Q: How do Microscopes Work?

ERIC Educational Resources Information Center

Zimov, Sarah

2004-01-01

Microscopes allow scientists to examine everyday objects in extraordinary ways. They provide high-resolution images that show objects in fine detail. This brief article describes the many types of microscopes and how they are used in different scientific venues.

Telecytology: Is it possible with smartphone images?

PubMed

Sahin, Davut; Hacisalihoglu, Uguray Payam; Kirimlioglu, Saime Hale

2018-01-01

This study aimed to discuss smartphone usage in telecytology and determine intraobserver concordance between microscopic cytopathological diagnoses and diagnoses derived via static smartphone images. The study was conducted with 172 cytologic material. A pathologist captured static images of the cytology slides from the ocular lens of a microscope using a smartphone. The images were transferred via WhatsApp® to a cytopathologist working in another center who made all the microscopic cytopathological diagnoses 5-27 months ago. The cytopathologist diagnosed images on a smartphone without knowledge of their previous microscopic diagnoses. The Kappa agreement between microscopic cytopathological diagnoses and smartphone image diagnoses was determined. The average image capturing, transfer, and remote cytopathological diagnostic time for one case was 6.20 minutes. The percentage of cases whose microscopic and smartphone image diagnoses were concordant was 84.30%, and the percentage of those whose diagnoses were discordant was 15.69%. The highest Kappa agreement was observed in endoscopic ultrasound-guided fine needle aspiration (1.000), and the lowest agreement was observed in urine cytology (0.665). Patient management changed with smart phone image diagnoses at 11.04%. This study showed that easy, fast, and high-quality image capturing and transfer is possible from cytology slides using smartphones. The intraobserver Kappa agreement between the microscopic cytopathological diagnoses and remote smartphone image diagnoses was high. It was found that remote diagnosis due to difficulties in telecytology might change patient management. The developments in the smartphone camera technology and transfer software make them efficient telepathology and telecytology tools. © 2017 Wiley Periodicals, Inc.

X ray imaging microscope for cancer research

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Shealy, David L.; Brinkley, B. R.; Baker, Phillip C.; Barbee, Troy W., Jr.; Walker, Arthur B. C., Jr.

1991-01-01

The NASA technology employed during the Stanford MSFC LLNL Rocket X Ray Spectroheliograph flight established that doubly reflecting, normal incidence multilayer optics can be designed, fabricated, and used for high resolution x ray imaging of the Sun. Technology developed as part of the MSFC X Ray Microscope program, showed that high quality, high resolution multilayer x ray imaging microscopes are feasible. Using technology developed at Stanford University and at the DOE Lawrence Livermore National Laboratory (LLNL), Troy W. Barbee, Jr. has fabricated multilayer coatings with near theoretical reflectivities and perfect bandpass matching for a new rocket borne solar observatory, the Multi-Spectral Solar Telescope Array (MSSTA). Advanced Flow Polishing has provided multilayer mirror substrates with sub-angstrom (rms) smoothnesss for the astronomical x ray telescopes and x ray microscopes. The combination of these important technological advancements has paved the way for the development of a Water Window Imaging X Ray Microscope for cancer research.

A surface science compatible epifluorescence microscope for inspection of samples under ultra high vacuum and cryogenic conditions.

PubMed

Marquardt, Christian; Paulheim, Alexander; Rohbohm, Nils; Merkel, Rudolf; Sokolowski, Moritz

2017-08-01

We modified an epi-illumination light microscope and mounted it on an ultra high vacuum chamber for investigating samples used in a surface science experiment. For easy access and bake out, all optical components are placed outside the vacuum and the sample is imaged through a glass window. The microscope can be operated in reflection brightfield or epifluorescence mode to image the sample surface or fluorescent dye molecules adsorbed on it. The homemade sample mounting was made compatible for the use under the microscope; sample temperatures as low as 6 K can be achieved. The performance of the microscope is demonstrated on two model samples: Brightfield-images of a well-prepared Ag(100) surface show a macroscopic corrugation of the surface, although low energy electron diffraction data indicate a highly ordered crystalline surface. The surface shows macroscopic protrusions with flat regions, about 20-200 μm in diameter, in between. Fluorescence images of diluted 3,4,9,10-perylene tetracarboxylicacid dianhydride (PTCDA) molecules adsorbed on an ultrathin epitaxial KCl film on the Ag(100) surface show a shading effect at surface protrusions due to an inclined angle of incidence of the PTCDA beam during deposition. For some preparations, the distribution of the fluorescence intensity is inhomogeneous and shows a dense network of bright patches about 5 μm in diameter related to the macroscopic corrugation of the surface. We propose that such a light microscope can aid many surface science experiments, especially those dealing with epitaxial growth or fluorescent materials.

Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Duckhoe; Sahin, Ozgur

2015-03-01

Scanning probe microscopes can be used to image and chemically characterize surfaces down to the atomic scale. However, the localized tip-sample interactions in scanning probe microscopes limit high-resolution images to the topmost atomic layer of surfaces, and characterizing the inner structures of materials and biomolecules is a challenge for such instruments. Here, we show that an atomic force microscope can be used to image and three-dimensionally reconstruct chemical groups inside a protein complex. We use short single-stranded DNAs as imaging labels that are linked to target regions inside a protein complex, and T-shaped atomic force microscope cantilevers functionalized with complementary probe DNAs allow the labels to be located with sequence specificity and subnanometre resolution. After measuring pairwise distances between labels, we reconstruct the three-dimensional structure formed by the target chemical groups within the protein complex using simple geometric calculations. Experiments with the biotin-streptavidin complex show that the predicted three-dimensional loci of the carboxylic acid groups of biotins are within 2 Å of their respective loci in the corresponding crystal structure, suggesting that scanning probe microscopes could complement existing structural biological techniques in solving structures that are difficult to study due to their size and complexity.

Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules.

PubMed

Elliott, Jonathan T; Dsouza, Alisha V; Marra, Kayla; Pogue, Brian W; Roberts, David W; Paulsen, Keith D

2016-09-01

Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system specifications are characterized, and in vivo efficacy of the system in detecting ABY-029 is evaluated in a rat orthotopic glioma model following microdose injections, showing the suitability of the device for microdose phase 0 clinical trials.

Microdose fluorescence imaging of ABY-029 on an operating microscope adapted by custom illumination and imaging modules

PubMed Central

Dsouza, Alisha V.; Marra, Kayla; Pogue, Brian W.; Roberts, David W.; Paulsen, Keith D.

2016-01-01

Fluorescence guided surgery has the potential to positively impact surgical oncology; current operating microscopes and stand-alone imaging systems are too insensitive or too cumbersome to maximally take advantage of new tumor-specific agents developed through the microdose pathway. To this end, a custom-built illumination and imaging module enabling picomolar-sensitive near-infrared fluorescence imaging on a commercial operating microscope is described. The limits of detection and system specifications are characterized, and in vivo efficacy of the system in detecting ABY-029 is evaluated in a rat orthotopic glioma model following microdose injections, showing the suitability of the device for microdose phase 0 clinical trials. PMID:27699098

Laser speckle contrast imaging using light field microscope approach

NASA Astrophysics Data System (ADS)

Ma, Xiaohui; Wang, Anting; Ma, Fenghua; Wang, Zi; Ming, Hai

2018-01-01

In this paper, a laser speckle contrast imaging (LSCI) system using light field (LF) microscope approach is proposed. As far as we known, it is first time to combine LSCI with LF. To verify this idea, a prototype consists of a modified LF microscope imaging system and an experimental device was built. A commercially used Lytro camera was modified for microscope imaging. Hollow glass tubes with different depth fixed in glass dish were used to simulate the vessels in brain and test the performance of the system. Compared with conventional LSCI, three new functions can be realized by using our system, which include refocusing, extending the depth of field (DOF) and gathering 3D information. Experiments show that the principle is feasible and the proposed system works well.

Scanning laser microscope for imaging nanostructured superconductors

NASA Astrophysics Data System (ADS)

Ishida, Takekazu; Arai, Kohei; Akita, Yukio; Miyanari, Mitsunori; Minami, Yusuke; Yotsuya, Tsutomu; Kato, Masaru; Satoh, Kazuo; Uno, Mayumi; Shimakage, Hisashi; Miki, Shigehito; Wang, Zhen

2010-10-01

The nanofabrication of superconductors yields various interesting features in superconducting properties. A variety of different imaging techniques have been developed for probing the local superconducting profiles. A scanning pulsed laser microscope has been developed by the combination of the XYZ piezo-driven stages and an optical fiber with an aspheric focusing lens. The scanning laser microscope is used to understand the position-dependent properties of a superconducting MgB 2 stripline of length 100 μm and width of 3 μm under constant bias current. Our results show that the superconducting stripline can clearly be seen in the contour image of the scanning laser microscope on the signal voltage. It is suggested from the observed image that the inhomogeneity is relevant in specifying the operating conditions such as detection efficiency of the sensor.

Algorithms for differentiating between images of heterogeneous tissue across fluorescence microscopes.

PubMed

Chitalia, Rhea; Mueller, Jenna; Fu, Henry L; Whitley, Melodi Javid; Kirsch, David G; Brown, J Quincy; Willett, Rebecca; Ramanujam, Nimmi

2016-09-01

Fluorescence microscopy can be used to acquire real-time images of tissue morphology and with appropriate algorithms can rapidly quantify features associated with disease. The objective of this study was to assess the ability of various segmentation algorithms to isolate fluorescent positive features (FPFs) in heterogeneous images and identify an approach that can be used across multiple fluorescence microscopes with minimal tuning between systems. Specifically, we show a variety of image segmentation algorithms applied to images of stained tumor and muscle tissue acquired with 3 different fluorescence microscopes. Results indicate that a technique called maximally stable extremal regions followed by thresholding (MSER + Binary) yielded the greatest contrast in FPF density between tumor and muscle images across multiple microscopy systems.

The Impact of the Condenser on Cytogenetic Image Quality in Digital Microscope System

PubMed Central

Ren, Liqiang; Li, Zheng; Li, Yuhua; Zheng, Bin; Li, Shibo; Chen, Xiaodong; Liu, Hong

2013-01-01

Background: Optimizing operational parameters of the digital microscope system is an important technique to acquire high quality cytogenetic images and facilitate the process of karyotyping so that the efficiency and accuracy of diagnosis can be improved. OBJECTIVE: This study investigated the impact of the condenser on cytogenetic image quality and system working performance using a prototype digital microscope image scanning system. Methods: Both theoretical analysis and experimental validations through objectively evaluating a resolution test chart and subjectively observing large numbers of specimen were conducted. Results: The results show that the optimal image quality and large depth of field (DOF) are simultaneously obtained when the numerical aperture of condenser is set as 60%–70% of the corresponding objective. Under this condition, more analyzable chromosomes and diagnostic information are obtained. As a result, the system shows higher working stability and less restriction for the implementation of algorithms such as autofocusing especially when the system is designed to achieve high throughput continuous image scanning. Conclusions: Although the above quantitative results were obtained using a specific prototype system under the experimental conditions reported in this paper, the presented evaluation methodologies can provide valuable guidelines for optimizing operational parameters in cytogenetic imaging using the high throughput continuous scanning microscopes in clinical practice. PMID:23676284

Microscopy refocusing and dark-field imaging by using a simple LED array.

PubMed

Zheng, Guoan; Kolner, Christopher; Yang, Changhuei

2011-10-15

The condenser is one of the main components in most transmitted light compound microscopes. In this Letter, we show that such a condenser can be replaced by a programmable LED array to achieve greater imaging flexibility and functionality. Without mechanically scanning the sample or changing the microscope setup, the proposed approach can be used for dark-field imaging, bright-field imaging, microscopy sectioning, and digital refocusing. Images of a starfish embryo were acquired by using such an approach for demonstration.

Point-of-care mobile digital microscopy and deep learning for the detection of soil-transmitted helminths and Schistosoma haematobium.

PubMed

Holmström, Oscar; Linder, Nina; Ngasala, Billy; Mårtensson, Andreas; Linder, Ewert; Lundin, Mikael; Moilanen, Hannu; Suutala, Antti; Diwan, Vinod; Lundin, Johan

2017-06-01

Microscopy remains the gold standard in the diagnosis of neglected tropical diseases. As resource limited, rural areas often lack laboratory equipment and trained personnel, new diagnostic techniques are needed. Low-cost, point-of-care imaging devices show potential in the diagnosis of these diseases. Novel, digital image analysis algorithms can be utilized to automate sample analysis. Evaluation of the imaging performance of a miniature digital microscopy scanner for the diagnosis of soil-transmitted helminths and Schistosoma haematobium, and training of a deep learning-based image analysis algorithm for automated detection of soil-transmitted helminths in the captured images. A total of 13 iodine-stained stool samples containing Ascaris lumbricoides, Trichuris trichiura and hookworm eggs and 4 urine samples containing Schistosoma haematobium were digitized using a reference whole slide-scanner and the mobile microscopy scanner. Parasites in the images were identified by visual examination and by analysis with a deep learning-based image analysis algorithm in the stool samples. Results were compared between the digital and visual analysis of the images showing helminth eggs. Parasite identification by visual analysis of digital slides captured with the mobile microscope was feasible for all analyzed parasites. Although the spatial resolution of the reference slide-scanner is higher, the resolution of the mobile microscope is sufficient for reliable identification and classification of all parasites studied. Digital image analysis of stool sample images captured with the mobile microscope showed high sensitivity for detection of all helminths studied (range of sensitivity = 83.3-100%) in the test set (n = 217) of manually labeled helminth eggs. In this proof-of-concept study, the imaging performance of a mobile, digital microscope was sufficient for visual detection of soil-transmitted helminths and Schistosoma haematobium. Furthermore, we show that deep learning-based image analysis can be utilized for the automated detection and classification of helminths in the captured images.

Point-of-care mobile digital microscopy and deep learning for the detection of soil-transmitted helminths and Schistosoma haematobium

PubMed Central

Holmström, Oscar; Linder, Nina; Ngasala, Billy; Mårtensson, Andreas; Linder, Ewert; Lundin, Mikael; Moilanen, Hannu; Suutala, Antti; Diwan, Vinod; Lundin, Johan

2017-01-01

ABSTRACT Background: Microscopy remains the gold standard in the diagnosis of neglected tropical diseases. As resource limited, rural areas often lack laboratory equipment and trained personnel, new diagnostic techniques are needed. Low-cost, point-of-care imaging devices show potential in the diagnosis of these diseases. Novel, digital image analysis algorithms can be utilized to automate sample analysis. Objective: Evaluation of the imaging performance of a miniature digital microscopy scanner for the diagnosis of soil-transmitted helminths and Schistosoma haematobium, and training of a deep learning-based image analysis algorithm for automated detection of soil-transmitted helminths in the captured images. Methods: A total of 13 iodine-stained stool samples containing Ascaris lumbricoides, Trichuris trichiura and hookworm eggs and 4 urine samples containing Schistosoma haematobium were digitized using a reference whole slide-scanner and the mobile microscopy scanner. Parasites in the images were identified by visual examination and by analysis with a deep learning-based image analysis algorithm in the stool samples. Results were compared between the digital and visual analysis of the images showing helminth eggs. Results: Parasite identification by visual analysis of digital slides captured with the mobile microscope was feasible for all analyzed parasites. Although the spatial resolution of the reference slide-scanner is higher, the resolution of the mobile microscope is sufficient for reliable identification and classification of all parasites studied. Digital image analysis of stool sample images captured with the mobile microscope showed high sensitivity for detection of all helminths studied (range of sensitivity = 83.3–100%) in the test set (n = 217) of manually labeled helminth eggs. Conclusions: In this proof-of-concept study, the imaging performance of a mobile, digital microscope was sufficient for visual detection of soil-transmitted helminths and Schistosoma haematobium. Furthermore, we show that deep learning-based image analysis can be utilized for the automated detection and classification of helminths in the captured images. PMID:28838305

Fusion of lens-free microscopy and mobile-phone microscopy images for high-color-accuracy and high-resolution pathology imaging

NASA Astrophysics Data System (ADS)

Zhang, Yibo; Wu, Yichen; Zhang, Yun; Ozcan, Aydogan

2017-03-01

Digital pathology and telepathology require imaging tools with high-throughput, high-resolution and accurate color reproduction. Lens-free on-chip microscopy based on digital in-line holography is a promising technique towards these needs, as it offers a wide field of view (FOV >20 mm2) and high resolution with a compact, low-cost and portable setup. Color imaging has been previously demonstrated by combining reconstructed images at three discrete wavelengths in the red, green and blue parts of the visible spectrum, i.e., the RGB combination method. However, this RGB combination method is subject to color distortions. To improve the color performance of lens-free microscopy for pathology imaging, here we present a wavelet-based color fusion imaging framework, termed "digital color fusion microscopy" (DCFM), which digitally fuses together a grayscale lens-free microscope image taken at a single wavelength and a low-resolution and low-magnification color-calibrated image taken by a lens-based microscope, which can simply be a mobile phone based cost-effective microscope. We show that the imaging results of an H&E stained breast cancer tissue slide with the DCFM technique come very close to a color-calibrated microscope using a 40x objective lens with 0.75 NA. Quantitative comparison showed 2-fold reduction in the mean color distance using the DCFM method compared to the RGB combination method, while also preserving the high-resolution features of the lens-free microscope. Due to the cost-effective and field-portable nature of both lens-free and mobile-phone microscopy techniques, their combination through the DCFM framework could be useful for digital pathology and telepathology applications, in low-resource and point-of-care settings.

Enhancing the performance of the light field microscope using wavefront coding.

PubMed

Cohen, Noy; Yang, Samuel; Andalman, Aaron; Broxton, Michael; Grosenick, Logan; Deisseroth, Karl; Horowitz, Mark; Levoy, Marc

2014-10-06

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.

Development of HiLo Microscope and its use in In-Vivo Applications

NASA Astrophysics Data System (ADS)

Patel, Shreyas J.

