretic separation characteristics of the chip were studied using fluorescein isothiocyanate (FITC)-derivatized amino acids as probe molecules. A mixture of FITC and four FITC-derivatized amino acids was successfully separated with 2-mm separation channel length.

Plate-shaped Yb:LuPO4 crystal for efficient CW and passively Q-switched microchip lasers

NASA Astrophysics Data System (ADS)

Liu, Junhai; Wang, Lisha; Han, Wenjuan; Xu, Honghao; Zhong, Degao; Teng, Bing

2016-10-01

It is demonstrated that plate-shaped crystals of Yb:LuPO4, which are grown from spontaneous nucleation by high-temperature solution method, can be utilized to make microchip lasers operating in continuous-wave (CW) or passively Q-switched mode. Efficient operation of such a microchip laser, which is built with a 0.3 mm thick crystal plate in a 2 mm long plane-parallel cavity, is realized at room temperature. With 2.37 W of pump power absorbed, 1.45 W of CW output power is generated with a slope efficiency of 73%. When passively Q-switched with a Cr4+:YAG crystal plate as saturable absorber, the laser produces a maximum pulsed output power of 0.53 W at 1013.3 nm, at a pulse repetition rate of 23.8 kHz, the resulting pulse energy, duration, and peak power are 22.3 μJ, 4.0 ns, and 5.6 kW, respectively.

Pump beam waist-dependent pulse energy generation in Nd:YAG/Cr4+:YAG passively Q-switched microchip laser

NASA Astrophysics Data System (ADS)

Li, Chao-yu; Dong, Jun

2016-08-01

The incident pump beam waist-dependent pulse energy generation in Nd:YAG/Cr4+:YAG composite crystal passively Q-switched microchip laser has been investigated experimentally and theoretically by moving the Nd:YAG/Cr4+:YAG composite crystal along the pump beam direction. Highest pulse energy of 0.4 mJ has been generated when the Nd:YAG/Cr4+:YAG composite crystal is moved about 6 mm away from the focused pump beam waist. Laser pulses with pulse width of 1.7 ns and peak power of over 235 kW have been achieved. The theoretically calculated effective laser beam area at different positions of Nd:YAG/Cr4+:YAG composite crystal along the pump beam direction is in good agreement with the experimental results. The highest peak power can be generated by adjusting the pump beam waist incident on the Nd:YAG/Cr4+:YAG composite crystal to optimize the effective laser beam area in passively Q-switched microchip laser.

Rapid fabrication of poly(dimethylsiloxane)-based microchip capillary electrophoresis devices using CO2 laser ablation.

PubMed

Fogarty, Barbara A; Heppert, Kathleen E; Cory, Theodore J; Hulbutta, Kalonie R; Martin, R Scott; Lunte, Susan M

2005-06-01

The use of CO(2) laser ablation for the patterning of capillary electrophoresis (CE) microchannels in poly(dimethylsiloxane)(PDMS) is described. Low-cost polymer devices were produced using a relatively inexpensive CO(2) laser system that facilitated rapid patterning and ablation of microchannels. Device designs were created using a commercially available software package. The effects of PDMS thickness, laser focusing, power, and speed on the resulting channel dimensions were investigated. Using optimized settings, the smallest channels that could be produced averaged 33 microm in depth (11.1% RSD, N= 6) and 110 microm in width (5.7% RSD, N= 6). The use of a PDMS substrate allowed reversible sealing of microchip components at room temperature without the need for cleanroom facilities. Using a layer of pre-cured polymer, devices were designed, ablated, and assembled within minutes. The final devices were used for microchip CE separation and detection of the fluorescently labeled neurotransmitters aspartate and glutamate.

Microchip laser operation of Tm,Ho:KLu(WO₄)₂ crystal.

PubMed

Loiko, Pavel; Serres, Josep Maria; Mateos, Xavier; Yumashev, Konstantin; Kuleshov, Nikolai; Petrov, Valentin; Griebner, Uwe; Aguiló, Magdalena; Díaz, Francesc

2014-11-17

A microchip laser is realized on the basis of a monoclinic Tm,Ho-codoped KLu(WO₄)₂crystal cut for light propagation along the Ng optical indicatrix axis. This crystal cut provides positive thermal lens with extremely weak astigmatism, S/M = 4%. High sensitivity factors, M = dD/dP(abs), of 24.9 and 24.1 m(-1)/W for the mg- and pg- tangential planes are calculated with respect to the absorbed pump power. Such thermo-optic behavior is responsible for mode stabilization in the plano-plano microchip laser cavity, as well as the demonstrated perfect circular beam profile (M(2) < 1.1). Maximum continuous-wave output power of 450 mW is obtained with a slope efficiency of 31%. A set of output couplers is employed to achieve lasing in the spectral range of 2060-2096 nm. The increase of output coupler transmission results in deterioration of the laser performance attributed to the increased up-conversion losses.

Microchip-Based Single-Cell Functional Proteomics for Biomedical Applications

PubMed Central

Lu, Yao; Yang, Liu; Wei, Wei; Shi, Qihui

2017-01-01

Cellular heterogeneity has been widely recognized but only recently have single cell tools become available that allow characterizing heterogeneity at the genomic and proteomic levels. We review the technological advances in microchip-based toolkits for single-cell functional proteomics. Each of these tools has distinct advantages and limitations, and a few have advanced toward being applied to address biological or clinical problems that fail to be addressed by traditional population-based methods. High-throughput single-cell proteomic assays generate high-dimensional data sets that contain new information and thus require developing new analytical framework to extract new biology. In this review article, we highlight a few biological and clinical applications in which the microchip-based single-cell proteomic tools provide unique advantages. The examples include resolving functional heterogeneity and dynamics of immune cells, dissecting cell-cell interaction by creating well-contolled on-chip microenvironment, capturing high-resolution snapshots of immune system functions in patients for better immunotherapy and elucidating phosphoprotein signaling networks in cancer cells for guiding effective molecularly targeted therapies. PMID:28280819

Tm:GdVO4 microchip laser Q-switched by a Sb2Te3 topological insulator

NASA Astrophysics Data System (ADS)

Loiko, Pavel; Bogusławski, Jakub; Serres, Josep Maria; Kifle, Esrom; Kowalczyk, Maciej; Mateos, Xavier; Sotor, Jarosław; Zybała, Rafał; Mars, Krzysztof; Mikuła, Andrzej; Aguiló, Magdalena; Díaz, Francesc; Griebner, Uwe; Petrov, Valentin

2018-02-01

We report on the first application of a topological insulator based on antimony telluride (Sb2Te3) as a saturable absorber (SA) in a bulk microchip laser. The transmission-type SA consisted of a thin film of Sb2Te3 (thickness: 3 nm) deposited on a glass substrate by pulsed magnetron sputtering. The saturable absorption of the Sb2Te3 film was confirmed for ns-long pulses. The microchip laser was based on a Tm:GdVO4 crystal diode-pumped at 802 nm. In the continuous-wave regime, this laser generated 3.54 W at 1905-1921 nm with a slope efficiency η of 37%. The Q-switched laser generated a maximum average output power of 0.70 W at 1913 nm. The pulse energy and duration were 3.5 μJ and 223 ns, respectively, at a repetition rate of 200 kHz. The Sb2Te3 SAs are promising for passively Q-switched waveguide lasers at 2 μm.

Variability of microchip capillary electrophoresis with conductivity detection.

PubMed

Tantra, Ratna; Robinson, Kenneth; Sikora, Aneta

2014-02-01

Microfluidic CE with conductivity detection platforms could have an impact on the future development of smaller, faster and portable devices. However, for the purpose of reliable identification and quantification, there is a need to understand the degree of irreproducibility associated with the analytical technique. In this study, a protocol was developed to remove baseline drift problems sometimes observed in such devices. The protocol, which consisted of pre-conditioning steps prior to analysis, was used to further assess measurement variability from 24 individual microchips fabricated from six separate batches of glass substrate. Results show acceptable RSD percentage for retention time measurements but large variability in their corresponding peak areas (with some microchips having variability of ∼50%). Sources of variability were not related to substrate batch but possibly to a number of factors such as applied voltage fluctuations or variations in microchannel quality, for example surface roughness that will subsequently affect microchannel dimensions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of prostate segmentation algorithms for MRI: the PROMISE12 challenge

PubMed Central

Litjens, Geert; Toth, Robert; van de Ven, Wendy; Hoeks, Caroline; Kerkstra, Sjoerd; van Ginneken, Bram; Vincent, Graham; Guillard, Gwenael; Birbeck, Neil; Zhang, Jindang; Strand, Robin; Malmberg, Filip; Ou, Yangming; Davatzikos, Christos; Kirschner, Matthias; Jung, Florian; Yuan, Jing; Qiu, Wu; Gao, Qinquan; Edwards, Philip “Eddie”; Maan, Bianca; van der Heijden, Ferdinand; Ghose, Soumya; Mitra, Jhimli; Dowling, Jason; Barratt, Dean; Huisman, Henkjan; Madabhushi, Anant

2014-01-01

Prostate MRI image segmentation has been an area of intense research due to the increased use of MRI as a modality for the clinical workup of prostate cancer. Segmentation is useful for various tasks, e.g. to accurately localize prostate boundaries for radiotherapy or to initialize multi-modal registration algorithms. In the past, it has been difficult for research groups to evaluate prostate segmentation algorithms on multi-center, multi-vendor and multi-protocol data. Especially because we are dealing with MR images, image appearance, resolution and the presence of artifacts are affected by differences in scanners and/or protocols, which in turn can have a large influence on algorithm accuracy. The Prostate MR Image Segmentation (PROMISE12) challenge was setup to allow a fair and meaningful comparison of segmentation methods on the basis of performance and robustness. In this work we will discuss the initial results of the online PROMISE12 challenge, and the results obtained in the live challenge workshop hosted by the MICCAI2012 conference. In the challenge, 100 prostate MR cases from 4 different centers were included, with differences in scanner manufacturer, field strength and protocol. A total of 11 teams from academic research groups and industry participated. Algorithms showed a wide variety in methods and implementation, including active appearance models, atlas registration and level sets. Evaluation was performed using boundary and volume based metrics which were combined into a single score relating the metrics to human expert performance. The winners of the challenge where the algorithms by teams Imorphics and ScrAutoProstate, with scores of 85.72 and 84.29 overall. Both algorithms where significantly better than all other algorithms in the challenge (p < 0.05) and had an efficient implementation with a run time of 8 minutes and 3 second per case respectively. Overall, active appearance model based approaches seemed to outperform other approaches like multi-atlas registration, both on accuracy and computation time. Although average algorithm performance was good to excellent and the Imorphics algorithm outperformed the second observer on average, we showed that algorithm combination might lead to further improvement, indicating that optimal performance for prostate segmentation is not yet obtained. All results are available online at http://promise12.grand-challenge.org/. PMID:24418598

Medical Image Segmentation by Combining Graph Cut and Oriented Active Appearance Models

PubMed Central

Chen, Xinjian; Udupa, Jayaram K.; Bağcı, Ulaş; Zhuge, Ying; Yao, Jianhua

2017-01-01

In this paper, we propose a novel 3D segmentation method based on the effective combination of the active appearance model (AAM), live wire (LW), and graph cut (GC). The proposed method consists of three main parts: model building, initialization, and segmentation. In the model building part, we construct the AAM and train the LW cost function and GC parameters. In the initialization part, a novel algorithm is proposed for improving the conventional AAM matching method, which effectively combines the AAM and LW method, resulting in Oriented AAM (OAAM). A multi-object strategy is utilized to help in object initialization. We employ a pseudo-3D initialization strategy, and segment the organs slice by slice via multi-object OAAM method. For the segmentation part, a 3D shape constrained GC method is proposed. The object shape generated from the initialization step is integrated into the GC cost computation, and an iterative GC-OAAM method is used for object delineation. The proposed method was tested in segmenting the liver, kidneys, and spleen on a clinical CT dataset and also tested on the MICCAI 2007 grand challenge for liver segmentation training dataset. The results show the following: (a) An overall segmentation accuracy of true positive volume fraction (TPVF) > 94.3%, false positive volume fraction (FPVF) < 0.2% can be achieved. (b) The initialization performance can be improved by combining AAM and LW. (c) The multi-object strategy greatly facilitates the initialization. (d) Compared to the traditional 3D AAM method, the pseudo 3D OAAM method achieves comparable performance while running 12 times faster. (e) The performance of proposed method is comparable to the state of the art liver segmentation algorithm. The executable version of 3D shape constrained GC with user interface can be downloaded from website http://xinjianchen.wordpress.com/research/. PMID:22311862