The functionality of achieving optical sectioning in biomedical research is invaluable as it allows for visualization of a biological sample at different depths while being free of background scattering. Most current microscopy techniques that offer optical sectioning, unfortunately, require complex instrumentation and thus are generally costly. HiLo microscopy, on the other hand, offers the same functionality and advantage at a relatively low cost. Hence, the work described in this thesis involves the design, build, and application of a HiLo microscope. More specifically, a standalone HiLo microscope was built in addition to implementing HiLo microscopy on a standard fluorescence microscope. In HiLo microscopy, optical sectioning is achieved by acquiring two different types of images per focal plane. One image is acquired under uniform illumination and the other is acquired under speckle illumination. These images are processed using an algorithm that extracts in-focus information and removes features and glare that occur as a result of background fluorescence. To show the benefits of the HiLo microscopy, several imaging experiments on various samples were performed under a HiLo microscope and compared against a traditional fluorescence microscope and a confocal microscope, which is considered the gold standard in optical imaging. In-vitro and ex-vivo imaging was performed on a set of pollen grains, and optically cleared mouse brain and heart slices. Each of these experiments showed great reduction in background scattering at different depths under HiLo microscopy. More importantly, HiLo imaging of optically cleared heart slice demonstrated emergence of different vasculature at different depths. Reduction of out-of-focus light increased the spatial resolution and allowed better visualization of capillary vessels. Furthermore, HiLo imaging was tested in an in-vivo model of a rodent dorsal window chamber model. When imaging the same sample under confocal microscope, the results were comparable between the two modalities. Additionally, a method of achieving blood flow maps at different depth using a combination of HiLo and LSI imaging is also discussed. The significance of this combined technique could help categorize blood flow to particular depths; this can help improve outcomes of medical treatments such pulse dye laser and photodynamic therapy treatments.

Internal scanning method as unique imaging method of optical vortex scanning microscope

NASA Astrophysics Data System (ADS)

Popiołek-Masajada, Agnieszka; Masajada, Jan; Szatkowski, Mateusz

2018-06-01

The internal scanning method is specific for the optical vortex microscope. It allows to move the vortex point inside the focused vortex beam with nanometer resolution while the whole beam stays in place. Thus the sample illuminated by the focused vortex beam can be scanned just by the vortex point. We show that this method enables high resolution imaging. The paper presents the preliminary experimental results obtained with the first basic image recovery procedure. A prospect of developing more powerful tools for topography recovery with the optical vortex scanning microscope is discussed shortly.

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

Juffmann, Thomas; Koppell, Stewart A.; Klopfer, Brannon B.

Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulations to show that an electron microscope based on a multi-pass measurement protocol enables imaging of single proteins, without averaging structures over multiple images. While we demonstrate the method for particular imaging targets, the approach is broadly applicable and is expected to improve resolution and sensitivity for a range of electron microscopy imaging modalities,more » including, for example, scanning and spectroscopic techniques. The approach implements a quantum mechanically optimal strategy which under idealized conditions can be considered interaction-free.« less

Cell-phone-based platform for biomedical device development and education applications.

PubMed

Smith, Zachary J; Chu, Kaiqin; Espenson, Alyssa R; Rahimzadeh, Mehdi; Gryshuk, Amy; Molinaro, Marco; Dwyre, Denis M; Lane, Stephen; Matthews, Dennis; Wachsmann-Hogiu, Sebastian

2011-03-02

In this paper we report the development of two attachments to a commercial cell phone that transform the phone's integrated lens and image sensor into a 350x microscope and visible-light spectrometer. The microscope is capable of transmission and polarized microscopy modes and is shown to have 1.5 micron resolution and a usable field-of-view of 150 x 50 with no image processing, and approximately 350 x 350 when post-processing is applied. The spectrometer has a 300 nm bandwidth with a limiting spectral resolution of close to 5 nm. We show applications of the devices to medically relevant problems. In the case of the microscope, we image both stained and unstained blood-smears showing the ability to acquire images of similar quality to commercial microscope platforms, thus allowing diagnosis of clinical pathologies. With the spectrometer we demonstrate acquisition of a white-light transmission spectrum through diffuse tissue as well as the acquisition of a fluorescence spectrum. We also envision the devices to have immediate relevance in the educational field.

Cell-Phone-Based Platform for Biomedical Device Development and Education Applications

PubMed Central

Smith, Zachary J.; Chu, Kaiqin; Espenson, Alyssa R.; Rahimzadeh, Mehdi; Gryshuk, Amy; Molinaro, Marco; Dwyre, Denis M.; Lane, Stephen; Matthews, Dennis; Wachsmann-Hogiu, Sebastian

2011-01-01

In this paper we report the development of two attachments to a commercial cell phone that transform the phone's integrated lens and image sensor into a 350× microscope and visible-light spectrometer. The microscope is capable of transmission and polarized microscopy modes and is shown to have 1.5 micron resolution and a usable field-of-view of 150×150 with no image processing, and approximately 350×350 when post-processing is applied. The spectrometer has a 300 nm bandwidth with a limiting spectral resolution of close to 5 nm. We show applications of the devices to medically relevant problems. In the case of the microscope, we image both stained and unstained blood-smears showing the ability to acquire images of similar quality to commercial microscope platforms, thus allowing diagnosis of clinical pathologies. With the spectrometer we demonstrate acquisition of a white-light transmission spectrum through diffuse tissue as well as the acquisition of a fluorescence spectrum. We also envision the devices to have immediate relevance in the educational field. PMID:21399693

Elemental and topographical imaging of microscopic variations in deposition on NSTX-U and DIII-D samples

NASA Astrophysics Data System (ADS)

Skinner, C. H.; Kaita, R.; Koel, B. E.; Chrobak, C. P.; Wampler, W. R.

2017-10-01

Tokamak plasma facing components (PFCs) have surface roughness that can cause microscopic spatial variations in erosion and deposition and hence influence material migration. Previous RBS measurements showed indirect evidence for this but the spatial (0.5mm) resolution was insufficient for direct imaging. We will present elemental images at sub-micron resolution of deposition on NSTX-U and DiMES samples that show strong microscopic variations and correlate this with 3D topographical maps of surface irregularities. The elemental imaging is performed with a Scanning Auger Microprobe (SAM) that measures element-specific Auger electrons excited by an SEM electron beam. 3D topographical maps of the samples are performed with a Leica DCM 3D confocal light microscope and compared to the elemental deposition pattern. The initial results appear consistent with erosion at the downstream edges of the surface pores exposed to the incident ion flux, whereas the deeper regions are shadowed and serve as deposition traps. Support was provided through DOE Contract Numbers DE-AC02-09CH11466, DE-FC02-04ER54698 and DE-NA0003525.

Microscopic vision modeling method by direct mapping analysis for micro-gripping system with stereo light microscope.

PubMed

Wang, Yuezong; Zhao, Zhizhong; Wang, Junshuai

2016-04-01

We present a novel and high-precision microscopic vision modeling method, which can be used for 3D data reconstruction in micro-gripping system with stereo light microscope. This method consists of four parts: image distortion correction, disparity distortion correction, initial vision model and residual compensation model. First, the method of image distortion correction is proposed. Image data required by image distortion correction comes from stereo images of calibration sample. The geometric features of image distortions can be predicted though the shape deformation of lines constructed by grid points in stereo images. Linear and polynomial fitting methods are applied to correct image distortions. Second, shape deformation features of disparity distribution are discussed. The method of disparity distortion correction is proposed. Polynomial fitting method is applied to correct disparity distortion. Third, a microscopic vision model is derived, which consists of two models, i.e., initial vision model and residual compensation model. We derive initial vision model by the analysis of direct mapping relationship between object and image points. Residual compensation model is derived based on the residual analysis of initial vision model. The results show that with maximum reconstruction distance of 4.1mm in X direction, 2.9mm in Y direction and 2.25mm in Z direction, our model achieves a precision of 0.01mm in X and Y directions and 0.015mm in Z direction. Comparison of our model with traditional pinhole camera model shows that two kinds of models have a similar reconstruction precision of X coordinates. However, traditional pinhole camera model has a lower precision of Y and Z coordinates than our model. The method proposed in this paper is very helpful for the micro-gripping system based on SLM microscopic vision. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lensless high-resolution on-chip optofluidic microscopes for Caenorhabditis elegans and cell imaging

PubMed Central

Cui, Xiquan; Lee, Lap Man; Heng, Xin; Zhong, Weiwei; Sternberg, Paul W.; Psaltis, Demetri; Yang, Changhuei

2008-01-01

Low-cost and high-resolution on-chip microscopes are vital for reducing cost and improving efficiency for modern biomedicine and bioscience. Despite the needs, the conventional microscope design has proven difficult to miniaturize. Here, we report the implementation and application of two high-resolution (≈0.9 μm for the first and ≈0.8 μm for the second), lensless, and fully on-chip microscopes based on the optofluidic microscopy (OFM) method. These systems abandon the conventional microscope design, which requires expensive lenses and large space to magnify images, and instead utilizes microfluidic flow to deliver specimens across array(s) of micrometer-size apertures defined on a metal-coated CMOS sensor to generate direct projection images. The first system utilizes a gravity-driven microfluidic flow for sample scanning and is suited for imaging elongate objects, such as Caenorhabditis elegans; and the second system employs an electrokinetic drive for flow control and is suited for imaging cells and other spherical/ellipsoidal objects. As a demonstration of the OFM for bioscience research, we show that the prototypes can be used to perform automated phenotype characterization of different Caenorhabditis elegans mutant strains, and to image spores and single cellular entities. The optofluidic microscope design, readily fabricable with existing semiconductor and microfluidic technologies, offers low-cost and highly compact imaging solutions. More functionalities, such as on-chip phase and fluorescence imaging, can also be readily adapted into OFM systems. We anticipate that the OFM can significantly address a range of biomedical and bioscience needs, and engender new microscope applications. PMID:18663227

Spectral confocal reflection microscopy using a white light source

NASA Astrophysics Data System (ADS)

Booth, M.; Juškaitis, R.; Wilson, T.

2008-08-01

We present a reflection confocal microscope incorporating a white light supercontinuum source and spectral detection. The microscope provides images resolved spatially in three-dimensions, in addition to spectral resolution covering the wavelength range 450-650nm. Images and reflection spectra of artificial and natural specimens are presented, showing features that are not normally revealed in conventional microscopes or confocal microscopes using discrete line lasers. The specimens include thin film structures on semiconductor chips, iridescent structures in Papilio blumei butterfly scales, nacre from abalone shells and opal gemstones. Quantitative size and refractive index measurements of transparent beads are derived from spectral interference bands.

Optical Coherence Tomography–Enhanced Microlaryngoscopy: Preliminary Report of a Noncontact Optical Coherence Tomography System Integrated With a Surgical Microscope

PubMed Central

Vokes, David E.; Jackson, Ryan; Guo, Shuguang; Perez, Jorge A.; Su, Jianping; Ridgway, James M.; Armstrong, William B.; Chen, Zhongping; Wong, Brian J. F.

2014-01-01

Objectives Optical coherence tomography (OCT) is a new imaging modality that uses near-infrared light to produce cross-sectional images of tissue with a resolution approaching that of light microscopy. We have previously reported use of OCT imaging of the vocal folds (VFs) during direct laryngoscopy with a probe held in contact or near-contact with the VFs. This aim of this study was to develop and evaluate a novel OCT system integrated with a surgical microscope to allow hands-free OCT imaging of the VFs, which could be performed simultaneously with microscopic visualization. Methods We performed a prospective evaluation of a new method of acquiring OCT images of the VFs. Results An OCT system was successfully integrated with a surgical microscope to permit noncontact OCT imaging of the VFs of 10 patients. With this novel device we were able to identify VF epithelium and lamina propria; however, the resolution was reduced compared to that achieved with the standard contact or near-contact OCT. Conclusions Optical coherence tomography is able to produce high-resolution images of vocal fold mucosa to a maximum depth of 1.6 mm. It may be used in the diagnosis of VF lesions, particularly early squamous cell carcinoma, in which OCT can show disruption of the basement membrane. Mounting the OCT device directly onto the operating microscope allows hands-free noncontact OCT imaging and simultaneous conventional microscopic visualization of the VFs. However, the lateral resolution of the OCT microscope system is 50 µm, in contrast to the conventional handheld probe system (10 µm). Although such images at this resolution are still useful clinically, improved resolution would enhance the system’s performance, potentially enabling real-time OCT-guided microsurgery of the larynx. PMID:18700431

Martian Dust Collected by Phoenix's Arm

NASA Technical Reports Server (NTRS)

2008-01-01

This image from NASA's Phoenix Lander's Optical Microscope shows particles of Martian dust lying on the microscope's silicon substrate. The Robotic Arm sprinkled a sample of the soil from the Snow White trench onto the microscope on July 2, 2008, the 38th Martian day, or sol, of the mission after landing.

Subsequently, the Atomic Force Microscope, or AFM, zoomed in one of the fine particles, creating the first-ever image of a particle of Mars' ubiquitous fine dust, the most highly magnified image ever seen from another world.

The Atomic Force Microscope was developed by a Swiss-led consortium in collaboration with Imperial College London. The AFM is part of Phoenix's Microscopy, Electrochemistry and Conductivity Analyzer instrument.

The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

Light field creating and imaging with different order intensity derivatives

NASA Astrophysics Data System (ADS)

Wang, Yu; Jiang, Huan

2014-10-01

Microscopic image restoration and reconstruction is a challenging topic in the image processing and computer vision, which can be widely applied to life science, biology and medicine etc. A microscopic light field creating and three dimensional (3D) reconstruction method is proposed for transparent or partially transparent microscopic samples, which is based on the Taylor expansion theorem and polynomial fitting. Firstly the image stack of the specimen is divided into several groups in an overlapping or non-overlapping way along the optical axis, and the first image of every group is regarded as reference image. Then different order intensity derivatives are calculated using all the images of every group and polynomial fitting method based on the assumption that the structure of the specimen contained by the image stack in a small range along the optical axis are possessed of smooth and linear property. Subsequently, new images located any position from which to reference image the distance is Δz along the optical axis can be generated by means of Taylor expansion theorem and the calculated different order intensity derivatives. Finally, the microscopic specimen can be reconstructed in 3D form using deconvolution technology and all the images including both the observed images and the generated images. The experimental results show the effectiveness and feasibility of our method.

Multi-pass transmission electron microscopy

DOE PAGES

Juffmann, Thomas; Koppell, Stewart A.; Klopfer, Brannon B.; ...

2017-05-10

Feynman once asked physicists to build better electron microscopes to be able to watch biology at work. While electron microscopes can now provide atomic resolution, electron beam induced specimen damage precludes high resolution imaging of sensitive materials, such as single proteins or polymers. Here, we use simulations to show that an electron microscope based on a multi-pass measurement protocol enables imaging of single proteins, without averaging structures over multiple images. While we demonstrate the method for particular imaging targets, the approach is broadly applicable and is expected to improve resolution and sensitivity for a range of electron microscopy imaging modalities,more » including, for example, scanning and spectroscopic techniques. The approach implements a quantum mechanically optimal strategy which under idealized conditions can be considered interaction-free.« less

Switched capacitor charge pump used for low-distortion imaging in atomic force microscope.

PubMed

Zhang, Jie; Zhang, Lian Sheng; Feng, Zhi Hua

2015-01-01

The switched capacitor charge pump (SCCP) is an effective method of linearizing charges on piezoelectric actuators and therefore constitute a significant approach to nano-positioning. In this work, it was for the first time implemented in an atomic force microscope for low-distortion imaging. Experimental results showed that the image quality was improved evidently under the SCCP drive compared with that under traditional linear voltage drive. © Wiley Periodicals, Inc.

Inverted light-sheet microscope for imaging mouse pre-implantation development.

PubMed

Strnad, Petr; Gunther, Stefan; Reichmann, Judith; Krzic, Uros; Balazs, Balint; de Medeiros, Gustavo; Norlin, Nils; Hiiragi, Takashi; Hufnagel, Lars; Ellenberg, Jan

2016-02-01

Despite its importance for understanding human infertility and congenital diseases, early mammalian development has remained inaccessible to in toto imaging. We developed an inverted light-sheet microscope that enabled us to image mouse embryos from zygote to blastocyst, computationally track all cells and reconstruct a complete lineage tree of mouse pre-implantation development. We used this unique data set to show that the first cell fate specification occurs at the 16-cell stage.

Fourier plane imaging microscopy

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

Dominguez, Daniel, E-mail: daniel.dominguez@ttu.edu; Peralta, Luis Grave de; Nano Tech Center, Texas Tech University, Lubbock, Texas 79409

We show how the image of an unresolved photonic crystal can be reconstructed using a single Fourier plane (FP) image obtained with a second camera that was added to a traditional compound microscope. We discuss how Fourier plane imaging microscopy is an application of a remarkable property of the obtained FP images: they contain more information about the photonic crystals than the images recorded by the camera commonly placed at the real plane of the microscope. We argue that the experimental results support the hypothesis that surface waves, contributing to enhanced resolution abilities, were optically excited in the studied photonicmore » crystals.« less

Compact Video Microscope Imaging System Implemented in Colloid Studies

NASA Technical Reports Server (NTRS)

McDowell, Mark

2002-01-01

Long description Photographs showing fiber-optic light source, microscope and charge-coupled discharge (CCD) camera head connected to camera body, CCD camera body feeding data to image acquisition board in PC, and Cartesian robot controlled via PC board. The Compact Microscope Imaging System (CMIS) is a diagnostic tool with intelligent controls for use in space, industrial, medical, and security applications. CMIS can be used in situ with a minimum amount of user intervention. This system can scan, find areas of interest in, focus on, and acquire images automatically. Many multiple-cell experiments require microscopy for in situ observations; this is feasible only with compact microscope systems. CMIS is a miniature machine vision system that combines intelligent image processing with remote control. The software also has a user-friendly interface, which can be used independently of the hardware for further post-experiment analysis. CMIS has been successfully developed in the SML Laboratory at the NASA Glenn Research Center and adapted for use for colloid studies and is available for telescience experiments. The main innovations this year are an improved interface, optimized algorithms, and the ability to control conventional full-sized microscopes in addition to compact microscopes. The CMIS software-hardware interface is being integrated into our SML Analysis package, which will be a robust general-purpose image-processing package that can handle over 100 space and industrial applications.