An automatic multi-atlas prostate segmentation in MRI using a multiscale representation and a label fusion strategy

NASA Astrophysics Data System (ADS)

Álvarez, Charlens; Martínez, Fabio; Romero, Eduardo

2015-01-01

The pelvic magnetic Resonance images (MRI) are used in Prostate cancer radiotherapy (RT), a process which is part of the radiation planning. Modern protocols require a manual delineation, a tedious and variable activity that may take about 20 minutes per patient, even for trained experts. That considerable time is an important work ow burden in most radiological services. Automatic or semi-automatic methods might improve the efficiency by decreasing the measure times while conserving the required accuracy. This work presents a fully automatic atlas- based segmentation strategy that selects the more similar templates for a new MRI using a robust multi-scale SURF analysis. Then a new segmentation is achieved by a linear combination of the selected templates, which are previously non-rigidly registered towards the new image. The proposed method shows reliable segmentations, obtaining an average DICE Coefficient of 79%, when comparing with the expert manual segmentation, under a leave-one-out scheme with the training database.

Homology Model of the GABAA Receptor Examined Using Brownian Dynamics

PubMed Central

O'Mara, Megan; Cromer, Brett; Parker, Michael; Chung, Shin-Ho

2005-01-01

We have developed a homology model of the GABAA receptor, using the subunit combination of α1β2γ2, the most prevalent type in the mammalian brain. The model is produced in two parts: the membrane-embedded channel domain and the extracellular N-terminal domain. The pentameric transmembrane domain model is built by modeling each subunit by homology with the equivalent subunit of the heteropentameric acetylcholine receptor transmembrane domain. This segment is then joined with the extracellular domain built by homology with the acetylcholine binding protein. The all-atom model forms a wide extracellular vestibule that is connected to an oval chamber near the external surface of the membrane. A narrow, cylindrical transmembrane channel links the outer segment of the pore to a shallow intracellular vestibule. The physiological properties of the model so constructed are examined using electrostatic calculations and Brownian dynamics simulations. A deep energy well of ∼80 kT accommodates three Cl− ions in the narrow transmembrane channel and seven Cl− ions in the external vestibule. Inward permeation takes place when one of the ions queued in the external vestibule enters the narrow segment and ejects the innermost ion. The model, when incorporated into Brownian dynamics, reproduces key experimental features, such as the single-channel current-voltage-concentration profiles. Finally, we simulate the γ2 K289M epilepsy inducing mutation and examine Cl− ion permeation through the mutant receptor. PMID:15749776

Recent developments in the Thomson Parabola Spectrometer diagnostic for laser-driven multi-species ion sources

NASA Astrophysics Data System (ADS)

Alejo, A.; Gwynne, D.; Doria, D.; Ahmed, H.; Carroll, D. C.; Clarke, R. J.; Neely, D.; Scott, G. G.; Borghesi, M.; Kar, S.

2016-10-01

Ongoing developments in laser-driven ion acceleration warrant appropriate modifications to the standard Thomson Parabola Spectrometer (TPS) arrangement in order to match the diagnostic requirements associated to the particular and distinctive properties of laser-accelerated beams. Here we present an overview of recent developments by our group of the TPS diagnostic aimed to enhance the capability of diagnosing multi-species high-energy ion beams. In order to facilitate discrimination between ions with same Z/A, a recursive differential filtering technique was implemented at the TPS detector in order to allow only one of the overlapping ion species to reach the detector, across the entire energy range detectable by the TPS. In order to mitigate the issue of overlapping ion traces towards the higher energy part of the spectrum, an extended, trapezoidal electric plates design was envisaged, followed by its experimental demonstration. The design allows achieving high energy-resolution at high energies without sacrificing the lower energy part of the spectrum. Finally, a novel multi-pinhole TPS design is discussed, that would allow angularly resolved, complete spectral characterization of the high-energy, multi-species ion beams.

Design of multi-body Lambert type orbits with specified departure and arrival positions

NASA Astrophysics Data System (ADS)

Ishii, Nobuaki; Kawaguchi, Jun'ichiro; Matsuo, Hiroki

1991-10-01

A new procedure for designing a multi-body Lambert type orbit comprising a multiple swingby process is developed, aiming at relieving a numerical difficulty inherent to a highly nonlinear swingby mechanism. The proposed algorithm, Recursive Multi-Step Linearization, first divides a whole orbit into several trajectory segments. Then, with a maximum use of piecewised transition matrices, a segmentized orbit is repeatedly upgraded until an approximated orbit initially based on a patched conics method eventually converges. In application to the four body earth-moon system with sun's gravitation, one of the double lunar swingby orbits including 12 lunar swingbys is successfully designed without any velocity mismatch.

Spectroscopic and laser characterization of Yb,Tm:KLu(WO4)2 crystal

NASA Astrophysics Data System (ADS)

Loiko, P. A.; Serres, J. M.; Mateos, X.; Demesh, M. P.; Yasukevich, A. S.; Yumashev, K. V.; Petrov, V.; Griebner, U.; Aguiló, M.; Díaz, F.

2016-01-01

We report on a comprehensive spectroscopic and laser characterization of monoclinic Yb,Tm:KLu(WO4)2 crystals. Stimulated-emission cross-section spectra corresponding to the 3F4 → 3H6 transition of Tm3+ ions are determined. The radiative lifetime of the 3F4 state of Tm3+ ions is 0.82 ms. The maximum Yb3+ → Tm3+ energy transfer efficiency is 83.9% for 5 at.% Yb - 8 at.% Tm doping. The fractional heat loading for Yb,Tm:KLu(WO4)2 is 0.45 ± 0.05. Using a hemispherical cavity and 5 at.% Yb - 6 at.% Tm doped crystal, a maximum CW power of 227 mW is achieved at 1.983-2.011 μm with a maximum slope efficiency η = 14%. In the microchip laser set-up, the highest slope efficiency is 20% for a 5 at.% Yb- 8 at.% Tm doped crystal with a maximum output power of 201 mW at 1.99-2.007 μm. Operation of Yb,Tm:KLu(WO4)2 as a vibronic laser emitting at 2.081-2.093 μm is also demonstrated.

Evaluation of the multiple-ion competition in the adsorption of As(V) onto reclaimed iron-oxide coated sands by fractional factorial design.

PubMed

Hsu, Jia-Chin; Lin, Chien-Jung; Liao, Chih-Hsiang; Chen, Shyi-Tien

2008-07-01

This study describes the competitive effects of selected ions and natural organic matter on As(V) removal using reclaimed iron-oxide coated sands (RIOCS) in the single- and multi-ion systems. A 2(7-3) factional factorial experimental design (FFD) was employed for screening main competitive factors in this adsorption process. As a result, the inhibitive competition effects of the anions on As(V) removal in the single ion system were in the following sequence: PO(4)(3-)>SiO(3)(2-)>HCO(3)(-)>humic acid (HA)>SO(4)(2-)>Cl(-), whereas the cation Ca(2+) was observed to enhance the As(V) removal. In addition, the optimum initial pH for As(V) removal in single-ion system was 5. Based on the estimates of major effects and interactions from the FFD, PO(4)(3-), SiO(3)(2-), Ca(2+) and HA were important factors on As(V) removal in the multi-ion system. The promoters for the As(V) removal were found to be Ca(2+) and, to a lesser extent, SO(4)(2-). The competitive effects of these ions on As(V) removal were in the order of PO(4)(3-), SiO(3)(2-), HA, HCO(3)(-), and Cl(-). In the single ion system, the efficiencies of As(V) removal range from 75% to 96%, much higher than those in the multi-ion system (44%) at the initial pH 5. Clearly, there were some complex anion interactions in the multi-ion system. To promote the removal of As(V) by RIOCS, it is proposed to lower the pH in the single-ion system, while in the multi-ion system, the increase of the Ca(2+) concentration, or decreases of PO(4)(3-), SiO(3)(2-) and HA concentrations is suggested.

Comparison of three methods of temperature measurement in hypothermic, euthermic, and hyperthermic dogs.

PubMed

Greer, Rebecca J; Cohn, Leah A; Dodam, John R; Wagner-Mann, Colette C; Mann, F A

2007-06-15

To assess the reliability and accuracy of a predictive rectal thermometer, an infrared auricular thermometer designed for veterinary use, and a subcutaneous temperature-sensing microchip for measurement of core body temperature over various temperature conditions in dogs. Prospective study. 8 purpose-bred dogs. A minimum of 7 days prior to study commencement, a subcutaneous temperature-sensing microchip was implanted in 1 of 3 locations (interscapular, lateral aspect of shoulder, or sacral region) in each dog. For comparison with temperatures measured via rectal thermometer, infrared auricular thermometer, and microchip, core body temperature was measured via a thermistor-tipped pulmonary artery (TTPA) catheter. Hypothermia was induced during anesthesia at the time of TTPA catheter placement; on 3 occasions after placement of the catheter, hyperthermia was induced via administration of a low dose of endotoxin. Near-simultaneous duplicate temperature measurements were recorded from the TTPA catheter, the rectal thermometer, auricular thermometer, and subcutaneous microchips during hypothermia, euthermia, and hyperthermia. Reliability (variability) of temperature measurement for each device and agreement between each device measurement and core body temperature were assessed. Variability between duplicate near-simultaneous temperature measurements was greatest for the auricular thermometer and least for the TTPA catheter. Measurements obtained by use of the rectal thermometer were in closest agreement with core body temperature; for all other devices, temperature readings typically underestimated core body temperature. Among the 3 methods of temperature measurement, rectal thermometry provided the most accurate estimation of core body temperature in dogs.

Microchip laser based on Yb:YAG/V:YAG monolith crystal

NASA Astrophysics Data System (ADS)

Nejezchleb, Karel; Šulc, Jan; Jelínková, Helena; Škoda, Václav

2016-03-01

V:YAG crystal was investigated as a passive Q-switch of longitudinally diode-pumped microchip laser, emitting radiation at wavelength 1030.5 nm. This laser was based on diffusion bonded monolith crystal (diameter 3 mm) which combines in one piece an active laser part (Yb:YAG crystal, 10 at.% Yb/Y, 3 mm long) and saturable absorber (V:YAG crystal, 2 mm long, initial transmission 86 % @ 1031 nm). The microchip resonator consisted of dielectric mirrors directly deposited on the monolith surfaces (pump mirror HT @ 968 nm and HR @ 1031 nm on Yb:YAG part, output coupler with reflection 55 % @ 1031 nm on the V:YAG part). For longitudinal CW pumping of Yb:YAG part, a fibre coupled (core diameter 100 μm, NA = 0.22, emission @ 968 nm) laser diode was used. The laser threshold was 3.8W. The laser slope efficiency for output mean in respect to incident pumping was 16 %. The linearly polarized generated transversal intensity beam profile was close to the fundamental Gaussian mode. The generated pulse length, stable and mostly independent on pumping power, was equal to 1.3 ns (FWHM). The single pulse energy was increasing with the pumping power and for the maximum pumping 9.7W it was 78 μJ which corresponds to the pulse peak-power 56 kW. The maximum Yb:YAG/V:YAG microchip laser mean output power of 1W was reached without observable thermal roll-over. The corresponding Q-switched pulses repetition rate was 13.1 kHz.

Microchip-based Integration of Cell Immobilization, Electrophoresis, Post-column Derivatization, and Fluorescence Detection for Monitoring the Release of Dopamine from PC 12 Cells

PubMed Central

Li, Michelle W.; Martin, R. Scott

2008-01-01

In this paper, we describe the fabrication and evaluation of a multilayer microchip device that can be used to quantitatively measure the amount of catecholamines released from PC 12 cells immobilized within the same device. This approach allows immobilized cells to be stimulated on-chip and, through rapid actuation of integrated microvalves, the products released from the cells are repeatedly injected into the electrophoresis portion of the microchip, where the analytes are separated based upon mass and charge and detected through post-column derivatization and fluorescence detection. Following optimization of the post-column derivatization detection scheme (using naphthalene-2,3-dicarboxaldehyde and 2-β-mercaptoethanol), off-chip cell stimulation experiments were performed to demonstrate the ability of this device to detect dopamine from a population of PC 12 cells. The final 3-dimensional device that integrates an immobilized PC 12 cell reactor with the bilayer continuous flow sampling/electrophoresis microchip was used to continuously monitor the on-chip stimulated release of dopamine from PC 12 cells. Similar dopamine release was seen when stimulating on-chip versus off-chip yet the on-chip immobilization studies could be carried out with 500 times fewer cells in a much reduced volume. While this paper is focused on PC 12 cells and neurotransmitter analysis, the final device is a general analytical tool that is amenable to immobilization of a variety of cell lines and analysis of various released analytes by electrophoretic means. PMID:18810283

Spontaneous Packaging and Hypothermic Storage of Mammalian Cells with a Cell-Membrane-Mimetic Polymer Hydrogel in a Microchip.