Enhancing the performance of the light field microscope using wavefront coding

PubMed Central

Cohen, Noy; Yang, Samuel; Andalman, Aaron; Broxton, Michael; Grosenick, Logan; Deisseroth, Karl; Horowitz, Mark; Levoy, Marc

2014-01-01

Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective’s back focal plane and at the microscope’s native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain. PMID:25322056

Bright-field scanning confocal electron microscopy using a double aberration-corrected transmission electron microscope.

PubMed

Wang, Peng; Behan, Gavin; Kirkland, Angus I; Nellist, Peter D; Cosgriff, Eireann C; D'Alfonso, Adrian J; Morgan, Andrew J; Allen, Leslie J; Hashimoto, Ayako; Takeguchi, Masaki; Mitsuishi, Kazutaka; Shimojo, Masayuki

2011-06-01

Scanning confocal electron microscopy (SCEM) offers a mechanism for three-dimensional imaging of materials, which makes use of the reduced depth of field in an aberration-corrected transmission electron microscope. The simplest configuration of SCEM is the bright-field mode. In this paper we present experimental data and simulations showing the form of bright-field SCEM images. We show that the depth dependence of the three-dimensional image can be explained in terms of two-dimensional images formed in the detector plane. For a crystalline sample, this so-called probe image is shown to be similar to a conventional diffraction pattern. Experimental results and simulations show how the diffracted probes in this image are elongated in thicker crystals and the use of this elongation to estimate sample thickness is explored. Copyright © 2010 Elsevier B.V. All rights reserved.

Adirondack Under the Microscope-2

NASA Technical Reports Server (NTRS)

2004-01-01

This overhead look at the martian rock dubbed Adirondack was captured by the Mars Exploration Rover Spirit's panoramic camera. It shows the approximate region where the rover's microscopic imager began its first close-up inspection.

Super-resolution imaging of ciliary microdomains in isolated olfactory sensory neurons using a custom two-color stimulated emission depletion microscope

NASA Astrophysics Data System (ADS)

Meyer, Stephanie A.; Ozbay, Baris N.; Potcoava, Mariana; Salcedo, Ernesto; Restrepo, Diego; Gibson, Emily A.

2016-06-01

We performed stimulated emission depletion (STED) imaging of isolated olfactory sensory neurons (OSNs) using a custom-built microscope. The STED microscope uses a single pulsed laser to excite two separate fluorophores, Atto 590 and Atto 647N. A gated timing circuit combined with temporal interleaving of the different color excitation/STED laser pulses filters the two channel detection and greatly minimizes crosstalk. We quantified the instrument resolution to be ˜81 and ˜44 nm, for the Atto 590 and Atto 647N channels. The spatial separation between the two channels was measured to be under 10 nm, well below the resolution limit. The custom-STED microscope is incorporated onto a commercial research microscope allowing brightfield, differential interference contrast, and epifluorescence imaging on the same field of view. We performed immunolabeling of OSNs in mice to image localization of ciliary membrane proteins involved in olfactory transduction. We imaged Ca2+-permeable cyclic nucleotide gated (CNG) channel (Atto 594) and adenylyl cyclase type III (ACIII) (Atto 647N) in distinct cilia. STED imaging resolved well-separated subdiffraction limited clusters for each protein. We quantified the size of each cluster to have a mean value of 88±48 nm and 124±43 nm, for CNG and ACIII, respectively. STED imaging showed separated clusters that were not resolvable in confocal images.

Automated system for characterization and classification of malaria-infected stages using light microscopic images of thin blood smears.

PubMed

Das, D K; Maiti, A K; Chakraborty, C

2015-03-01

In this paper, we propose a comprehensive image characterization cum classification framework for malaria-infected stage detection using microscopic images of thin blood smears. The methodology mainly includes microscopic imaging of Leishman stained blood slides, noise reduction and illumination correction, erythrocyte segmentation, feature selection followed by machine classification. Amongst three-image segmentation algorithms (namely, rule-based, Chan-Vese-based and marker-controlled watershed methods), marker-controlled watershed technique provides better boundary detection of erythrocytes specially in overlapping situations. Microscopic features at intensity, texture and morphology levels are extracted to discriminate infected and noninfected erythrocytes. In order to achieve subgroup of potential features, feature selection techniques, namely, F-statistic and information gain criteria are considered here for ranking. Finally, five different classifiers, namely, Naive Bayes, multilayer perceptron neural network, logistic regression, classification and regression tree (CART), RBF neural network have been trained and tested by 888 erythrocytes (infected and noninfected) for each features' subset. Performance evaluation of the proposed methodology shows that multilayer perceptron network provides higher accuracy for malaria-infected erythrocytes recognition and infected stage classification. Results show that top 90 features ranked by F-statistic (specificity: 98.64%, sensitivity: 100%, PPV: 99.73% and overall accuracy: 96.84%) and top 60 features ranked by information gain provides better results (specificity: 97.29%, sensitivity: 100%, PPV: 99.46% and overall accuracy: 96.73%) for malaria-infected stage classification. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Correlation of EBIC and SWBXT Imaged Defects and Epilayer Growth Pits in 6H-SiC Schottky Diodes

NASA Technical Reports Server (NTRS)

Schnable, C. M.; Tabib-Azar, M.; Neudeck, P. G.; Bailey, S. G.; Su, H. B.; Dudley, M.; Raffaelle, R. P.

2000-01-01

We show the first direct experimental correlation between the presence of closed core screw dislocations in 6H-SiC epilayers with recombination centers, as well as with some of the small growth pits on the epilayer surface in lightly-doped 6H-SiC Schottky diodes. At every Synchrotron White-Beam X-ray Topography (SWBXT)-identified closed core screw dislocation, an Electron Beam Induced Current (EBIC) image showed a dark spot indicating a recombination center, and Nomarski optical microscope and Atomic Force Microscope (AFM) images showed a corresponding small growth pit with a sharp apex on the surface of the epilayer.

Microscope Image of Scavenged Particles

NASA Technical Reports Server (NTRS)

2008-01-01

This image from NASA's Phoenix Mars Lander's Optical Microscope shows a strongly magnetic surface which has scavenged particles from within the microscope enclosure before a sample delivery from the lander's Robotic Arm. The particles correspond to the larger grains seen in fine orange material that makes up most of the soil at the Phoenix site. They vary in color, but are of similar size, about one-tenth of a millimeter.

As the microscope's sample wheel moved during operation, these particles also shifted, clearing a thin layer of the finer orange particles that have also been collected. Together with the previous image, this shows that the larger grains are much more magnetic than the fine orange particles with a much larger volume of the grains being collected by the magnet. The image is 2 milimeters across.

It is speculated that the orange material particles are a weathering product from the larger grains, with the weathering process both causing a color change and a loss of magnetism.

The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by JPL, Pasadena, Calif. Spacecraft development was by Lockheed Martin Space Systems, Denver.

In vivo observation of age-related structural changes of dermal collagen in human facial skin using collagen-sensitive second harmonic generation microscope equipped with 1250-nm mode-locked Cr:Forsterite laser

NASA Astrophysics Data System (ADS)

Yasui, Takeshi; Yonetsu, Makoto; Tanaka, Ryosuke; Tanaka, Yuji; Fukushima, Shu-ichiro; Yamashita, Toyonobu; Ogura, Yuki; Hirao, Tetsuji; Murota, Hiroyuki; Araki, Tsutomu

2013-03-01

In vivo visualization of human skin aging is demonstrated using a Cr:Forsterite (Cr:F) laser-based, collagen-sensitive second harmonic generation (SHG) microscope. The deep penetration into human skin, as well as the specific sensitivity to collagen molecules, achieved by this microscope enables us to clearly visualize age-related structural changes of collagen fiber in the reticular dermis. Here we investigated intrinsic aging and/or photoaging in the male facial skin. Young subjects show dense distributions of thin collagen fibers, whereas elderly subjects show coarse distributions of thick collagen fibers. Furthermore, a comparison of SHG images between young and elderly subjects with and without a recent life history of excessive sun exposure show that a combination of photoaging with intrinsic aging significantly accelerates skin aging. We also perform image analysis based on two-dimensional Fourier transformation of the SHG images and extracted an aging parameter for human skin. The in vivo collagen-sensitive SHG microscope will be a powerful tool in fields such as cosmeceutical sciences and anti-aging dermatology.

Visualizing Morphological Changes of Abscission Zone Cells in Arabidopsis by Scanning Electron Microscope.

PubMed

Shi, Chun-Lin; Butenko, Melinka A

2018-01-01

Scanning electron microscope (SEM) is a type of electron microscope which produces detailed images of surface structures. It has been widely used in plants and animals to study cellular structures. Here, we describe a detailed protocol to prepare samples of floral abscission zones (AZs) for SEM, as well as further image analysis. We show that it is a powerful tool to detect morphologic changes at the cellular level during the course of abscission in wild-type plants and to establish the details of phenotypic alteration in abscission mutants.

Mars Life? - Microscopic Tubular Structures

NASA Image and Video Library

1996-08-09

This electron microscope image shows tubular structures of likely Martian origin. These structures are very similar in size and shape to extremely tiny microfossils found in some Earth rocks. http://photojournal.jpl.nasa.gov/catalog/PIA00287

k-Space Image Correlation Spectroscopy: A Method for Accurate Transport Measurements Independent of Fluorophore Photophysics

PubMed Central

Kolin, David L.; Ronis, David; Wiseman, Paul W.

2006-01-01

We present the theory and application of reciprocal space image correlation spectroscopy (kICS). This technique measures the number density, diffusion coefficient, and velocity of fluorescently labeled macromolecules in a cell membrane imaged on a confocal, two-photon, or total internal reflection fluorescence microscope. In contrast to r-space correlation techniques, we show kICS can recover accurate dynamics even in the presence of complex fluorophore photobleaching and/or “blinking”. Furthermore, these quantities can be calculated without nonlinear curve fitting, or any knowledge of the beam radius of the exciting laser. The number densities calculated by kICS are less sensitive to spatial inhomogeneity of the fluorophore distribution than densities measured using image correlation spectroscopy. We use simulations as a proof-of-principle to show that number densities and transport coefficients can be extracted using this technique. We present calibration measurements with fluorescent microspheres imaged on a confocal microscope, which recover Stokes-Einstein diffusion coefficients, and flow velocities that agree with single particle tracking measurements. We also show the application of kICS to measurements of the transport dynamics of α5-integrin/enhanced green fluorescent protein constructs in a transfected CHO cell imaged on a total internal reflection fluorescence microscope using charge-coupled device area detection. PMID:16861272

New innovations for contrast enhancement in electron microscopy

NASA Astrophysics Data System (ADS)

Mohan, A.

In this study two techniques for producing and improving contrast in Electron Microscopy are discussed. The first technique deals with the production of secondary contrast in a Variable Pressure SEM under poor vacuum conditions using the specimen current signal. A review of the prior work in this field shows that the presence of the gas ions in the microscope column results in the amplification of the specimen current signal which is enriched in secondary content. The focus of this study is to establish practical conditions for imaging samples in the microscope using specimen current with gas amplification. This is done by understanding the different variables in the microscope which affect the image formation process and then finding out optimum conditions for obtaining the best possible image, i.e., the image most enhanced in secondary contrast. A few 'real life' samples analyzed using this technique show that the gas amplified specimen current images contain secondary information and, in some cases, provide clear advantages to imaging with conventional secondary and backscattered detectors. The second technique dealing with the production of phase contrast in the TEM for extremely thin, electron transparent samples, is analyzed. A review of the literature regarding prior work in the field shows that, while the theoretical aspects of production of phase contrast in the TEM using a phase plate are well understood, there have been problems in practically implementing this in the microscope. One major assumption with most of the studies is that a fiber, partially coated with gold, results in the formation of point charges which is an essential requirement for symmetrically shifting the phase of the electron beam. The focus of this portion of the dissertation is to image the type of fields associated with such a phase plate using the technique of electron holography. It is found that there are two types of fields associated with a phase plate of this sort. One is a cylindrical field which extends along the length of the fiber while the other is a localized spherically symmetric field. A series of simulations show that the spherical field can produce phase contrast in the TEM and also improve the contrast transfer properties of the microscope.

Thrombus segmentation by texture dynamics from microscopic image sequences

NASA Astrophysics Data System (ADS)

Brieu, Nicolas; Serbanovic-Canic, Jovana; Cvejic, Ana; Stemple, Derek; Ouwehand, Willem; Navab, Nassir; Groher, Martin

2010-03-01

The genetic factors of thrombosis are commonly explored by microscopically imaging the coagulation of blood cells induced by injuring a vessel of mice or of zebrafish mutants. The latter species is particularly interesting since skin transparency permits to non-invasively acquire microscopic images of the scene with a CCD camera and to estimate the parameters characterizing the thrombus development. These parameters are currently determined by manual outlining, which is both error prone and extremely time consuming. Even though a technique for automatic thrombus extraction would be highly valuable for gene analysts, little work can be found, which is mainly due to very low image contrast and spurious structures. In this work, we propose to semi-automatically segment the thrombus over time from microscopic image sequences of wild-type zebrafish larvae. To compensate the lack of valuable spatial information, our main idea consists of exploiting the temporal information by modeling the variations of the pixel intensities over successive temporal windows with a linear Markov-based dynamic texture formalization. We then derive an image from the estimated model parameters, which represents the probability of a pixel to belong to the thrombus. We employ this probability image to accurately estimate the thrombus position via an active contour segmentation incorporating also prior and spatial information of the underlying intensity images. The performance of our approach is tested on three microscopic image sequences. We show that the thrombus is accurately tracked over time in each sequence if the respective parameters controlling prior influence and contour stiffness are correctly chosen.

FIMic: design for ultimate 3D-integral microscopy of in-vivo biological samples

PubMed Central

Scrofani, G.; Sola-Pikabea, J.; Llavador, A.; Sanchez-Ortiga, E.; Barreiro, J. C.; Saavedra, G.; Garcia-Sucerquia, J.; Martínez-Corral, M.

2017-01-01

In this work, Fourier integral microscope (FIMic), an ultimate design of 3D-integral microscopy, is presented. By placing a multiplexing microlens array at the aperture stop of the microscope objective of the host microscope, FIMic shows extended depth of field and enhanced lateral resolution in comparison with regular integral microscopy. As FIMic directly produces a set of orthographic views of the 3D-micrometer-sized sample, it is suitable for real-time imaging. Following regular integral-imaging reconstruction algorithms, a 2.75-fold enhanced depth of field and 2-time better spatial resolution in comparison with conventional integral microscopy is reported. Our claims are supported by theoretical analysis and experimental images of a resolution test target, cotton fibers, and in-vivo 3D-imaging of biological specimens. PMID:29359107

SIL-STED microscopy technique enhancing super-resolution of fluorescence microscopy

NASA Astrophysics Data System (ADS)

Park, No-Cheol; Lim, Geon; Lee, Won-sup; Moon, Hyungbae; Choi, Guk-Jong; Park, Young-Pil

2017-08-01

We have characterized a new type STED microscope which combines a high numerical aperture (NA) optical head with a solid immersion lens (SIL), and we call it as SIL-STED microscope. The advantage of a SIL-STED microscope is that its high NA of the SIL makes it superior to a general STED microscope in lateral resolution, thus overcoming the optical diffraction limit at the macromolecular level and enabling advanced super-resolution imaging of cell surface or cell membrane structure and function Do. This study presents the first implementation of higher NA illumination in a STED microscope limiting the fluorescence lateral resolution to about 40 nm. The refractive index of the SIL which is made of material KTaO3 is about 2.23 and 2.20 at a wavelength of 633 nm and 780 nm which are used for excitation and depletion in STED imaging, respectively. Based on the vector diffraction theory, the electric field focused by the SILSTED microscope is numerically calculated so that the numerical results of the point dispersion function of the microscope and the expected resolution could be analyzed. For further investigation, fluorescence imaging of nano size fluorescent beads is fulfilled to show improved performance of the technique.

Quantitative Phase Imaging in a Volume Holographic Microscope

NASA Astrophysics Data System (ADS)

Waller, Laura; Luo, Yuan; Barbastathis, George

2010-04-01

We demonstrate a method for quantitative phase imaging in a Volume Holographic Microscope (VHM) from a single exposure, describe the properties of the system and show experimental results. The VHM system uses a multiplexed volume hologram (VH) to laterally separate images from different focal planes. This 3D intensity information is then used to solve the transport of intensity (TIE) equation and recover phase quantitatively. We discuss the modifications to the technique that were made in order to give accurate results.

Focal depth measurement of scanning helium ion microscope

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

Guo, Hongxuan, E-mail: Guo.hongxuan@nims.go.jp; Itoh, Hiroshi; Wang, Chunmei

2014-07-14

When facing the challenges of critical dimension measurement of complicated nanostructures, such as of the three dimension integrated circuit, characterization of the focal depth of microscopes is important. In this Letter, we developed a method for characterizing the focal depth of a scanning helium ion microscope (HIM) by using an atomic force microscope tip characterizer (ATC). The ATC was tilted in a sample chamber at an angle to the scanning plan. Secondary electron images (SEIs) were obtained at different positions of the ATC. The edge resolution of the SEIs shows the nominal diameters of the helium ion beam at differentmore » focal levels. With this method, the nominal shapes of the helium ion beams were obtained with different apertures. Our results show that a small aperture is necessary to get a high spatial resolution and high depth of field images with HIM. This work provides a method for characterizing and improving the performance of HIM.« less

Focal depth measurement of scanning helium ion microscope

NASA Astrophysics Data System (ADS)

Guo, Hongxuan; Itoh, Hiroshi; Wang, Chunmei; Zhang, Han; Fujita, Daisuke

2014-07-01

When facing the challenges of critical dimension measurement of complicated nanostructures, such as of the three dimension integrated circuit, characterization of the focal depth of microscopes is important. In this Letter, we developed a method for characterizing the focal depth of a scanning helium ion microscope (HIM) by using an atomic force microscope tip characterizer (ATC). The ATC was tilted in a sample chamber at an angle to the scanning plan. Secondary electron images (SEIs) were obtained at different positions of the ATC. The edge resolution of the SEIs shows the nominal diameters of the helium ion beam at different focal levels. With this method, the nominal shapes of the helium ion beams were obtained with different apertures. Our results show that a small aperture is necessary to get a high spatial resolution and high depth of field images with HIM. This work provides a method for characterizing and improving the performance of HIM.