PubMed

Xu, Yan; Mawatari, Kazuma; Konno, Tomohiro; Kitamori, Takehiko; Ishihara, Kazuhiko

2015-10-21

Currently, continuous culture/passage and cryopreservation are two major, well-established methods to provide cultivated mammalian cells for experiments in laboratories. Due to the lack of flexibility, however, both laboratory-oriented methods are unable to meet the need for rapidly growing cell-based applications, which require cell supply in a variety of occasions outside of laboratories. Herein, we report spontaneous packaging and hypothermic storage of mammalian cells under refrigerated (4 °C) and ambient conditions (25 °C) using a cell-membrane-mimetic methacryloyloxyethyl phosphorylcholine (MPC) polymer hydrogel incorporated within a glass microchip. Its capability for hypothermic storage of cells was comparatively evaluated over 16 days. The results reveal that the cytocompatible MPC polymer hydrogel, in combination with the microchip structure, enabled hypothermic storage of cells with quite high viability, high intracellular esterase activity, maintained cell membrane integrity, and small morphological change for more than 1 week at 4 °C and at least 4 days at 25 °C. Furthermore, the stored cells could be released from the hydrogel and exhibited the ability to adhere to a surface and achieve confluence under standard cell culture conditions. Both hypothermic storage conditions are ordinary flexible conditions which can be easily established in places outside of laboratories. Therefore, cell packaging and storage using the hydrogel incorporated within the microchip would be a promising miniature and portable solution for flexible supply and delivery of small amounts of cells from bench to bedside.

Multi-scale learning based segmentation of glands in digital colonrectal pathology images.

PubMed

Gao, Yi; Liu, William; Arjun, Shipra; Zhu, Liangjia; Ratner, Vadim; Kurc, Tahsin; Saltz, Joel; Tannenbaum, Allen

2016-02-01

Digital histopathological images provide detailed spatial information of the tissue at micrometer resolution. Among the available contents in the pathology images, meso-scale information, such as the gland morphology, texture, and distribution, are useful diagnostic features. In this work, focusing on the colon-rectal cancer tissue samples, we propose a multi-scale learning based segmentation scheme for the glands in the colon-rectal digital pathology slides. The algorithm learns the gland and non-gland textures from a set of training images in various scales through a sparse dictionary representation. After the learning step, the dictionaries are used collectively to perform the classification and segmentation for the new image.

Multi-scale learning based segmentation of glands in digital colonrectal pathology images

NASA Astrophysics Data System (ADS)

Gao, Yi; Liu, William; Arjun, Shipra; Zhu, Liangjia; Ratner, Vadim; Kurc, Tahsin; Saltz, Joel; Tannenbaum, Allen

2016-03-01

Digital histopathological images provide detailed spatial information of the tissue at micrometer resolution. Among the available contents in the pathology images, meso-scale information, such as the gland morphology, texture, and distribution, are useful diagnostic features. In this work, focusing on the colon-rectal cancer tissue samples, we propose a multi-scale learning based segmentation scheme for the glands in the colon-rectal digital pathology slides. The algorithm learns the gland and non-gland textures from a set of training images in various scales through a sparse dictionary representation. After the learning step, the dictionaries are used collectively to perform the classification and segmentation for the new image.

Novel product ions of 2-aminoanilide and benzimidazole Ag(I) complexes using electrospray ionization with multi-stage tandem mass spectrometry.

PubMed

Johnson, Byron S; Burinsky, David J; Burova, Svetlana A; Davis, Roman; Fitzgerald, Russ N; Matsuoka, Richard T

2012-05-15

The 2-aminoaniline scaffold is of significant value to the pharmaceutical industry and is embedded in a number of pharmacophores including 2-aminoanilides and benzimidazoles. A novel application of coordination ion spray mass spectrometry (CIS-MS) for interrogating the silver ion (Ag(+)) complexes of a homologous series of these compounds using multi-stage tandem mass spectrometry is described. Unlike the ubiquitous alkali metal ion complexes, Ag(+) complexes of 2-aminoanilides and benzimidazoles were found to yield [M - H](+) ions in significant abundance via gas-phase elimination of the metal hydride (AgH) resulting in unique product ion cascades. Sample introduction was by liquid chromatography with mass spectrometry analysis performed on a hybrid linear ion trap/orbitrap instrument capable of high-resolution measurements. Rigorous structural characterization by multi-stage tandem mass spectrometry using [M +  H](+), [M - H](-) and [M - H](+) precursor ions derived from ESI and CIS experiments was performed for the homologous series of 2-aminoanilide and benzimidazole compounds. A full tabular comparison of structural information resulting from these product ion cascades was produced. Multi-stage tandem mass spectrometry of [M - H](+) ions resulting from Ag(+) complexes of 2-aminoanilides and benzimidazoles in CIS-MS experiments produced unique product ion cascades that exhibited complementary structural information to that obtained from tandem mass spectrometry of [M  +  H](+) and [M - H](-) ions by electrospray ionization (ESI). These observations may be broadly applicable to other compounds that are observed to form Ag(+) complexes and eliminate AgH. Copyright © 2012 John Wiley & Sons, Ltd.

Molecular Dynamics Simulations of Ion Transport and Mechanisms in Polymer Nanocomposites

NASA Astrophysics Data System (ADS)

Mogurampelly, Santosh; Ganesan, Venkat

2015-03-01

Using all atom molecular dynamics and trajectory-extending kinetic Monte Carlo simulations, we study the influence of Al2O3 nanoparticles on the transport properties of Li+ ions in polymer electrolytes consisting of polyethylene oxide (PEO) melt solvated with LiBF4 salt. We observe that the nanoparticles have a strong influence on polymer segmental dynamics which in turn correlates with the mobility of Li+ ions. Explicitly, polymer segmental relaxation times and Li+ ion residence times around polymer were found to increase with the addition of nanoparticles. We also observe that increasing short range repulsive interactions between nanoparticles and polymer membrane leads to increasing polymer dynamics and ion mobility. Overall, our simulation results suggest that nanoparticle induced changes in conformational and dynamic properties of the polymer influences the ion mobilities in polymer electrolytes and suggests possible directions for using such findings to improve the polymer matrix conductivity. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing computing resources that have contributed to the research.

Performing label-fusion-based segmentation using multiple automatically generated templates.

PubMed

Chakravarty, M Mallar; Steadman, Patrick; van Eede, Matthijs C; Calcott, Rebecca D; Gu, Victoria; Shaw, Philip; Raznahan, Armin; Collins, D Louis; Lerch, Jason P

2013-10-01

Classically, model-based segmentation procedures match magnetic resonance imaging (MRI) volumes to an expertly labeled atlas using nonlinear registration. The accuracy of these techniques are limited due to atlas biases, misregistration, and resampling error. Multi-atlas-based approaches are used as a remedy and involve matching each subject to a number of manually labeled templates. This approach yields numerous independent segmentations that are fused using a voxel-by-voxel label-voting procedure. In this article, we demonstrate how the multi-atlas approach can be extended to work with input atlases that are unique and extremely time consuming to construct by generating a library of multiple automatically generated templates of different brains (MAGeT Brain). We demonstrate the efficacy of our method for the mouse and human using two different nonlinear registration algorithms (ANIMAL and ANTs). The input atlases consist a high-resolution mouse brain atlas and an atlas of the human basal ganglia and thalamus derived from serial histological data. MAGeT Brain segmentation improves the identification of the mouse anterior commissure (mean Dice Kappa values (κ = 0.801), but may be encountering a ceiling effect for hippocampal segmentations. Applying MAGeT Brain to human subcortical structures improves segmentation accuracy for all structures compared to regular model-based techniques (κ = 0.845, 0.752, and 0.861 for the striatum, globus pallidus, and thalamus, respectively). Experiments performed with three manually derived input templates suggest that MAGeT Brain can approach or exceed the accuracy of multi-atlas label-fusion segmentation (κ = 0.894, 0.815, and 0.895 for the striatum, globus pallidus, and thalamus, respectively). Copyright © 2012 Wiley Periodicals, Inc.

Trafficking Mechanisms Underlying Neuronal Voltage-gated Ion Channel Localization at the Axon Initial Segment

PubMed Central

Vacher, Helene; Trimmer, James S.

2012-01-01

Summary Voltage-gated ion channels are diverse and fundamental determinants of neuronal intrinsic excitability. Voltage-gated K+ (Kv) and Na+ (Nav) channels play complex yet fundamentally important roles in determining intrinsic excitability. The Kv and Nav channels located at the axon initial segment (AIS) play a unique and especially important role in generating neuronal output in the form of anterograde axonal and backpropagating action potentials, Aberrant intrinsic excitability in individual neurons within networks contributes to synchronous neuronal activity leading to seizures. Mutations in ion channel genes gives rise to a variety of seizure-related “Channelopathies”, and many of the ion channel subunits associated with epilepsy mutations are localized at the AIS, making this a hotspot for epileptogenesis. Here we review the cellular mechanisms that underlie the trafficking of Kv and Nav channels found at the AIS, and how Kv and Nav channel mutations associated with epilepsy can alter these processes. PMID:23216576

The Segregated Expression of Voltage-Gated Potassium and Sodium Channels in Neuronal Membranes: Functional Implications and Regulatory Mechanisms

PubMed Central

Duménieu, Maël; Oulé, Marie; Kreutz, Michael R.; Lopez-Rojas, Jeffrey

2017-01-01

Neurons are highly polarized cells with apparent functional and morphological differences between dendrites and axon. A critical determinant for the molecular and functional identity of axonal and dendritic segments is the restricted expression of voltage-gated ion channels (VGCs). Several studies show an uneven distribution of ion channels and their differential regulation within dendrites and axons, which is a prerequisite for an appropriate integration of synaptic inputs and the generation of adequate action potential (AP) firing patterns. This review article will focus on the signaling pathways leading to segmented expression of voltage-gated potassium and sodium ion channels at the neuronal plasma membrane and the regulatory mechanisms ensuring segregated functions. We will also discuss the relevance of proper ion channel targeting for neuronal physiology and how alterations in polarized distribution contribute to neuronal pathology. PMID:28484374

The effect of morphometric atlas selection on multi-atlas-based automatic brachial plexus segmentation.

PubMed

Van de Velde, Joris; Wouters, Johan; Vercauteren, Tom; De Gersem, Werner; Achten, Eric; De Neve, Wilfried; Van Hoof, Tom

2015-12-23

The present study aimed to measure the effect of a morphometric atlas selection strategy on the accuracy of multi-atlas-based BP autosegmentation using the commercially available software package ADMIRE® and to determine the optimal number of selected atlases to use. Autosegmentation accuracy was measured by comparing all generated automatic BP segmentations with anatomically validated gold standard segmentations that were developed using cadavers. Twelve cadaver computed tomography (CT) atlases were included in the study. One atlas was selected as a patient in ADMIRE®, and multi-atlas-based BP autosegmentation was first performed with a group of morphometrically preselected atlases. In this group, the atlases were selected on the basis of similarity in the shoulder protraction position with the patient. The number of selected atlases used started at two and increased up to eight. Subsequently, a group of randomly chosen, non-selected atlases were taken. In this second group, every possible combination of 2 to 8 random atlases was used for multi-atlas-based BP autosegmentation. For both groups, the average Dice similarity coefficient (DSC), Jaccard index (JI) and Inclusion index (INI) were calculated, measuring the similarity of the generated automatic BP segmentations and the gold standard segmentation. Similarity indices of both groups were compared using an independent sample t-test, and the optimal number of selected atlases was investigated using an equivalence trial. For each number of atlases, average similarity indices of the morphometrically selected atlas group were significantly higher than the random group (p < 0,05). In this study, the highest similarity indices were achieved using multi-atlas autosegmentation with 6 selected atlases (average DSC = 0,598; average JI = 0,434; average INI = 0,733). Morphometric atlas selection on the basis of the protraction position of the patient significantly improves multi-atlas-based BP autosegmentation accuracy. In this study, the optimal number of selected atlases used was six, but for definitive conclusions about the optimal number of atlases and to improve the autosegmentation accuracy for clinical use, more atlases need to be included.