Sharp Tips on the Atomic Force Microscope

NASA Technical Reports Server (NTRS)

2008-01-01

This image shows the eight sharp tips of the NASA's Phoenix Mars Lander's Atomic Force Microscope, or AFM. The AFM is part of Phoenix's Microscopy, Electrochemistry, and Conductivity Analyzer, or MECA.

The microscope maps the shape of particles in three dimensions by scanning them with one of the tips at the end of a beam. For the AFM image taken, the tip at the end of the upper right beam was used. The tip pointing up in the enlarged image is the size of a smoke particle at its base, or 2 microns. This image was taken with a scanning electron microscope before Phoenix launched on August 4, 2007.

The AFM was developed by a Swiss-led consortium in collaboration with Imperial College London.

The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

In vivo cellular imaging with microscopes enabled by MEMS scanners

NASA Astrophysics Data System (ADS)

Ra, Hyejun

High-resolution optical imaging plays an important role in medical diagnosis and biomedical research. Confocal microscopy is a widely used imaging method for obtaining cellular and sub-cellular images of biological tissue in reflectance and fluorescence modes. Its characteristic optical sectioning capability also enables three-dimensional (3-D) image reconstruction. However, its use has mostly been limited to excised tissues due to the requirement of high numerical aperture (NA) lenses for cellular resolution. Microscope miniaturization can enable in vivo imaging to make possible early cancer diagnosis and biological studies in the innate environment. In this dissertation, microscope miniaturization for in vivo cellular imaging is presented. The dual-axes confocal (DAC) architecture overcomes limitations of the conventional single-axis confocal (SAC) architecture to allow for miniaturization with high resolution. A microelectromechanical systems (MEMS) scanner is the central imaging component that is key in miniaturization of the DAC architecture. The design, fabrication, and characterization of the two-dimensional (2-D) MEMS scanner are presented. The gimbaled MEMS scanner is fabricated on a double silicon-on-insulator (SOI) wafer and is actuated by self-aligned vertical electrostatic combdrives. The imaging performance of the MEMS scanner in a DAC configuration is shown in a breadboard microscope setup, where reflectance and fluorescence imaging is demonstrated. Then, the MEMS scanner is integrated into a miniature DAC microscope. The whole imaging system is integrated into a portable unit for research in small animal models of human biology and disease. In vivo 3-D imaging is demonstrated on mouse skin models showing gene transfer and siRNA silencing. The siRNA silencing process is sequentially imaged in one mouse over time.

Compact Microscope Imaging System with Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark

2004-01-01

The figure presents selected views of a compact microscope imaging system (CMIS) that includes a miniature video microscope, a Cartesian robot (a computer- controlled three-dimensional translation stage), and machine-vision and control subsystems. The CMIS was built from commercial off-the-shelf instrumentation, computer hardware and software, and custom machine-vision software. The machine-vision and control subsystems include adaptive neural networks that afford a measure of artificial intelligence. The CMIS can perform several automated tasks with accuracy and repeatability . tasks that, heretofore, have required the full attention of human technicians using relatively bulky conventional microscopes. In addition, the automation and control capabilities of the system inherently include a capability for remote control. Unlike human technicians, the CMIS is not at risk of becoming fatigued or distracted: theoretically, it can perform continuously at the level of the best human technicians. In its capabilities for remote control and for relieving human technicians of tedious routine tasks, the CMIS is expected to be especially useful in biomedical research, materials science, inspection of parts on industrial production lines, and space science. The CMIS can automatically focus on and scan a microscope sample, find areas of interest, record the resulting images, and analyze images from multiple samples simultaneously. Automatic focusing is an iterative process: The translation stage is used to move the microscope along its optical axis in a succession of coarse, medium, and fine steps. A fast Fourier transform (FFT) of the image is computed at each step, and the FFT is analyzed for its spatial-frequency content. The microscope position that results in the greatest dispersal of FFT content toward high spatial frequencies (indicating that the image shows the greatest amount of detail) is deemed to be the focal position.

Secondary electron imaging of monolayer materials inside a transmission electron microscope

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

Cretu, Ovidiu, E-mail: cretu.ovidiu@nims.go.jp; Lin, Yung-Chang; Suenaga, Kazutomo

2015-08-10

A scanning transmission electron microscope equipped with a backscattered and secondary electron detector is shown capable to image graphene and hexagonal boron nitride monolayers. Secondary electron contrasts of the two lightest monolayer materials are clearly distinguished from the vacuum level. A signal difference between these two materials is attributed to electronic structure differences, which will influence the escape probabilities of the secondary electrons. Our results show that the secondary electron signal can be used to distinguish between the electronic structures of materials with atomic layer sensitivity, enhancing its applicability as a complementary signal in the analytical microscope.

High-speed image processing system and its micro-optics application

NASA Astrophysics Data System (ADS)

Ohba, Kohtaro; Ortega, Jesus C. P.; Tanikawa, Tamio; Tanie, Kazuo; Tajima, Kenji; Nagai, Hiroshi; Tsuji, Masataka; Yamada, Shigeru

2003-07-01

In this paper, a new application system with high speed photography, i.e. an observational system for the tele-micro-operation, has been proposed with a dynamic focusing system and a high-speed image processing system using the "Depth From Focus (DFF)" criteria. In micro operation, such as for the microsurgery, DNA operation and etc., the small depth of a focus on the microscope makes bad observation. For example, if the focus is on the object, the actuator cannot be seen with the microscope. On the other hand, if the focus is on the actuator, the object cannot be observed. In this sense, the "all-in-focus image," which holds the in-focused texture all over the image, is useful to observe the microenvironments on the microscope. It is also important to obtain the "depth map" which could show the 3D micro virtual environments in real-time to actuate the micro objects, intuitively. To realize the real-time micro operation with DFF criteria, which has to integrate several images to obtain "all-in-focus image" and "depth map," at least, the 240 frames par second based image capture and processing system should be required. At first, this paper briefly reviews the criteria of "depth from focus" to achieve the all-in-focus image and the 3D microenvironments' reconstruction, simultaneously. After discussing the problem in our past system, a new frame-rate system is constructed with the high-speed video camera and FPGA hardware with 240 frames par second. To apply this system in the real microscope, a new criterion "ghost filtering" technique to reconstruct the all-in-focus image is proposed. Finally, the micro observation shows the validity of this system.

Digital imaging and image analysis applied to numerical applications in forensic hair examination.

PubMed

Brooks, Elizabeth; Comber, Bruce; McNaught, Ian; Robertson, James

2011-03-01

A method that provides objective data to complement the hair analysts' microscopic observations, which is non-destructive, would be of obvious benefit in the forensic examination of hairs. This paper reports on the use of objective colour measurement and image analysis techniques of auto-montaged images. Brown Caucasian telogen scalp hairs were chosen as a stern test of the utility of these approaches. The results show the value of using auto-montaged images and the potential for the use of objective numerical measures of colour and pigmentation to complement microscopic observations. 2010. Published by Elsevier Ireland Ltd. All rights reserved.

Calibration of Wide-Field Deconvolution Microscopy for Quantitative Fluorescence Imaging

PubMed Central

Lee, Ji-Sook; Wee, Tse-Luen (Erika); Brown, Claire M.

2014-01-01

Deconvolution enhances contrast in fluorescence microscopy images, especially in low-contrast, high-background wide-field microscope images, improving characterization of features within the sample. Deconvolution can also be combined with other imaging modalities, such as confocal microscopy, and most software programs seek to improve resolution as well as contrast. Quantitative image analyses require instrument calibration and with deconvolution, necessitate that this process itself preserves the relative quantitative relationships between fluorescence intensities. To ensure that the quantitative nature of the data remains unaltered, deconvolution algorithms need to be tested thoroughly. This study investigated whether the deconvolution algorithms in AutoQuant X3 preserve relative quantitative intensity data. InSpeck Green calibration microspheres were prepared for imaging, z-stacks were collected using a wide-field microscope, and the images were deconvolved using the iterative deconvolution algorithms with default settings. Afterwards, the mean intensities and volumes of microspheres in the original and the deconvolved images were measured. Deconvolved data sets showed higher average microsphere intensities and smaller volumes than the original wide-field data sets. In original and deconvolved data sets, intensity means showed linear relationships with the relative microsphere intensities given by the manufacturer. Importantly, upon normalization, the trend lines were found to have similar slopes. In original and deconvolved images, the volumes of the microspheres were quite uniform for all relative microsphere intensities. We were able to show that AutoQuant X3 deconvolution software data are quantitative. In general, the protocol presented can be used to calibrate any fluorescence microscope or image processing and analysis procedure. PMID:24688321

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy

PubMed Central

Lim, Daryl; Ford, Tim N.; Chu, Kengyeh K.; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish. PMID:21280920

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy.

PubMed

Lim, Daryl; Ford, Tim N; Chu, Kengyeh K; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish.

Optically sectioned in vivo imaging with speckle illumination HiLo microscopy

NASA Astrophysics Data System (ADS)

Lim, Daryl; Ford, Tim N.; Chu, Kengyeh K.; Mertz, Jerome

2011-01-01

We present a simple wide-field imaging technique, called HiLo microscopy, that is capable of producing optically sectioned images in real time, comparable in quality to confocal laser scanning microscopy. The technique is based on the fusion of two raw images, one acquired with speckle illumination and another with standard uniform illumination. The fusion can be numerically adjusted, using a single parameter, to produce optically sectioned images of varying thicknesses with the same raw data. Direct comparison between our HiLo microscope and a commercial confocal laser scanning microscope is made on the basis of sectioning strength and imaging performance. Specifically, we show that HiLo and confocal 3-D imaging of a GFP-labeled mouse brain hippocampus are comparable in quality. Moreover, HiLo microscopy is capable of faster, near video rate imaging over larger fields of view than attainable with standard confocal microscopes. The goal of this paper is to advertise the simplicity, robustness, and versatility of HiLo microscopy, which we highlight with in vivo imaging of common model organisms including planaria, C. elegans, and zebrafish.

Extended morphological processing: a practical method for automatic spot detection of biological markers from microscopic images.

PubMed

Kimori, Yoshitaka; Baba, Norio; Morone, Nobuhiro

2010-07-08

A reliable extraction technique for resolving multiple spots in light or electron microscopic images is essential in investigations of the spatial distribution and dynamics of specific proteins inside cells and tissues. Currently, automatic spot extraction and characterization in complex microscopic images poses many challenges to conventional image processing methods. A new method to extract closely located, small target spots from biological images is proposed. This method starts with a simple but practical operation based on the extended morphological top-hat transformation to subtract an uneven background. The core of our novel approach is the following: first, the original image is rotated in an arbitrary direction and each rotated image is opened with a single straight line-segment structuring element. Second, the opened images are unified and then subtracted from the original image. To evaluate these procedures, model images of simulated spots with closely located targets were created and the efficacy of our method was compared to that of conventional morphological filtering methods. The results showed the better performance of our method. The spots of real microscope images can be quantified to confirm that the method is applicable in a given practice. Our method achieved effective spot extraction under various image conditions, including aggregated target spots, poor signal-to-noise ratio, and large variations in the background intensity. Furthermore, it has no restrictions with respect to the shape of the extracted spots. The features of our method allow its broad application in biological and biomedical image information analysis.

Noise removal in extended depth of field microscope images through nonlinear signal processing.

PubMed

Zahreddine, Ramzi N; Cormack, Robert H; Cogswell, Carol J

2013-04-01

Extended depth of field (EDF) microscopy, achieved through computational optics, allows for real-time 3D imaging of live cell dynamics. EDF is achieved through a combination of point spread function engineering and digital image processing. A linear Wiener filter has been conventionally used to deconvolve the image, but it suffers from high frequency noise amplification and processing artifacts. A nonlinear processing scheme is proposed which extends the depth of field while minimizing background noise. The nonlinear filter is generated via a training algorithm and an iterative optimizer. Biological microscope images processed with the nonlinear filter show a significant improvement in image quality and signal-to-noise ratio over the conventional linear filter.

Generic Features of Tertiary Chromatin Structure as Detected in Natural Chromosomes

PubMed Central

Müller, Waltraud G.; Rieder, Dietmar; Kreth, Gregor; Cremer, Christoph; Trajanoski, Zlatko; McNally, James G.

2004-01-01

Knowledge of tertiary chromatin structure in mammalian interphase chromosomes is largely derived from artificial tandem arrays. In these model systems, light microscope images reveal fibers or beaded fibers after high-density targeting of transactivators to insertional domains spanning several megabases. These images of fibers have lent support to chromonema fiber models of tertiary structure. To assess the relevance of these studies to natural mammalian chromatin, we identified two different ∼400-kb regions on human chromosomes 6 and 22 and then examined light microscope images of interphase tertiary chromatin structure when the regions were transcriptionally active and inactive. When transcriptionally active, these natural chromosomal regions elongated, yielding images characterized by a series of adjacent puncta or “beads”, referred to hereafter as beaded images. These elongated structures required transcription for their maintenance. Thus, despite marked differences in the density and the mode of transactivation, the natural and artificial systems showed similarities, suggesting that beaded images are generic features of transcriptionally active tertiary chromatin. We show here, however, that these images do not necessarily favor chromonema fiber models but can also be explained by a radial-loop model or even a simple nucleosome affinity, random-chain model. Thus, light microscope images of tertiary structure cannot distinguish among competing models, although they do impose key constraints: chromatin must be clustered to yield beaded images and then packaged within each cluster to enable decondensation into adjacent clusters. PMID:15485905

Adaptive and automatic red blood cell counting method based on microscopic hyperspectral imaging technology

NASA Astrophysics Data System (ADS)

Liu, Xi; Zhou, Mei; Qiu, Song; Sun, Li; Liu, Hongying; Li, Qingli; Wang, Yiting

2017-12-01

Red blood cell counting, as a routine examination, plays an important role in medical diagnoses. Although automated hematology analyzers are widely used, manual microscopic examination by a hematologist or pathologist is still unavoidable, which is time-consuming and error-prone. This paper proposes a full-automatic red blood cell counting method which is based on microscopic hyperspectral imaging of blood smears and combines spatial and spectral information to achieve high precision. The acquired hyperspectral image data of the blood smear in the visible and near-infrared spectral range are firstly preprocessed, and then a quadratic blind linear unmixing algorithm is used to get endmember abundance images. Based on mathematical morphological operation and an adaptive Otsu’s method, a binaryzation process is performed on the abundance images. Finally, the connected component labeling algorithm with magnification-based parameter setting is applied to automatically select the binary images of red blood cell cytoplasm. Experimental results show that the proposed method can perform well and has potential for clinical applications.

EnLightenment: High resolution smartphone microscopy as an educational and public engagement platform.

PubMed

Wicks, Laura C; Cairns, Gemma S; Melnyk, Jacob; Bryce, Scott; Duncan, Rory R; Dalgarno, Paul A

2017-01-01

We developed a simple, cost-effective smartphone microscopy platform for use in educational and public engagement programs. We demonstrated its effectiveness, and potential for citizen science through a national imaging initiative, EnLightenment . The cost effectiveness of the instrument allowed for the program to deliver over 500 microscopes to more than 100 secondary schools throughout Scotland, targeting 1000's of 12-14 year olds. Through careful, quantified, selection of a high power, low-cost objective lens, our smartphone microscope has an imaging resolution of microns, with a working distance of 3 mm. It is therefore capable of imaging single cells and sub-cellular features, and retains usability for young children. The microscopes were designed in kit form and provided an interdisciplinary educational tool. By providing full lesson plans and support material, we developed a framework to explore optical design, microscope performance, engineering challenges on construction and real-world applications in life sciences, biological imaging, marine biology, art, and technology. A national online imaging competition framed EnLightenment ; with over 500 high quality images submitted of diverse content, spanning multiple disciplines. With examples of cellular and sub-cellular features clearly identifiable in some submissions, we show how young public can use these instruments for research-level imaging applications, and the potential of the instrument for citizen science programs.

Color calibration and fusion of lens-free and mobile-phone microscopy images for high-resolution and accurate color reproduction

NASA Astrophysics Data System (ADS)

Zhang, Yibo; Wu, Yichen; Zhang, Yun; Ozcan, Aydogan

2016-06-01

Lens-free holographic microscopy can achieve wide-field imaging in a cost-effective and field-portable setup, making it a promising technique for point-of-care and telepathology applications. However, due to relatively narrow-band sources used in holographic microscopy, conventional colorization methods that use images reconstructed at discrete wavelengths, corresponding to e.g., red (R), green (G) and blue (B) channels, are subject to color artifacts. Furthermore, these existing RGB colorization methods do not match the chromatic perception of human vision. Here we present a high-color-fidelity and high-resolution imaging method, termed “digital color fusion microscopy” (DCFM), which fuses a holographic image acquired at a single wavelength with a color-calibrated image taken by a low-magnification lens-based microscope using a wavelet transform-based colorization method. We demonstrate accurate color reproduction of DCFM by imaging stained tissue sections. In particular we show that a lens-free holographic microscope in combination with a cost-effective mobile-phone-based microscope can generate color images of specimens, performing very close to a high numerical-aperture (NA) benchtop microscope that is corrected for color distortions and chromatic aberrations, also matching the chromatic response of human vision. This method can be useful for wide-field imaging needs in telepathology applications and in resource-limited settings, where whole-slide scanning microscopy systems are not available.