Residual Shuffling Convolutional Neural Networks for Deep Semantic Image Segmentation Using Multi-Modal Data

NASA Astrophysics Data System (ADS)

Chen, K.; Weinmann, M.; Gao, X.; Yan, M.; Hinz, S.; Jutzi, B.; Weinmann, M.

2018-05-01

In this paper, we address the deep semantic segmentation of aerial imagery based on multi-modal data. Given multi-modal data composed of true orthophotos and the corresponding Digital Surface Models (DSMs), we extract a variety of hand-crafted radiometric and geometric features which are provided separately and in different combinations as input to a modern deep learning framework. The latter is represented by a Residual Shuffling Convolutional Neural Network (RSCNN) combining the characteristics of a Residual Network with the advantages of atrous convolution and a shuffling operator to achieve a dense semantic labeling. Via performance evaluation on a benchmark dataset, we analyze the value of different feature sets for the semantic segmentation task. The derived results reveal that the use of radiometric features yields better classification results than the use of geometric features for the considered dataset. Furthermore, the consideration of data on both modalities leads to an improvement of the classification results. However, the derived results also indicate that the use of all defined features is less favorable than the use of selected features. Consequently, data representations derived via feature extraction and feature selection techniques still provide a gain if used as the basis for deep semantic segmentation.

Trunk lean gait decreases multi-segmental coordination in the vertical direction.

PubMed

Tokuda, Kazuki; Anan, Masaya; Sawada, Tomonori; Tanimoto, Kenji; Takeda, Takuya; Ogata, Yuta; Takahashi, Makoto; Kito, Nobuhiro; Shinkoda, Koichi

2017-11-01

[Purpose] The strategy of trunk lean gait to reduce external knee adduction moment (KAM) may affect multi-segmental synergy control of center of mass (COM) displacement. Uncontrolled manifold (UCM) analysis is an evaluation index to understand motor variability. The purpose of this study was to investigate how motor variability is affected by using UCM analysis on adjustment of the trunk lean angle. [Subjects and Methods] Fifteen healthy young adults walked at their preferred speed under two conditions: normal and trunk lean gait. UCM analysis was performed with respect to the COM displacement during the stance phase. The KAM data were analyzed at the points of the first KAM peak during the stance phase. [Results] The KAM during trunk lean gait was smaller than during normal gait. Despite a greater segmental configuration variance with respect to mediolateral COM displacement during trunk lean gait, the synergy index was not significantly different between the two conditions. The synergy index with respect to vertical COM displacement during trunk lean gait was smaller than that during normal gait. [Conclusion] These results suggest that trunk lean gait is effective in reducing KAM; however, it may decrease multi-segmental movement coordination of COM control in the vertical direction.

Resolving Controversies Concerning the Kinetic Structure of Multi-Ion Plasma Shocks

NASA Astrophysics Data System (ADS)

Keenan, Brett; Simakov, Andrei; Chacon, Luis; Taitano, William

2017-10-01

Strong collisional shocks in multi-ion plasmas are featured in several high-energy-density environments, including Inertial Confinement Fusion (ICF) implosions. Yet, basic structural features of these shocks remain poorly understood (e.g., the shock width's dependence on the Mach number and the plasma ion composition, and temperature decoupling between ion species), causing controversies in the literature; even for stationary shocks in planar geometry [cf., Ref. and Ref.]. Using a LANL-developed, high-fidelity, 1D-2V Vlasov-Fokker-Planck code (iFP), as well as direct comparisons to multi-ion hydrodynamic simulations and semi-analytic predictions, we critically examine steady-state, planar shocks in two-ion species plasmas and put forward resolutions to these controversies. This work was supported by the Los Alamos National Laboratory LDRD Program, Metropolis Postdoctoral Fellowship for W.T.T., and used resources provided by the Los Alamos National Laboratory Institutional Computing Program.

Development of a compact filament-discharge multi-cusp H- ion source.

PubMed

Jia, XianLu; Zhang, TianJue; Zheng, Xia; Qin, JiuChang

2012-02-01

A 14 MeV medical cyclotron with the external ion source has been designed and is being constructed at China Institute of Atomic Energy. The H(-) ion will be accelerated by this machine and the proton beam will be extracted by carbon strippers in dual opposite direction. The compact multi-cusp H(-) ion source has been developed for the cyclotron. The 79.5 mm long ion source is 48 mm in diameter, which is consisting of a special shape filament, ten columns of permanent magnets providing a multi-cusp field, and a three-electrode extraction system. So far, the 3 mA∕25 keV H(-) beam with an emittance of 0.3 π mm mrad has been obtained from the ion source. The paper gives the design details and the beam test results. Further experimental study is under way and an extracted beam of 5 mA is expected.

Multi-class segmentation of neuronal electron microscopy images using deep learning

NASA Astrophysics Data System (ADS)

Khobragade, Nivedita; Agarwal, Chirag

2018-03-01

Study of connectivity of neural circuits is an essential step towards a better understanding of functioning of the nervous system. With the recent improvement in imaging techniques, high-resolution and high-volume images are being generated requiring automated segmentation techniques. We present a pixel-wise classification method based on Bayesian SegNet architecture. We carried out multi-class segmentation on serial section Transmission Electron Microscopy (ssTEM) images of Drosophila third instar larva ventral nerve cord, labeling the four classes of neuron membranes, neuron intracellular space, mitochondria and glia / extracellular space. Bayesian SegNet was trained using 256 ssTEM images of 256 x 256 pixels and tested on 64 different ssTEM images of the same size, from the same serial stack. Due to high class imbalance, we used a class-balanced version of Bayesian SegNet by re-weighting each class based on their relative frequency. We achieved an overall accuracy of 93% and a mean class accuracy of 88% for pixel-wise segmentation using this encoder-decoder approach. On evaluating the segmentation results using similarity metrics like SSIM and Dice Coefficient, we obtained scores of 0.994 and 0.886 respectively. Additionally, we used the network trained using the 256 ssTEM images of Drosophila third instar larva for multi-class labeling of ISBI 2012 challenge ssTEM dataset.