Color calibration and fusion of lens-free and mobile-phone microscopy images for high-resolution and accurate color reproduction

PubMed Central

Zhang, Yibo; Wu, Yichen; Zhang, Yun; Ozcan, Aydogan

2016-01-01

Lens-free holographic microscopy can achieve wide-field imaging in a cost-effective and field-portable setup, making it a promising technique for point-of-care and telepathology applications. However, due to relatively narrow-band sources used in holographic microscopy, conventional colorization methods that use images reconstructed at discrete wavelengths, corresponding to e.g., red (R), green (G) and blue (B) channels, are subject to color artifacts. Furthermore, these existing RGB colorization methods do not match the chromatic perception of human vision. Here we present a high-color-fidelity and high-resolution imaging method, termed “digital color fusion microscopy” (DCFM), which fuses a holographic image acquired at a single wavelength with a color-calibrated image taken by a low-magnification lens-based microscope using a wavelet transform-based colorization method. We demonstrate accurate color reproduction of DCFM by imaging stained tissue sections. In particular we show that a lens-free holographic microscope in combination with a cost-effective mobile-phone-based microscope can generate color images of specimens, performing very close to a high numerical-aperture (NA) benchtop microscope that is corrected for color distortions and chromatic aberrations, also matching the chromatic response of human vision. This method can be useful for wide-field imaging needs in telepathology applications and in resource-limited settings, where whole-slide scanning microscopy systems are not available. PMID:27283459

Color calibration and fusion of lens-free and mobile-phone microscopy images for high-resolution and accurate color reproduction.

PubMed

Zhang, Yibo; Wu, Yichen; Zhang, Yun; Ozcan, Aydogan

2016-06-10

Lens-free holographic microscopy can achieve wide-field imaging in a cost-effective and field-portable setup, making it a promising technique for point-of-care and telepathology applications. However, due to relatively narrow-band sources used in holographic microscopy, conventional colorization methods that use images reconstructed at discrete wavelengths, corresponding to e.g., red (R), green (G) and blue (B) channels, are subject to color artifacts. Furthermore, these existing RGB colorization methods do not match the chromatic perception of human vision. Here we present a high-color-fidelity and high-resolution imaging method, termed "digital color fusion microscopy" (DCFM), which fuses a holographic image acquired at a single wavelength with a color-calibrated image taken by a low-magnification lens-based microscope using a wavelet transform-based colorization method. We demonstrate accurate color reproduction of DCFM by imaging stained tissue sections. In particular we show that a lens-free holographic microscope in combination with a cost-effective mobile-phone-based microscope can generate color images of specimens, performing very close to a high numerical-aperture (NA) benchtop microscope that is corrected for color distortions and chromatic aberrations, also matching the chromatic response of human vision. This method can be useful for wide-field imaging needs in telepathology applications and in resource-limited settings, where whole-slide scanning microscopy systems are not available.

A fourth order PDE based fuzzy c- means approach for segmentation of microscopic biopsy images in presence of Poisson noise for cancer detection.

PubMed

Kumar, Rajesh; Srivastava, Subodh; Srivastava, Rajeev

2017-07-01

For cancer detection from microscopic biopsy images, image segmentation step used for segmentation of cells and nuclei play an important role. Accuracy of segmentation approach dominate the final results. Also the microscopic biopsy images have intrinsic Poisson noise and if it is present in the image the segmentation results may not be accurate. The objective is to propose an efficient fuzzy c-means based segmentation approach which can also handle the noise present in the image during the segmentation process itself i.e. noise removal and segmentation is combined in one step. To address the above issues, in this paper a fourth order partial differential equation (FPDE) based nonlinear filter adapted to Poisson noise with fuzzy c-means segmentation method is proposed. This approach is capable of effectively handling the segmentation problem of blocky artifacts while achieving good tradeoff between Poisson noise removals and edge preservation of the microscopic biopsy images during segmentation process for cancer detection from cells. The proposed approach is tested on breast cancer microscopic biopsy data set with region of interest (ROI) segmented ground truth images. The microscopic biopsy data set contains 31 benign and 27 malignant images of size 896 × 768. The region of interest selected ground truth of all 58 images are also available for this data set. Finally, the result obtained from proposed approach is compared with the results of popular segmentation algorithms; fuzzy c-means, color k-means, texture based segmentation, and total variation fuzzy c-means approaches. The experimental results shows that proposed approach is providing better results in terms of various performance measures such as Jaccard coefficient, dice index, Tanimoto coefficient, area under curve, accuracy, true positive rate, true negative rate, false positive rate, false negative rate, random index, global consistency error, and variance of information as compared to other segmentation approaches used for cancer detection. Copyright © 2017 Elsevier B.V. All rights reserved.

Co-registration of In-Vivo Human MRI Brain Images to Postmortem Histological Microscopic Images

PubMed Central

Singh, M.; Rajagopalan, A.; Kim, T.-S.; Hwang, D.; Chui, H.; Zhang, X.-L.; Lee, A.-Y.; Zarow, C.

2009-01-01

Certain features such as small vascular lesions seen in human MRI are detected reliably only in postmortem histological samples by microscopic imaging. Co-registration of these microscopically detected features to their corresponding locations in the in-vivo images would be of great benefit to understanding the MRI signatures of specific diseases. Using non-linear Polynomial transformation, we report a method to co-register in-vivo MRIs to microscopic images of histological samples drawn off the postmortem brain. The approach utilizes digital photographs of postmortem slices as an intermediate reference to co-register the MRIs to microscopy. The overall procedure is challenging due to gross structural deformations in the postmortem brain during extraction and subsequent distortions in the histological preparations. Hemispheres of the brain were co-registered separately to mitigate these effects. Approaches relying on matching single-slices, multiple-slices and entire volumes in conjunction with different similarity measures suggested that using four slices at a time in combination with two sequential measures, Pearson correlation coefficient followed by mutual information, produced the best MRI-postmortem co-registration according to a voxel mismatch count. The accuracy of the overall registration was evaluated by measuring the 3D Euclidean distance between the locations of microscopically identified lesions on postmortem slices and their MRI-postmortem co-registered locations. The results show a mean 3D displacement of 5.1 ± 2.0 mm between the in-vivo MRI and microscopically determined locations for 21 vascular lesions in 11 subjects. PMID:19169415

In Vivo Near Infrared Virtual Intraoperative Surgical Photoacoustic Optical Coherence Tomography

PubMed Central

Lee, Donghyun; Lee, Changho; Kim, Sehui; Zhou, Qifa; Kim, Jeehyun; Kim, Chulhong

2016-01-01

Since its first implementation in otolaryngological surgery nearly a century ago, the surgical microscope has improved the accuracy and the safety of microsurgeries. However, the microscope shows only a magnified surface view of the surgical region. To overcome this limitation, either optical coherence tomography (OCT) or photoacoustic microscopy (PAM) has been independently combined with conventional surgical microscope. Herein, we present a near-infrared virtual intraoperative photoacoustic optical coherence tomography (NIR-VISPAOCT) system that combines both PAM and OCT with a conventional surgical microscope. Using optical scattering and absorption, the NIR-VISPAOCT system simultaneously provides surgeons with real-time comprehensive biological information such as tumor margins, tissue structure, and a magnified view of the region of interest. Moreover, by utilizing a miniaturized beam projector, it can back-project 2D cross-sectional PAM and OCT images onto the microscopic view plane. In this way, both microscopic and cross-sectional PAM and OCT images are concurrently displayed on the ocular lens of the microscope. To verify the usability of the NIR-VISPAOCT system, we demonstrate simulated surgeries, including in vivo image-guided melanoma resection surgery and in vivo needle injection of carbon particles into a mouse thigh. The proposed NIR-VISPAOCT system has potential applications in neurosurgery, ophthalmological surgery, and other microsurgeries. PMID:27731390

'Blueberry' Triplets Born in Rock

NASA Technical Reports Server (NTRS)

2004-01-01

This microscopic image, taken at the outcrop region dubbed 'Berry Bowl' near the Mars Exploration Rover Opportunity's landing site, shows the sphere-like grains or 'blueberries' that fill Berry Bowl. Of particular interest is the blueberry triplet, which indicates that these geologic features grew in pre-existing wet sediments. Other sphere-like grains that form in the air, such as impact spherules or ejected volcanic material called lapilli, are unlikely to fuse along a line and form triplets. This image was taken by the rover's microscopic imager on the 46th martian day, or sol, of its mission.

Fast and Accurate Cell Tracking by a Novel Optical-Digital Hybrid Method

NASA Astrophysics Data System (ADS)

Torres-Cisneros, M.; Aviña-Cervantes, J. G.; Pérez-Careta, E.; Ambriz-Colín, F.; Tinoco, Verónica; Ibarra-Manzano, O. G.; Plascencia-Mora, H.; Aguilera-Gómez, E.; Ibarra-Manzano, M. A.; Guzman-Cabrera, R.; Debeir, Olivier; Sánchez-Mondragón, J. J.

2013-09-01

An innovative methodology to detect and track cells using microscope images enhanced by optical cross-correlation techniques is proposed in this paper. In order to increase the tracking sensibility, image pre-processing has been implemented as a morphological operator on the microscope image. Results show that the pre-processing process allows for additional frames of cell tracking, therefore increasing its robustness. The proposed methodology can be used in analyzing different problems such as mitosis, cell collisions, and cell overlapping, ultimately designed to identify and treat illnesses and malignancies.

Prototype through-pellicle coherent imaging using a 30nm tabletop EUV source

NASA Astrophysics Data System (ADS)

Bevis, Charles S.; Karl, Robert M.; Wang, Bin; Esashi, Yuka; Tanksalvala, Michael; Porter, Christina L.; Johnsen, Peter; Adams, Daniel E.; Murnane, Margaret M.; Kapteyn, Henry C.

2018-03-01

We present preliminary through-pellicle imaging using a 30nm tabletop extreme ultraviolet (EUV) coherent diffractive imaging microscope. We show that even in a non-optimized setup, this technique enables through-pellicle imaging of a sample with no detectable impact on image fidelity or resolution.

Understanding Imaging and Metrology with the Helium Ion Microscope

NASA Astrophysics Data System (ADS)

Postek, Michael T.; Vladár, András E.; Ming, Bin

2009-09-01

One barrier to innovation confronting all phases of nanotechnology is the lack of accurate metrology for the characterization of nanomaterials. Ultra-high resolution microscopy is a key technology needed to achieve this goal. But, current microscope technology is being pushed to its limits. The scanning and transmission electron microscopes have incrementally improved in performance and other scanned probe technologies such as atomic force microscopy, scanning tunneling microscopy and focused ion beam microscopes have all been applied to nanotechnology with various levels of success. A relatively new tool for nanotechnology is the scanning helium ion microscope (HIM). The HIM is a new complementary imaging and metrology technology for nanotechnology which may be able to push the current resolution barrier lower. But, successful imaging and metrology with this instrument entails new ion beam/specimen interaction physics which must be fully understood. As a new methodology, HIM is beginning to show promise and the abundance of potentially advantageous applications for nanotechnology have yet to be fully exploited. This presentation will discuss some of the progress made at NIST in understanding the science behind this new technique.

Quantitative orientation-independent differential interference contrast (DIC) microscopy

NASA Astrophysics Data System (ADS)

Shribak, Michael; LaFountain, James; Biggs, David; Inoué, Shinya

2007-02-01

We describe a new DIC technique, which records phase gradients within microscopic specimens independently of their orientation. The proposed system allows the generation of images representing the distribution of dry mass (optical path difference) in the specimen. Unlike in other forms of interference microscopes, this approach does not require a narrow illuminating cone. The orientation-independent differential interference contrast (OI-DIC) system can also be combined with orientation-independent polarization (OI-Pol) measurements to yield two complementary images: one showing dry mass distribution (which is proportional to refractive index) and the other showing distribution of birefringence (due to structural or internal anisotropy). With a model specimen used for this work -- living spermatocytes from the crane fly, Nephrotoma suturalis --- the OI-DIC image clearly reveals the detailed shape of the chromosomes while the polarization image quantitatively depicts the distribution of the birefringent microtubules in the spindle, both without any need for staining or other modifications of the cell. We present examples of a pseudo-color combined image incorporating both orientation-independent DIC and polarization images of a spermatocyte at diakinesis and metaphase of meiosis I. Those images provide clear evidence that the proposed technique can reveal fine architecture and molecular organization in live cells without perturbation associated with staining or fluorescent labeling. The phase image was obtained using optics having a numerical aperture 1.4, thus achieving a level of resolution never before achieved with any interference microscope.

Sensing of Streptococcus mutans by microscopic imaging ellipsometry

NASA Astrophysics Data System (ADS)

Khaleel, Mai Ibrahim; Chen, Yu-Da; Chien, Ching-Hang; Chang, Yia-Chung

2017-05-01

Microscopic imaging ellipsometry is an optical technique that uses an objective and sensing procedure to measure the ellipsometric parameters Ψ and Δ in the form of microscopic maps. This technique is well known for being noninvasive and label-free. Therefore, it can be used to detect and characterize biological species without any impact. Microscopic imaging ellipsometry was used to measure the optical response of dried Streptococcus mutans cells on a glass substrate. The ellipsometric Ψ and Δ maps were obtained with the Optrel Multiskop system for specular reflection in the visible range (λ=450 to 750 nm). The Ψ and Δ images at 500, 600, and 700 nm were analyzed using three different theoretical models with single-bounce, two-bounce, and multibounce light paths to obtain the optical constants and height distribution. The obtained images of the optical constants show different aspects when comparing the single-bounce analysis with the two-bounce or multibounce analysis in detecting S. mutans samples. Furthermore, the height distributions estimated by two-bounce and multibounce analyses of S. mutans samples were in agreement with the thickness values measured by AFM, which implies that the two-bounce and multibounce analyses can provide information complementary to that obtained by a single-bounce light path.

Review of current progress in nanometrology with the helium ion microscope

NASA Astrophysics Data System (ADS)

Postek, Michael T.; Vladár, András; Archie, Charles; Ming, Bin

2011-02-01

Scanning electron microscopy has been employed as an imaging and measurement tool for more than 50 years and it continues as a primary tool in many research and manufacturing facilities across the world. A new challenger to this work is the helium ion microscope (HIM). The HIM is a new imaging and metrology technology. Essentially, substitution of the electron source with a helium ion source yields a tool visually similar in function to the scanning electron microscope, but very different in the fundamental imaging and measurement process. The imaged and measured signal originates differently than in the scanning electron microscope and that fact and its single atom source diameter may be able to push the obtainable resolution lower, provide greater depth-of-field and ultimately improve the metrology. Successful imaging and metrology with this instrument entails understanding and modeling of new ion beam/specimen interaction physics. As a new methodology, HIM is beginning to show promise and the abundance of potentially advantageous applications for nanometrology has yet to be fully exploited. This paper discusses some of the progress made at NIST in collaboration with IBM to understand the science behind this new technology.

Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications.

PubMed

Zhang, Yu Shrike; Chang, Jae-Byum; Alvarez, Mario Moisés; Trujillo-de Santiago, Grissel; Aleman, Julio; Batzaya, Byambaa; Krishnadoss, Vaishali; Ramanujam, Aishwarya Aravamudhan; Kazemzadeh-Narbat, Mehdi; Chen, Fei; Tillberg, Paul W; Dokmeci, Mehmet Remzi; Boyden, Edward S; Khademhosseini, Ali

2016-03-15

To date, much effort has been expended on making high-performance microscopes through better instrumentation. Recently, it was discovered that physical magnification of specimens was possible, through a technique called expansion microscopy (ExM), raising the question of whether physical magnification, coupled to inexpensive optics, could together match the performance of high-end optical equipment, at a tiny fraction of the price. Here we show that such "hybrid microscopy" methods--combining physical and optical magnifications--can indeed achieve high performance at low cost. By physically magnifying objects, then imaging them on cheap miniature fluorescence microscopes ("mini-microscopes"), it is possible to image at a resolution comparable to that previously attainable only with benchtop microscopes that present costs orders of magnitude higher. We believe that this unprecedented hybrid technology that combines expansion microscopy, based on physical magnification, and mini-microscopy, relying on conventional optics--a process we refer to as Expansion Mini-Microscopy (ExMM)--is a highly promising alternative method for performing cost-effective, high-resolution imaging of biological samples. With further advancement of the technology, we believe that ExMM will find widespread applications for high-resolution imaging particularly in research and healthcare scenarios in undeveloped countries or remote places.

Distinction between amorphous and healed planar deformation features in shocked quartz using composite color scanning electron microscope cathodoluminescence (SEM-CL) imaging

NASA Astrophysics Data System (ADS)

Hamers, Maartje F.; Pennock, Gill M.; Herwegh, Marco; Drury, Martyn R.

2016-10-01

Planar deformation features (PDFs) in quartz are one of the most reliable and most widely used forms of evidence for hypervelocity impact. PDFs can be identified in scanning electron microscope cathodoluminescence (SEM-CL) images, but not all PDFs show the same CL behavior: there are nonluminescent and red luminescent PDFs. This study aims to explain the origin of the different CL emissions in PDFs. Focused ion beam (FIB) thin foils were prepared of specific sample locations selected in composite color SEM-CL images and were analyzed in a transmission electron microscope (TEM). The FIB preparation technique allowed a direct, often one-to-one correlation between the CL images and the defect structure observed in TEM. This correlation shows that composite color SEM-CL imaging allows distinction between amorphous PDFs on one hand and healed PDFs and basal Brazil twins on the other: nonluminescent PDFs are amorphous, while healed PDFs and basal Brazil twins are red luminescent, with a dominant emission peak at 650 nm. We suggest that the red luminescence is the result of preferential beam damage along dislocations, fluid inclusions, and twin boundaries. Furthermore, a high-pressure phase (possibly stishovite) in PDFs can be detected in color SEM-CL images by its blue luminescence.