Segmentation of pelvic structures for planning CT using a geometrical shape model tuned by a multi-scale edge detector

PubMed Central

Martínez, Fabio; Romero, Eduardo; Dréan, Gaël; Simon, Antoine; Haigron, Pascal; De Crevoisier, Renaud; Acosta, Oscar

2014-01-01

Accurate segmentation of the prostate and organs at risk in computed tomography (CT) images is a crucial step for radiotherapy (RT) planning. Manual segmentation, as performed nowadays, is a time consuming process and prone to errors due to the a high intra- and inter-expert variability. This paper introduces a new automatic method for prostate, rectum and bladder segmentation in planning CT using a geometrical shape model under a Bayesian framework. A set of prior organ shapes are first built by applying Principal Component Analysis (PCA) to a population of manually delineated CT images. Then, for a given individual, the most similar shape is obtained by mapping a set of multi-scale edge observations to the space of organs with a customized likelihood function. Finally, the selected shape is locally deformed to adjust the edges of each organ. Experiments were performed with real data from a population of 116 patients treated for prostate cancer. The data set was split in training and test groups, with 30 and 86 patients, respectively. Results show that the method produces competitive segmentations w.r.t standard methods (Averaged Dice = 0.91 for prostate, 0.94 for bladder, 0.89 for Rectum) and outperforms the majority-vote multi-atlas approaches (using rigid registration, free-form deformation (FFD) and the demons algorithm) PMID:24594798

Multi-atlas and label fusion approach for patient-specific MRI based skull estimation.

PubMed

Torrado-Carvajal, Angel; Herraiz, Joaquin L; Hernandez-Tamames, Juan A; San Jose-Estepar, Raul; Eryaman, Yigitcan; Rozenholc, Yves; Adalsteinsson, Elfar; Wald, Lawrence L; Malpica, Norberto

2016-04-01

MRI-based skull segmentation is a useful procedure for many imaging applications. This study describes a methodology for automatic segmentation of the complete skull from a single T1-weighted volume. The skull is estimated using a multi-atlas segmentation approach. Using a whole head computed tomography (CT) scan database, the skull in a new MRI volume is detected by nonrigid image registration of the volume to every CT, and combination of the individual segmentations by label-fusion. We have compared Majority Voting, Simultaneous Truth and Performance Level Estimation (STAPLE), Shape Based Averaging (SBA), and the Selective and Iterative Method for Performance Level Estimation (SIMPLE) algorithms. The pipeline has been evaluated quantitatively using images from the Retrospective Image Registration Evaluation database (reaching an overlap of 72.46 ± 6.99%), a clinical CT-MR dataset (maximum overlap of 78.31 ± 6.97%), and a whole head CT-MRI pair (maximum overlap 78.68%). A qualitative evaluation has also been performed on MRI acquisition of volunteers. It is possible to automatically segment the complete skull from MRI data using a multi-atlas and label fusion approach. This will allow the creation of complete MRI-based tissue models that can be used in electromagnetic dosimetry applications and attenuation correction in PET/MR. © 2015 Wiley Periodicals, Inc.

Adaptive surrogate model based multi-objective transfer trajectory optimization between different libration points

NASA Astrophysics Data System (ADS)

Peng, Haijun; Wang, Wei

2016-10-01

An adaptive surrogate model-based multi-objective optimization strategy that combines the benefits of invariant manifolds and low-thrust control toward developing a low-computational-cost transfer trajectory between libration orbits around the L1 and L2 libration points in the Sun-Earth system has been proposed in this paper. A new structure for a multi-objective transfer trajectory optimization model that divides the transfer trajectory into several segments and gives the dominations for invariant manifolds and low-thrust control in different segments has been established. To reduce the computational cost of multi-objective transfer trajectory optimization, a mixed sampling strategy-based adaptive surrogate model has been proposed. Numerical simulations show that the results obtained from the adaptive surrogate-based multi-objective optimization are in agreement with the results obtained using direct multi-objective optimization methods, and the computational workload of the adaptive surrogate-based multi-objective optimization is only approximately 10% of that of direct multi-objective optimization. Furthermore, the generating efficiency of the Pareto points of the adaptive surrogate-based multi-objective optimization is approximately 8 times that of the direct multi-objective optimization. Therefore, the proposed adaptive surrogate-based multi-objective optimization provides obvious advantages over direct multi-objective optimization methods.

Optimal graph based segmentation using flow lines with application to airway wall segmentation.

PubMed

Petersen, Jens; Nielsen, Mads; Lo, Pechin; Saghir, Zaigham; Dirksen, Asger; de Bruijne, Marleen

2011-01-01

This paper introduces a novel optimal graph construction method that is applicable to multi-dimensional, multi-surface segmentation problems. Such problems are often solved by refining an initial coarse surface within the space given by graph columns. Conventional columns are not well suited for surfaces with high curvature or complex shapes but the proposed columns, based on properly generated flow lines, which are non-intersecting, guarantee solutions that do not self-intersect and are better able to handle such surfaces. The method is applied to segment human airway walls in computed tomography images. Comparison with manual annotations on 649 cross-sectional images from 15 different subjects shows significantly smaller contour distances and larger area of overlap than are obtained with recently published graph based methods. Airway abnormality measurements obtained with the method on 480 scan pairs from a lung cancer screening trial are reproducible and correlate significantly with lung function.

Brain Tumor Segmentation Using Deep Belief Networks and Pathological Knowledge.

PubMed

Zhan, Tianming; Chen, Yi; Hong, Xunning; Lu, Zhenyu; Chen, Yunjie

2017-01-01

In this paper, we propose an automatic brain tumor segmentation method based on Deep Belief Networks (DBNs) and pathological knowledge. The proposed method is targeted against gliomas (both low and high grade) obtained in multi-sequence magnetic resonance images (MRIs). Firstly, a novel deep architecture is proposed to combine the multi-sequences intensities feature extraction with classification to get the classification probabilities of each voxel. Then, graph cut based optimization is executed on the classification probabilities to strengthen the spatial relationships of voxels. At last, pathological knowledge of gliomas is applied to remove some false positives. Our method was validated in the Brain Tumor Segmentation Challenge 2012 and 2013 databases (BRATS 2012, 2013). The performance of segmentation results demonstrates our proposal providing a competitive solution with stateof- the-art methods. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.