A compact CCD-monitored atomic force microscope with optical vision and improved performances.

PubMed

Mingyue, Liu; Haijun, Zhang; Dongxian, Zhang

2013-09-01

A novel CCD-monitored atomic force microscope (AFM) with optical vision and improved performances has been developed. Compact optical paths are specifically devised for both tip-sample microscopic monitoring and cantilever's deflection detecting with minimized volume and optimal light-amplifying ratio. The ingeniously designed AFM probe with such optical paths enables quick and safe tip-sample approaching, convenient and effective tip-sample positioning, and high quality image scanning. An image stitching method is also developed to build a wider-range AFM image under monitoring. Experiments show that this AFM system can offer real-time optical vision for tip-sample monitoring with wide visual field and/or high lateral optical resolution by simply switching the objective; meanwhile, it has the elegant performances of nanometer resolution, high stability, and high scan speed. Furthermore, it is capable of conducting wider-range image measurement while keeping nanometer resolution. Copyright © 2013 Wiley Periodicals, Inc.

Multispectral digital lensless holographic microscopy: from femtosecond laser to white light LED

NASA Astrophysics Data System (ADS)

Garcia-Sucerquia, J.

2015-04-01

The use of femtosecond laser radiation and super bright white LED in digital lensless holographic microscopy is presented. For the ultrafast laser radiation two different configurations of operation of the microscope are presented and the dissimilar performance of each one analyzed. The microscope operating with a super bright white light LED in combination with optical filters shows very competitive performance as it is compared with more expensive optical sources. The broadband emission of both radiation sources allows the multispectral imaging of biological samples to obtain spectral responses and/or full color images of the microscopic specimens; sections of the head of a Drosophila melanogaster fly are imaged in this contribution. The simple, solid, compact, lightweight, and reliable architecture of digital lensless holographic microscopy operating with broadband light sources to image biological specimens exhibiting micrometer-sized details is evaluated in the present contribution.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

2011-06-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

2010-07-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

Quantitative comparison between full-spectrum and filter-based imaging in hyperspectral fluorescence microscopy

PubMed Central

GAO, L.; HAGEN, N.; TKACZYK, T.S.

2012-01-01

Summary We implement a filterless illumination scheme on a hyperspectral fluorescence microscope to achieve full-range spectral imaging. The microscope employs polarisation filtering, spatial filtering and spectral unmixing filtering to replace the role of traditional filters. Quantitative comparisons between full-spectrum and filter-based microscopy are provided in the context of signal dynamic range and accuracy of measured fluorophores’ emission spectra. To show potential applications, a five-colour cell immunofluorescence imaging experiment is theoretically simulated. Simulation results indicate that the use of proposed full-spectrum imaging technique may result in three times improvement in signal dynamic range compared to that can be achieved in the filter-based imaging. PMID:22356127

Hyperlens-array-implemented optical microscopy

NASA Astrophysics Data System (ADS)

Iwanaga, Masanobu

2014-08-01

Limit of resolution of conventional optical microscopes has never reached below 100 nm under visible light illumination. We show that numerically designed high-transmittance hyperlens array (HLA) is implemented in an optical microscope and works in practice for achieving one-shot-recording optical images of in-situ placed objects with sub 50 nm resolution in lateral direction. Direct resolution test employing well-defined nanopatterns proves that the HLA-implemented imaging is super-resolution optical microscopy, which works even under nW/mm2 visible illumination for objects. The HLA implementation makes the resolution of conventional microscopes one-scale higher, leading to the 1/10 illumination wavelength range, that is, mesoscopic range.

[Remote Slit Lamp Microscope Consultation System Based on Web].

PubMed

Chen, Junfa; Zhuo, Yong; Liu, Zuguo; Chen, Yanping

2015-11-01

To realize the remote operation of the slit lamp microscope for department of ophthalmology consultation, and visual display the real-time status of remote slit lamp microscope, a remote slit lamp microscope consultation system based on B/S structure is designed and implemented. Through framing the slit lamp microscope on the website system, the realtime acquisition and transmission of remote control and image data is realized. The three dimensional model of the slit lamp microscope is established and rendered on the web by using WebGL technology. The practical application results can well show the real-time interactive of the remote consultation system.

Ophthalmic applications of confocal microscopy: diagnostics, refractive surgery, and eye banking

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1990-11-01

Confocal microscopy of ocular tissue provides two advantages over traditional imaging techniques: increased range and transverse resolution and increased contrast. The semitransparent cornea and ocular lens in the living eye can be optically sectioned and observed by reflected light confocal microscopy. Within the cornea we observed various cell components nerve fibers nerve cell bodies and fibrous networks. The confocal microscopic images from the in-situ ocular lens show the lens capsule the lens epithelium and the individual lens fibrils. All of the reflected light confocal microscopic images have high contrast and high resolution. Some of the applications of confocal imaging in ophthalmology include: diagnostics of the cornea and the ocular lens examination prior to and after refractive surgery examination of intraocular lenses (IOL) and examination of eye bank material. Other ophthalmic uses of confocal imaging include: studies of wound healing therapeutics and the effects of contact lenses on the cornea. The proposed features of a clinical confocal microscope are reviewed. 2.

Rapid detection of parasite in muscle fibers of fishes using a portable microscope imaging technique (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Jayoung; Lee, Hoonsoo; Kim, Moon S.; Cho, Byoungkwan

2017-05-01

Fishes are a widely used food material in the world. Recently about 4% of the fishes are infected with Kudoa thyrsites in Asian ocean. Kudoa thyrsites is a parasite that is found within the muscle fibers of fishes. The infected fishes can be a reason of food poisoning, which should be sorted out before distribution and consumption. Although Kudoa thyrsites is visible to the naked eye, it could be easily overlooked due to the micro-scale size and similar color with fish tissue. In addition, the visual inspection is labor intensive works resulting in loss of money and time. In this study, a portable microscopic camera was utilized to obtain images of raw fish slices. The optimized image processing techniques with polarized transmittance images provided reliable performance. The result shows that the portable microscopic imaging method can be used to detect parasites rapidly and non-destructively, which could be an alternative to manual inspections.

Grayscale inhomogeneity correction method for multiple mosaicked electron microscope images

NASA Astrophysics Data System (ADS)

Zhou, Fangxu; Chen, Xi; Sun, Rong; Han, Hua

2018-04-01

Electron microscope image stitching is highly desired to acquire microscopic resolution images of large target scenes in neuroscience. However, the result of multiple Mosaicked electron microscope images may exist severe gray scale inhomogeneity due to the instability of the electron microscope system and registration errors, which degrade the visual effect of the mosaicked EM images and aggravate the difficulty of follow-up treatment, such as automatic object recognition. Consequently, the grayscale correction method for multiple mosaicked electron microscope images is indispensable in these areas. Different from most previous grayscale correction methods, this paper designs a grayscale correction process for multiple EM images which tackles the difficulty of the multiple images monochrome correction and achieves the consistency of grayscale in the overlap regions. We adjust overall grayscale of the mosaicked images with the location and grayscale information of manual selected seed images, and then fuse local overlap regions between adjacent images using Poisson image editing. Experimental result demonstrates the effectiveness of our proposed method.

Interior tomography in microscopic CT with image reconstruction constrained by full field of view scan at low spatial resolution

NASA Astrophysics Data System (ADS)

Luo, Shouhua; Shen, Tao; Sun, Yi; Li, Jing; Li, Guang; Tang, Xiangyang

2018-04-01

In high resolution (microscopic) CT applications, the scan field of view should cover the entire specimen or sample to allow complete data acquisition and image reconstruction. However, truncation may occur in projection data and results in artifacts in reconstructed images. In this study, we propose a low resolution image constrained reconstruction algorithm (LRICR) for interior tomography in microscopic CT at high resolution. In general, the multi-resolution acquisition based methods can be employed to solve the data truncation problem if the project data acquired at low resolution are utilized to fill up the truncated projection data acquired at high resolution. However, most existing methods place quite strict restrictions on the data acquisition geometry, which greatly limits their utility in practice. In the proposed LRICR algorithm, full and partial data acquisition (scan) at low and high resolutions, respectively, are carried out. Using the image reconstructed from sparse projection data acquired at low resolution as the prior, a microscopic image at high resolution is reconstructed from the truncated projection data acquired at high resolution. Two synthesized digital phantoms, a raw bamboo culm and a specimen of mouse femur, were utilized to evaluate and verify performance of the proposed LRICR algorithm. Compared with the conventional TV minimization based algorithm and the multi-resolution scout-reconstruction algorithm, the proposed LRICR algorithm shows significant improvement in reduction of the artifacts caused by data truncation, providing a practical solution for high quality and reliable interior tomography in microscopic CT applications. The proposed LRICR algorithm outperforms the multi-resolution scout-reconstruction method and the TV minimization based reconstruction for interior tomography in microscopic CT.

The Tunneling Microscope: A New Look at the Atomic World.

ERIC Educational Resources Information Center

Golovchenko, J. A.

1986-01-01

A new instrument called the tunneling microscope has recently been developed that is capable of generating real-space images of surfaces showing atomic structure. Discusses current capabilities, limitations, and the physics involved in the technique. Includes results from a study of silicon crystal surfaces. (JN)

Noninvasive, label-free, three-dimensional imaging of melanoma with confocal photothermal microscopy: Differentiate malignant melanoma from benign tumor tissue

NASA Astrophysics Data System (ADS)

He, Jinping; Wang, Nan; Tsurui, Hiromichi; Kato, Masashi; Iida, Machiko; Kobayashi, Takayoshi

2016-07-01

Skin cancer is one of the most common cancers. Melanoma accounts for less than 2% of skin cancer cases but causes a large majority of skin cancer deaths. Early detection of malignant melanoma remains the key factor in saving lives. However, the melanoma diagnosis is still clinically challenging. Here, we developed a confocal photothermal microscope for noninvasive, label-free, three-dimensional imaging of melanoma. The axial resolution of confocal photothermal microscope is ~3 times higher than that of commonly used photothermal microscope. Three-dimensional microscopic distribution of melanin in pigmented lesions of mouse skin is obtained directly with this setup. Classic morphometric and fractal analysis of sixteen 3D images (eight for benign melanoma and eight for malignant) showed a capability of pathology of melanoma: melanin density and size become larger during the melanoma growth, and the melanin distribution also becomes more chaotic and unregulated. The results suggested new options for monitoring the melanoma growth and also for the melanoma diagnosis.

RGB digital lensless holographic microscopy

NASA Astrophysics Data System (ADS)

Garcia-Sucerquia, Jorge

2013-11-01

The recent introduction of color digital lensless holographic microscopy (CDLHM) has shown the possibility of imaging microscopic specimens at full color without the need of lenses. Owing to the simplicity, robustness, and compactness of the digital lensless holographic microscopes (DLHM), they have been presented as the ideal candidates to being developed into portable holographic microscopes. However, in the case of CDLHM the utilization of three independent lasers hinders the portability option for this microscope. In this contribution an alternative to reduce the complexity of CDLHM aimed to recover the portability of this microscopy technology is presented. A super-bright white-light light-emitting diode (LED) is spectrally and spatially filtered to produce the needed illumination by CDLHM to work. CDLHM with LED illumination is used to image at full color a section of the head of a drosophila melanogaster fly (fruit fly). The LED-CDLHM method shows the capability of imaging objects of 2μm size in comparison with the micrometer resolution reported for LASER-CDLHM.

Multi-scale image segmentation and numerical modeling in carbonate rocks

NASA Astrophysics Data System (ADS)

Alves, G. C.; Vanorio, T.

2016-12-01

Numerical methods based on computational simulations can be an important tool in estimating physical properties of rocks. These can complement experimental results, especially when time constraints and sample availability are a problem. However, computational models created at different scales can yield conflicting results with respect to the physical laboratory. This problem is exacerbated in carbonate rocks due to their heterogeneity at all scales. We developed a multi-scale approach performing segmentation of the rock images and numerical modeling across several scales, accounting for those heterogeneities. As a first step, we measured the porosity and the elastic properties of a group of carbonate samples with varying micrite content. Then, samples were imaged by Scanning Electron Microscope (SEM) as well as optical microscope at different magnifications. We applied three different image segmentation techniques to create numerical models from the SEM images and performed numerical simulations of the elastic wave-equation. Our results show that a multi-scale approach can efficiently account for micro-porosities in tight micrite-supported samples, yielding acoustic velocities comparable to those obtained experimentally. Nevertheless, in high-porosity samples characterized by larger grain/micrite ratio, results show that SEM scale images tend to overestimate velocities, mostly due to their inability to capture macro- and/or intragranular- porosity. This suggests that, for high-porosity carbonate samples, optical microscope images would be more suited for numerical simulations.

EnLightenment: High resolution smartphone microscopy as an educational and public engagement platform

PubMed Central

Wicks, Laura C.; Cairns, Gemma S.; Melnyk, Jacob; Bryce, Scott; Duncan, Rory R.; Dalgarno, Paul A.

2018-01-01

We developed a simple, cost-effective smartphone microscopy platform for use in educational and public engagement programs. We demonstrated its effectiveness, and potential for citizen science through a national imaging initiative, EnLightenment. The cost effectiveness of the instrument allowed for the program to deliver over 500 microscopes to more than 100 secondary schools throughout Scotland, targeting 1000’s of 12-14 year olds. Through careful, quantified, selection of a high power, low-cost objective lens, our smartphone microscope has an imaging resolution of microns, with a working distance of 3 mm. It is therefore capable of imaging single cells and sub-cellular features, and retains usability for young children. The microscopes were designed in kit form and provided an interdisciplinary educational tool. By providing full lesson plans and support material, we developed a framework to explore optical design, microscope performance, engineering challenges on construction and real-world applications in life sciences, biological imaging, marine biology, art, and technology. A national online imaging competition framed EnLightenment ; with over 500 high quality images submitted of diverse content, spanning multiple disciplines. With examples of cellular and sub-cellular features clearly identifiable in some submissions, we show how young public can use these instruments for research-level imaging applications, and the potential of the instrument for citizen science programs. PMID:29623296

A method for fast automated microscope image stitching.

PubMed

Yang, Fan; Deng, Zhen-Sheng; Fan, Qiu-Hong

2013-05-01

Image stitching is an important technology to produce a panorama or larger image by combining several images with overlapped areas. In many biomedical researches, image stitching is highly desirable to acquire a panoramic image which represents large areas of certain structures or whole sections, while retaining microscopic resolution. In this study, we develop a fast normal light microscope image stitching algorithm based on feature extraction. At first, an algorithm of scale-space reconstruction of speeded-up robust features (SURF) was proposed to extract features from the images to be stitched with a short time and higher repeatability. Then, the histogram equalization (HE) method was employed to preprocess the images to enhance their contrast for extracting more features. Thirdly, the rough overlapping zones of the images preprocessed were calculated by phase correlation, and the improved SURF was used to extract the image features in the rough overlapping areas. Fourthly, the features were corresponded by matching algorithm and the transformation parameters were estimated, then the images were blended seamlessly. Finally, this procedure was applied to stitch normal light microscope images to verify its validity. Our experimental results demonstrate that the improved SURF algorithm is very robust to viewpoint, illumination, blur, rotation and zoom of the images and our method is able to stitch microscope images automatically with high precision and high speed. Also, the method proposed in this paper is applicable to registration and stitching of common images as well as stitching the microscope images in the field of virtual microscope for the purpose of observing, exchanging, saving, and establishing a database of microscope images. Copyright © 2013 Elsevier Ltd. All rights reserved.

Novel snapshot hyperspectral imager for fluorescence imaging

NASA Astrophysics Data System (ADS)

Chandler, Lynn; Chandler, Andrea; Periasamy, Ammasi

2018-02-01

Hyperspectral imaging has emerged as a new technique for the identification and classification of biological tissue1. Benefitting recent developments in sensor technology, the new class of hyperspectral imagers can capture entire hypercubes with single shot operation and it shows great potential for real-time imaging in biomedical sciences. This paper explores the use of a SnapShot imager in fluorescence imaging via microscope for the very first time. Utilizing the latest imaging sensor, the Snapshot imager is both compact and attachable via C-mount to any commercially available light microscope. Using this setup, fluorescence hypercubes of several cells were generated, containing both spatial and spectral information. The fluorescence images were acquired with one shot operation for all the emission range from visible to near infrared (VIS-IR). The paper will present the hypercubes obtained images from example tissues (475-630nm). This study demonstrates the potential of application in cell biology or biomedical applications for real time monitoring.

Microscopic fluorescence spectral analysis of basal cell carcinomas

NASA Astrophysics Data System (ADS)

He, Qingli; Lui, Harvey; Zloty, David; Cowan, Bryce; Warshawski, Larry; McLean, David I.; Zeng, Haishan

2007-05-01

Background and Objectives. Laser-induced autofluorescence (LIAF) is a promising tool for cancer diagnosis. This method is based on the differences in autofluorescence spectra between normal and cancerous tissues, but the underlined mechanisms are not well understood. The objective of this research is to study the microscopic origins and intrinsic fluorescence properties of basal cell carcinoma (BCC) for better understanding of the mechanism of in vivo fluorescence detection and margin delineation of BCCs on skin patients. A home-made micro- spectrophotometer (MSP) system was used to image the fluorophore distribution and to measure the fluorescence spectra of various microscopic structures and regions on frozen tissue sections. Materials and Methods. BCC tissue samples were obtained from 14 patients undergoing surgical resections. After surgical removal, each tissue sample was immediately embedded in OCT medium and snap-frozen in liquid nitrogen. The frozen tissue block was then cut into 16-μm thickness sections using a cryostat microtome and placed on microscopic glass slides. The sections for fluorescence study were kept unstained and unfixed, and then analyzed by the MSP system. The adjacent tissue sections were H&E stained for histopathological examination and also served to help identify various microstructures on the adjacent unstained sections. The MSP system has all the functions of a conventional microscope, plus the ability of performing spectral analysis on selected micro-areas of a microscopic sample. For tissue fluorescence analysis, 442nm He-Cd laser light is used to illuminate and excite the unstained tissue sections. A 473-nm long pass filter was inserted behind the microscope objective to block the transmitted laser light while passing longer wavelength fluorescence signal. The fluorescence image of the sample can be viewed through the eyepieces and also recorded by a CCD camera. An optical fiber is mounted onto the image plane of the photograph port of the microscope to collect light from a specific micro area of the sample. The collected light is transmitted via the fiber to a disperserve type CCD spectrometer for spectral analysis. Results. The measurement results showed significant spectral differences between normal and cancerous tissues. For normal tissue regions, the spectral results agreed with our previous findings on autofluorescence of normal skin sections. For the cancerous regions, the epidermis showed very weak fluorescence signal, while the stratum corneum exhibited fluorescence emissions peaking at about 510 nm. In the dermis, the basal cell island and a band of surrounding areas showed very weak fluorescence signal, while distal dermis above and below the basal cell island showed greater fluorescence signal but with different spectral shapes. The very weak autofluorescence from the basal cell island and its surrounding area may be attributed to their degenerative properties that limited the production of collagens. Conclusions. The obtained microscopic results very well explain the in vivo fluorescence properties of BCC lesions in that they have decreased fluorescence intensity compared to the surrounding normal skin. The intrinsic spectra of various microstructures and the microscopic fluorescence images (corresponding fluorophore distribution in tissue) obtained in this study will be used for further theoretical modeling of in vivo fluorescence spectroscopy and imaging of skin cancers.

Observation of Phase Objects by Using an X-ray Microscope with a Foucault Knife-Edge

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

Watanabe, N.; Sasaya, T.; Imai, Y.

2011-09-09

An x-ray microscope with a zone plate was assembled at the synchrotron radiation source of BL3C, Photon Factory. A Foucault knife-edge was set at the back focal plate of the objective zone plate and phase retrieval was tested by scanning the knife-edge. A preliminary result shows that scanning the knife-edge during exposure was effective for phase retrieval. Phase-contrast tomography was investigated using differential projection images calculated from two Schlieren images with the oppositely oriented knife-edges. Fairly good reconstruction images of polystyrene beads and spores could be obtained.

Mars Life? - Microscopic Tube-like Structures

NASA Image and Video Library

1996-08-09

This high-resolution scanning electron microscope image shows an unusual tube-like structural form that is less than 1/100th the width of a human hair in size found in meteorite ALH84001, a meteorite believed to be of Martian origin. http://photojournal.jpl.nasa.gov/catalog/PIA00288

Differentiating characteristic microstructural features of cancerous tissues using Mueller matrix microscope.

PubMed

Wang, Ye; He, Honghui; Chang, Jintao; Zeng, Nan; Liu, Shaoxiong; Li, Migao; Ma, Hui

2015-12-01

Polarized light imaging can provide rich microstructural information of samples, and has been applied to the detections of various abnormal tissues. In this paper, we report a polarized light microscope based on Mueller matrix imaging by adding the polarization state generator and analyzer (PSG and PSA) to a commercial transmission optical microscope. The maximum errors for the absolute values of Mueller matrix elements are reduced to 0.01 after calibration. This Mueller matrix microscope has been used to examine human cervical and liver cancerous tissues with fibrosis. Images of the transformed Mueller matrix parameters provide quantitative assessment on the characteristic features of the pathological tissues. Contrast mechanism of the experimental results are backed up by Monte Carlo simulations based on the sphere-cylinder birefringence model, which reveal the relationship between the pathological features in the cancerous tissues at the cellular level and the polarization parameters. Both the experimental and simulated data indicate that the microscopic transformed Mueller matrix parameters can distinguish the breaking down of birefringent normal tissues for cervical cancer, or the formation of birefringent surrounding structures accompanying the inflammatory reaction for liver cancer. With its simple structure, fast measurement and high precision, polarized light microscope based on Mueller matrix shows a good diagnosis application prospect. Copyright © 2015 Elsevier Ltd. All rights reserved.

Hyperspectral imaging with laser-scanning sum-frequency generation microscopy

PubMed Central

Hanninen, Adam; Shu, Ming Wai; Potma, Eric O.

2017-01-01

Vibrationally sensitive sum-frequency generation (SFG) microscopy is a chemically selective imaging technique sensitive to non-centrosymmetric molecular arrangements in biological samples. The routine use of SFG microscopy has been hampered by the difficulty of integrating the required mid-infrared excitation light into a conventional, laser-scanning nonlinear optical (NLO) microscope. In this work, we describe minor modifications to a regular laser-scanning microscope to accommodate SFG microscopy as an imaging modality. We achieve vibrationally sensitive SFG imaging of biological samples with sub-μm resolution at image acquisition rates of 1 frame/s, almost two orders of magnitude faster than attained with previous point-scanning SFG microscopes. Using the fast scanning capability, we demonstrate hyperspectral SFG imaging in the CH-stretching vibrational range and point out its use in the study of molecular orientation and arrangement in biologically relevant samples. We also show multimodal imaging by combining SFG microscopy with second-harmonic generation (SHG) and coherent anti-Stokes Raman scattering (CARS) on the same imaging platfrom. This development underlines that SFG microscopy is a unique modality with a spatial resolution and image acquisition time comparable to that of other NLO imaging techniques, making point-scanning SFG microscopy a valuable member of the NLO imaging family. PMID:28966861

ARC-1996-AC96-0345-11

NASA Image and Video Library

1996-10-10

Martian Meteorite (ALH84001): This high resolution transmission electron microscope image is of a cast, or replica, from a chip of a Martian meteorite, labeled ALH84001, that shows the outline of what are believed to be possible microscopic fossils of bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. The tubular features in this image are less than a micrometer in size, or about 1/500th the diameter of a human hair. (JSC ref: S96-12637)

Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

PubMed

Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

2015-01-01

Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Cluster secondary ion mass spectrometry microscope mode mass spectrometry imaging.

PubMed

Kiss, András; Smith, Donald F; Jungmann, Julia H; Heeren, Ron M A

2013-12-30

Microscope mode imaging for secondary ion mass spectrometry is a technique with the promise of simultaneous high spatial resolution and high-speed imaging of biomolecules from complex surfaces. Technological developments such as new position-sensitive detectors, in combination with polyatomic primary ion sources, are required to exploit the full potential of microscope mode mass spectrometry imaging, i.e. to efficiently push the limits of ultra-high spatial resolution, sample throughput and sensitivity. In this work, a C60 primary source was combined with a commercial mass microscope for microscope mode secondary ion mass spectrometry imaging. The detector setup is a pixelated detector from the Medipix/Timepix family with high-voltage post-acceleration capabilities. The system's mass spectral and imaging performance is tested with various benchmark samples and thin tissue sections. The high secondary ion yield (with respect to 'traditional' monatomic primary ion sources) of the C60 primary ion source and the increased sensitivity of the high voltage detector setup improve microscope mode secondary ion mass spectrometry imaging. The analysis time and the signal-to-noise ratio are improved compared with other microscope mode imaging systems, all at high spatial resolution. We have demonstrated the unique capabilities of a C60 ion microscope with a Timepix detector for high spatial resolution microscope mode secondary ion mass spectrometry imaging. Copyright © 2013 John Wiley & Sons, Ltd.

A deep learning framework to discern and count microscopic nematode eggs.

PubMed

Akintayo, Adedotun; Tylka, Gregory L; Singh, Asheesh K; Ganapathysubramanian, Baskar; Singh, Arti; Sarkar, Soumik

2018-06-14

In order to identify and control the menace of destructive pests via microscopic image-based identification state-of-the art deep learning architecture is demonstrated on the parasitic worm, the soybean cyst nematode (SCN), Heterodera glycines. Soybean yield loss is negatively correlated with the density of SCN eggs that are present in the soil. While there has been progress in automating extraction of egg-filled cysts and eggs from soil samples counting SCN eggs obtained from soil samples using computer vision techniques has proven to be an extremely difficult challenge. Here we show that a deep learning architecture developed for rare object identification in clutter-filled images can identify and count the SCN eggs. The architecture is trained with expert-labeled data to effectively build a machine learning model for quantifying SCN eggs via microscopic image analysis. We show dramatic improvements in the quantification time of eggs while maintaining human-level accuracy and avoiding inter-rater and intra-rater variabilities. The nematode eggs are correctly identified even in complex, debris-filled images that are often difficult for experts to identify quickly. Our results illustrate the remarkable promise of applying deep learning approaches to phenotyping for pest assessment and management.

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Mars Life? - Microscopic Egg-shaped Structures

NASA Technical Reports Server (NTRS)

1996-01-01

This electron microscope image shows egg-shaped structures, some of which may be possible microscopic fossils of Martian origin as discussed by NASA research published in the Aug. 16, 1996, issue of the journal Science. A two-year investigation found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller.

Tomographic imaging of transparent biological samples using the pyramid phase microscope

PubMed Central

Iglesias, Ignacio

2016-01-01

We show how a pyramid phase microscope can be used to obtain tomographic information of the spatial variation of refractive index in biological samples using the Radon transform. A method that uses the information provided by the phase microscope for axial and lateral repositioning of the sample when it rotates is also described. Its application to the reconstruction of mouse embryos in the blastocyst stage is demonstrated. PMID:27570696

Physics and engineering aspects of cell and tissue imaging systems: microscopic devices and computer assisted diagnosis.

PubMed

Chen, Xiaodong; Ren, Liqiang; Zheng, Bin; Liu, Hong

2013-01-01

The conventional optical microscopes have been used widely in scientific research and in clinical practice. The modern digital microscopic devices combine the power of optical imaging and computerized analysis, archiving and communication techniques. It has a great potential in pathological examinations for improving the efficiency and accuracy of clinical diagnosis. This chapter reviews the basic optical principles of conventional microscopes, fluorescence microscopes and electron microscopes. The recent developments and future clinical applications of advanced digital microscopic imaging methods and computer assisted diagnosis schemes are also discussed.

Performance evaluation of image segmentation algorithms on microscopic image data.

PubMed

Beneš, Miroslav; Zitová, Barbara

2015-01-01

In our paper, we present a performance evaluation of image segmentation algorithms on microscopic image data. In spite of the existence of many algorithms for image data partitioning, there is no universal and 'the best' method yet. Moreover, images of microscopic samples can be of various character and quality which can negatively influence the performance of image segmentation algorithms. Thus, the issue of selecting suitable method for a given set of image data is of big interest. We carried out a large number of experiments with a variety of segmentation methods to evaluate the behaviour of individual approaches on the testing set of microscopic images (cross-section images taken in three different modalities from the field of art restoration). The segmentation results were assessed by several indices used for measuring the output quality of image segmentation algorithms. In the end, the benefit of segmentation combination approach is studied and applicability of achieved results on another representatives of microscopic data category - biological samples - is shown. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Root dentine and endodontic instrumentation: cutting edge microscopic imaging

PubMed Central

2016-01-01

Cutting of the dental hard tissues is an integral part of restorative dentistry. Cutting of the root dentine is also needed in preparation prior to endodontic treatment, with significant commercial investment for the development of flexible cutting instruments based around nickel titanium (NiTi) alloys. This paper describes the evolution of endodontic cutting instruments, both in materials used, e.g. the transition from stainless steel to NiTi, and the design of the actual instruments themselves and their method of activation—by hand or motor driven. We have been examining tooth-cutting interactions microscopically for over 25 years using a variety of microscopic techniques; in particular, video-rate confocal microscopy. This has given a unique insight into how many of the procedures that we take for granted are achieved in clinical practice, by showing microscopic video images of the cutting as it occurs within the tooth. This technology has now been extended to allow imaging of the endodontic instrument and the root canal wall for the first time. We are able to image dentine distortion and crack propagation during endodontic filing of the root canal space. We are also able to visualize the often claimed, but seldom seen action of contemporary endodontic instruments. PMID:27274802

Root dentine and endodontic instrumentation: cutting edge microscopic imaging.

PubMed

Atmeh, Amre R; Watson, Timothy F

2016-06-06

Cutting of the dental hard tissues is an integral part of restorative dentistry. Cutting of the root dentine is also needed in preparation prior to endodontic treatment, with significant commercial investment for the development of flexible cutting instruments based around nickel titanium (NiTi) alloys. This paper describes the evolution of endodontic cutting instruments, both in materials used, e.g. the transition from stainless steel to NiTi, and the design of the actual instruments themselves and their method of activation-by hand or motor driven. We have been examining tooth-cutting interactions microscopically for over 25 years using a variety of microscopic techniques; in particular, video-rate confocal microscopy. This has given a unique insight into how many of the procedures that we take for granted are achieved in clinical practice, by showing microscopic video images of the cutting as it occurs within the tooth. This technology has now been extended to allow imaging of the endodontic instrument and the root canal wall for the first time. We are able to image dentine distortion and crack propagation during endodontic filing of the root canal space. We are also able to visualize the often claimed, but seldom seen action of contemporary endodontic instruments.

Quantitative Imaging with a Mobile Phone Microscope

PubMed Central

Skandarajah, Arunan; Reber, Clay D.; Switz, Neil A.; Fletcher, Daniel A.

2014-01-01

Use of optical imaging for medical and scientific applications requires accurate quantification of features such as object size, color, and brightness. High pixel density cameras available on modern mobile phones have made photography simple and convenient for consumer applications; however, the camera hardware and software that enables this simplicity can present a barrier to accurate quantification of image data. This issue is exacerbated by automated settings, proprietary image processing algorithms, rapid phone evolution, and the diversity of manufacturers. If mobile phone cameras are to live up to their potential to increase access to healthcare in low-resource settings, limitations of mobile phone–based imaging must be fully understood and addressed with procedures that minimize their effects on image quantification. Here we focus on microscopic optical imaging using a custom mobile phone microscope that is compatible with phones from multiple manufacturers. We demonstrate that quantitative microscopy with micron-scale spatial resolution can be carried out with multiple phones and that image linearity, distortion, and color can be corrected as needed. Using all versions of the iPhone and a selection of Android phones released between 2007 and 2012, we show that phones with greater than 5 MP are capable of nearly diffraction-limited resolution over a broad range of magnifications, including those relevant for single cell imaging. We find that automatic focus, exposure, and color gain standard on mobile phones can degrade image resolution and reduce accuracy of color capture if uncorrected, and we devise procedures to avoid these barriers to quantitative imaging. By accommodating the differences between mobile phone cameras and the scientific cameras, mobile phone microscopes can be reliably used to increase access to quantitative imaging for a variety of medical and scientific applications. PMID:24824072

Automated in-chamber specimen coating for serial block-face electron microscopy.

PubMed

Titze, B; Denk, W

2013-05-01

When imaging insulating specimens in a scanning electron microscope, negative charge accumulates locally ('sample charging'). The resulting electric fields distort signal amplitude, focus and image geometry, which can be avoided by coating the specimen with a conductive film prior to introducing it into the microscope chamber. This, however, is incompatible with serial block-face electron microscopy (SBEM), where imaging and surface removal cycles (by diamond knife or focused ion beam) alternate, with the sample remaining in place. Here we show that coating the sample after each cutting cycle with a 1-2 nm metallic film, using an electron beam evaporator that is integrated into the microscope chamber, eliminates charging effects for both backscattered (BSE) and secondary electron (SE) imaging. The reduction in signal-to-noise ratio (SNR) caused by the film is smaller than that caused by the widely used low-vacuum method. Sample surfaces as large as 12 mm across were coated and imaged without charging effects at beam currents as high as 25 nA. The coatings also enabled the use of beam deceleration for non-conducting samples, leading to substantial SNR gains for BSE contrast. We modified and automated the evaporator to enable the acquisition of SBEM stacks, and demonstrated the acquisition of stacks of over 1000 successive cut/coat/image cycles and of stacks using beam deceleration or SE contrast. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

Microscope basics.

PubMed

Sluder, Greenfield; Nordberg, Joshua J

2013-01-01

This chapter provides information on how microscopes work and discusses some of the microscope issues to be considered in using a video camera on the microscope. There are two types of microscopes in use today for research in cell biology-the older finite tube-length (typically 160mm mechanical tube length) microscopes and the infinity optics microscopes that are now produced. The objective lens forms a magnified, real image of the specimen at a specific distance from the objective known as the intermediate image plane. All objectives are designed to be used with the specimen at a defined distance from the front lens element of the objective (the working distance) so that the image formed is located at a specific location in the microscope. Infinity optics microscopes differ from the finite tube-length microscopes in that the objectives are designed to project the image of the specimen to infinity and do not, on their own, form a real image of the specimen. Three types of objectives are in common use today-plan achromats, plan apochromats, and plan fluorite lenses. The concept of mounting video cameras on the microscope is also presented in the chapter. Copyright © 2003 Elsevier Inc. All rights reserved.

Detection of cervical intraepithelial neoplasia by using optical coherence tomography in combination with microscopy

NASA Astrophysics Data System (ADS)

Gallwas, Julia; Jalilova, Aydan; Ladurner, Roland; Kolben, Theresa Maria; Kolben, Thomas; Ditsch, Nina; Homann, Christian; Lankenau, Eva; Dannecker, Christian

2017-01-01

Optical coherence tomography (OCT) is a noninvasive high-resolution imaging technique that permits the detection of cancerous and precancerous lesions of the uterine cervix. The purpose of this study was to evaluate a new system that integrates an OCT device into a microscope. OCT images were taken from loop electrosurgical excision procedure (LEEP) specimens under microscopic guidance. The images were blinded with respect to their origin within the microscopic image and analyzed independently by two investigators using initially defined criteria and later compared to the corresponding histology. Sensitivity and specificity were calculated with respect to the correct identification of high-grade squamous intraepithelial lesions (HSIL). The interinvestigator agreement was assessed by using Cohen's kappa statistics. About 160 OCT images were obtained from 20 LEEP specimens. Sixty randomly chosen images were used to define reproducible criteria for evaluation. The assessment of the remaining 100 images showed a sensitivity of 88% (second investigator 84%) and a specificity of 69% (65%) in detecting HSIL. Surgical microscopy-guided OCT appears to be a promising technique for immediate assessment of microanatomical changes. In the gynecological setting, the combination of OCT with a colposcope may improve the detection of high-grade squamous intraepithelial lesions.

Color digital lensless holographic microscopy: laser versus LED illumination.

PubMed

Garcia-Sucerquia, Jorge

2016-08-20

A comparison of the performance of color digital lensless holographic microscopy (CDLHM) as utilized for illumination of RGB lasers or a super-bright white-light LED with a set of spectral filters is presented. As the use of lasers in CDLHM conceals the possibility of having a compact, lightweight, portable, and low cost microscope, and additionally the limited available laser radiation wavelengths limit a real multispectral imaging microscope, here we present the use of super-bright white-light LED and spectral filters for illuminating the sample. The performance of RGB laser-CDLHM and LED-CDLHM is evaluated on imaging a section of the head of a Drosophila melanogaster fly. This comparison shows that there is trade-off between the spatial resolution of the microscope and the light sources utilized, which can be understood with regard to the coherence properties of the illuminating light. Despite the smaller spatial coherence features of LED-CDLHM in comparison with laser-CDLHM, the former shows promise as a portable RGB digital lensless holographic microscope that could be extended to other wavelengths by the use of different spectral filters.

Integration of a Spectral Domain Optical Coherence Tomography System into a Surgical Microscope for Intraoperative Imaging

PubMed Central

Ehlers, Justis P.; Tao, Yuankai K.; Farsiu, Sina; Maldonado, Ramiro; Izatt, Joseph A.

2011-01-01

Purpose. To demonstrate an operating microscope-mounted spectral domain optical coherence tomography (MMOCT) system for human retinal and model surgery imaging. Methods. A prototype MMOCT system was developed to interface directly with an ophthalmic surgical microscope, to allow SDOCT imaging during surgical viewing. Nonoperative MMOCT imaging was performed in an Institutional Review Board–approved protocol in four healthy volunteers. The effect of surgical instrument materials on MMOCT imaging was evaluated while performing retinal surface, intraretinal, and subretinal maneuvers in cadaveric porcine eyes. The instruments included forceps, metallic and polyamide subretinal needles, and soft silicone-tipped instruments, with and without diamond dusting. Results. High-resolution images of the human retina were successfully obtained with the MMOCT system. The optical properties of surgical instruments affected the visualization of the instrument and the underlying retina. Metallic instruments (e.g., forceps and needles) showed high reflectivity with total shadowing below the instrument. Polyamide material had a moderate reflectivity with subtotal shadowing. Silicone instrumentation showed moderate reflectivity with minimal shadowing. Summed voxel projection MMOCT images provided clear visualization of the instruments, whereas the B-scans from the volume revealed details of the interactions between the tissues and the instrumentation (e.g., subretinal space cannulation, retinal elevation, or retinal holes). Conclusions. High-quality retinal imaging is feasible with an MMOCT system. Intraoperative imaging with model eyes provides high-resolution depth information including visualization of the instrument and intraoperative tissue manipulation. This study demonstrates a key component of an interactive platform that could provide enhanced information for the vitreoretinal surgeon. PMID:21282565

Integration of a spectral domain optical coherence tomography system into a surgical microscope for intraoperative imaging.

PubMed

Ehlers, Justis P; Tao, Yuankai K; Farsiu, Sina; Maldonado, Ramiro; Izatt, Joseph A; Toth, Cynthia A

2011-05-16

To demonstrate an operating microscope-mounted spectral domain optical coherence tomography (MMOCT) system for human retinal and model surgery imaging. A prototype MMOCT system was developed to interface directly with an ophthalmic surgical microscope, to allow SDOCT imaging during surgical viewing. Nonoperative MMOCT imaging was performed in an Institutional Review Board-approved protocol in four healthy volunteers. The effect of surgical instrument materials on MMOCT imaging was evaluated while performing retinal surface, intraretinal, and subretinal maneuvers in cadaveric porcine eyes. The instruments included forceps, metallic and polyamide subretinal needles, and soft silicone-tipped instruments, with and without diamond dusting. High-resolution images of the human retina were successfully obtained with the MMOCT system. The optical properties of surgical instruments affected the visualization of the instrument and the underlying retina. Metallic instruments (e.g., forceps and needles) showed high reflectivity with total shadowing below the instrument. Polyamide material had a moderate reflectivity with subtotal shadowing. Silicone instrumentation showed moderate reflectivity with minimal shadowing. Summed voxel projection MMOCT images provided clear visualization of the instruments, whereas the B-scans from the volume revealed details of the interactions between the tissues and the instrumentation (e.g., subretinal space cannulation, retinal elevation, or retinal holes). High-quality retinal imaging is feasible with an MMOCT system. Intraoperative imaging with model eyes provides high-resolution depth information including visualization of the instrument and intraoperative tissue manipulation. This study demonstrates a key component of an interactive platform that could provide enhanced information for the vitreoretinal surgeon.

Quantum Cascade Laser-Based Infrared Microscopy for Label-Free and Automated Cancer Classification in Tissue Sections.

PubMed

Kuepper, Claus; Kallenbach-Thieltges, Angela; Juette, Hendrik; Tannapfel, Andrea; Großerueschkamp, Frederik; Gerwert, Klaus

2018-05-16

A feasibility study using a quantum cascade laser-based infrared microscope for the rapid and label-free classification of colorectal cancer tissues is presented. Infrared imaging is a reliable, robust, automated, and operator-independent tissue classification method that has been used for differential classification of tissue thin sections identifying tumorous regions. However, long acquisition time by the so far used FT-IR-based microscopes hampered the clinical translation of this technique. Here, the used quantum cascade laser-based microscope provides now infrared images for precise tissue classification within few minutes. We analyzed 110 patients with UICC-Stage II and III colorectal cancer, showing 96% sensitivity and 100% specificity of this label-free method as compared to histopathology, the gold standard in routine clinical diagnostics. The main hurdle for the clinical translation of IR-Imaging is overcome now by the short acquisition time for high quality diagnostic images, which is in the same time range as frozen sections by pathologists.

Automated detection of analyzable metaphase chromosome cells depicted on scanned digital microscopic images

NASA Astrophysics Data System (ADS)

Qiu, Yuchen; Wang, Xingwei; Chen, Xiaodong; Li, Yuhua; Liu, Hong; Li, Shibo; Zheng, Bin

2010-02-01

Visually searching for analyzable metaphase chromosome cells under microscopes is quite time-consuming and difficult. To improve detection efficiency, consistency, and diagnostic accuracy, an automated microscopic image scanning system was developed and tested to directly acquire digital images with sufficient spatial resolution for clinical diagnosis. A computer-aided detection (CAD) scheme was also developed and integrated into the image scanning system to search for and detect the regions of interest (ROI) that contain analyzable metaphase chromosome cells in the large volume of scanned images acquired from one specimen. Thus, the cytogeneticists only need to observe and interpret the limited number of ROIs. In this study, the high-resolution microscopic image scanning and CAD performance was investigated and evaluated using nine sets of images scanned from either bone marrow (three) or blood (six) specimens for diagnosis of leukemia. The automated CAD-selection results were compared with the visual selection. In the experiment, the cytogeneticists first visually searched for the analyzable metaphase chromosome cells from specimens under microscopes. The specimens were also automated scanned and followed by applying the CAD scheme to detect and save ROIs containing analyzable cells while deleting the others. The automated selected ROIs were then examined by a panel of three cytogeneticists. From the scanned images, CAD selected more analyzable cells than initially visual examinations of the cytogeneticists in both blood and bone marrow specimens. In general, CAD had higher performance in analyzing blood specimens. Even in three bone marrow specimens, CAD selected 50, 22, 9 ROIs, respectively. Except matching with the initially visual selection of 9, 7, and 5 analyzable cells in these three specimens, the cytogeneticists also selected 41, 15 and 4 new analyzable cells, which were missed in initially visual searching. This experiment showed the feasibility of applying this CAD-guided high-resolution microscopic image scanning system to prescreen and select ROIs that may contain analyzable metaphase chromosome cells. The success and the further improvement of this automated scanning system may have great impact on the future clinical practice in genetic laboratories to detect and diagnose diseases.

Real-time Image Processing for Microscopy-based Label-free Imaging Flow Cytometry in a Microfluidic Chip.

PubMed

Heo, Young Jin; Lee, Donghyeon; Kang, Junsu; Lee, Keondo; Chung, Wan Kyun

2017-09-14

Imaging flow cytometry (IFC) is an emerging technology that acquires single-cell images at high-throughput for analysis of a cell population. Rich information that comes from high sensitivity and spatial resolution of a single-cell microscopic image is beneficial for single-cell analysis in various biological applications. In this paper, we present a fast image-processing pipeline (R-MOD: Real-time Moving Object Detector) based on deep learning for high-throughput microscopy-based label-free IFC in a microfluidic chip. The R-MOD pipeline acquires all single-cell images of cells in flow, and identifies the acquired images as a real-time process with minimum hardware that consists of a microscope and a high-speed camera. Experiments show that R-MOD has the fast and reliable accuracy (500 fps and 93.3% mAP), and is expected to be used as a powerful tool for biomedical and clinical applications.

Scanning Probe Platform | Materials Science | NREL

Science.gov Websites

level; this image obtained using a scanning tunneling microscope shows gray and white clusters of produce high-resolution color images or maps like this one obtained using scanning tunneling luminescence gray clusters. Gold substrate: (Left) STM image reveals the terraces of the H2 flamed substrate. (Right

Quantification of incisal tooth wear in upper anterior teeth: conventional vs new method using toolmakers microscope and a three-dimensional measuring technique.

PubMed

Al-Omiri, Mahmoud K; Sghaireen, Mohd G; Alzarea, Bader K; Lynch, Edward

2013-12-01

This study aimed to quantify tooth wear in upper anterior teeth using a new CAD-CAM Laser scanning machine, tool maker microscope and conventional tooth wear index. Fifty participants (25 males and 25 females, mean age = 25 ± 4 years) were assessed for incisal tooth wear of upper anterior teeth using Smith and Knight clinical tooth wear index (TWI) on two occasions, the study baseline and 1 year later. Stone dies for each tooth were prepared and scanned using the CAD-CAM Laser Cercon System. Scanned images were printed and examined under a toolmaker microscope to quantify tooth wear and then the dies were directly assessed under the microscope to measure tooth wear. The Wilcoxon Signed Ranks Test was used to analyze the data. TWI scores for incisal edges were 0-3 and were similar at both occasions. Score 4 was not detected. Wear values measured by directly assessing the dies under the toolmaker microscope (range = 113 - 150 μm, mean = 130 ± 20 μm) were significantly more than those measured from Cercon Digital Machine images (range=52-80 μm, mean = 68 ± 23 μm) and both showed significant differences between the two occasions. Wear progression in upper anterior teeth was effectively detected by directly measuring the dies or the images of dies under toolmaker microscope. Measuring the dies of worn dentition directly under tool maker microscope enabled detection of wear progression more accurately than measuring die images obtained with Cercon Digital Machine. Conventional method was the least sensitive for tooth wear quantification and was unable to identify wear progression in most cases. Copyright © 2013 Elsevier Ltd. All rights reserved.

Real-time restoration of white-light confocal microscope optical sections

PubMed Central

Balasubramanian, Madhusudhanan; Iyengar, S. Sitharama; Beuerman, Roger W.; Reynaud, Juan; Wolenski, Peter

2009-01-01

Confocal microscopes (CM) are routinely used for building 3-D images of microscopic structures. Nonideal imaging conditions in a white-light CM introduce additive noise and blur. The optical section images need to be restored prior to quantitative analysis. We present an adaptive noise filtering technique using Karhunen–Loéve expansion (KLE) by the method of snapshots and a ringing metric to quantify the ringing artifacts introduced in the images restored at various iterations of iterative Lucy–Richardson deconvolution algorithm. The KLE provides a set of basis functions that comprise the optimal linear basis for an ensemble of empirical observations. We show that most of the noise in the scene can be removed by reconstructing the images using the KLE basis vector with the largest eigenvalue. The prefiltering scheme presented is faster and does not require prior knowledge about image noise. Optical sections processed using the KLE prefilter can be restored using a simple inverse restoration algorithm; thus, the methodology is suitable for real-time image restoration applications. The KLE image prefilter outperforms the temporal-average prefilter in restoring CM optical sections. The ringing metric developed uses simple binary morphological operations to quantify the ringing artifacts and confirms with the visual observation of ringing artifacts in the restored images. PMID:20186290

'Stucco' Walls

NASA Technical Reports Server (NTRS)

2004-01-01

This projected mosaic image, taken by the microscopic imager, an instrument located on the Mars Exploration Rover Opportunity 's instrument deployment device, or 'arm,' shows the partial clotting or cement-like properties of the sand-sized grains within the trench wall. The area in this image measures approximately 3 centimeters (1.2 inches) wide and 5 centimeters (2 inches) tall.(This image also appears as an inset on a separate image from the rover's navigation camera, showing the location of this particular spot within the trench wall.)

Berries on the Ground 2 3-D

NASA Image and Video Library

2004-02-12

This 3-D anaglyph, from NASA Mars Exploration Rover Spirit, shows a microscopic image taken of soil featuring round, blueberry-shaped rock formations on the crater floor at Meridiani Planum, Mars. 3D glasses are necessary to view this image.

Two-photon laser scanning microscopy with electrowetting-based prism scanning

PubMed Central

Supekar, Omkar D.; Ozbay, Baris N.; Zohrabi, Mo; Nystrom, Philip D.; Futia, Gregory L.; Restrepo, Diego; Gibson, Emily A.; Gopinath, Juliet T.; Bright, Victor M.

2017-01-01

Laser scanners are an integral part of high resolution biomedical imaging systems such as confocal or 2-photon excitation (2PE) microscopes. In this work, we demonstrate the utility of electrowetting on dielectric (EWOD) prisms as a lateral laser-scanning element integrated in a conventional 2PE microscope. To the best of our knowledge, this is the first such demonstration for EWOD prisms. EWOD devices provide a transmissive, low power consuming, and compact alternative to conventional adaptive optics, and hence this technology has tremendous potential. We demonstrate 2PE microscope imaging of cultured mouse hippocampal neurons with a FOV of 130 × 130 μm2 using EWOD prism scanning. In addition, we show simulations of the optical system with the EWOD prism, to evaluate the effect of propagating a Gaussian beam through the EWOD prism on the imaging quality. Based on the simulation results a beam size of 0.91 mm full width half max was chosen to conduct the imaging experiments, resulting in a numerical aperture of 0.17 of the imaging system. PMID:29296477

Portable smartphone based quantitative phase microscope

NASA Astrophysics Data System (ADS)

Meng, Xin; Tian, Xiaolin; Yu, Wei; Kong, Yan; Jiang, Zhilong; Liu, Fei; Xue, Liang; Liu, Cheng; Wang, Shouyu

2018-01-01

To realize portable device with high contrast imaging capability, we designed a quantitative phase microscope using transport of intensity equation method based on a smartphone. The whole system employs an objective and an eyepiece as imaging system and a cost-effective LED as illumination source. A 3-D printed cradle is used to align these components. Images of different focal planes are captured by manual focusing, followed by calculation of sample phase via a self-developed Android application. To validate its accuracy, we first tested the device by measuring a random phase plate with known phases, and then red blood cell smear, Pap smear, broad bean epidermis sections and monocot root were also measured to show its performance. Owing to its advantages as accuracy, high-contrast, cost-effective and portability, the portable smartphone based quantitative phase microscope is a promising tool which can be future adopted in remote healthcare and medical diagnosis.

Scanning electron microscope cathodoluminescence imaging of subgrain boundaries, twins and planar deformation features in quartz

NASA Astrophysics Data System (ADS)

Hamers, M. F.; Pennock, G. M.; Drury, M. R.

2017-04-01

The study of deformation features has been of great importance to determine deformation mechanisms in quartz. Relevant microstructures in both growth and deformation processes include dislocations, subgrains, subgrain boundaries, Brazil and Dauphiné twins and planar deformation features (PDFs). Dislocations and twin boundaries are most commonly imaged using a transmission electron microscope (TEM), because these cannot directly be observed using light microscopy, in contrast to PDFs. Here, we show that red-filtered cathodoluminescence imaging in a scanning electron microscope (SEM) is a useful method to visualise subgrain boundaries, Brazil and Dauphiné twin boundaries. Because standard petrographic thin sections can be studied in the SEM, the observed structures can be directly and easily correlated to light microscopy studies. In contrast to TEM preparation methods, SEM techniques are non-destructive to the area of interest on a petrographic thin section.

Identification of staphylococcus species with hyperspectral microscope imaging and classification algrorithms

USDA-ARS?s Scientific Manuscript database

Hyperspectral microscope imaging is presented as a rapid and efficient tool to classify foodborne bacteria species. The spectral data were obtained from five different species of Staphylococcus spp. with a hyperspectral microscope imaging system that provided a maximum of 89 contiguous spectral imag...

Recent progress in understanding the imaging and metrology using the helium ion microscope

NASA Astrophysics Data System (ADS)

Postek, Michael T.; Vladar, Andras E.; Ming, Bin

2009-05-01

Nanotechnology is pushing imaging and measurement instrument technology to high levels of required performance. As this continues, new barriers confronting innovation in this field are encountered. Particle beam instrument resolution remains one of these barriers. A new tool for imaging and metrology for nanotechnology is the scanning Helium Ion Microscope (HIM). The HIM is a new approach to imaging and metrology for nanotechnology which may be able to push this barrier lower. As a new methodology, it is just beginning to show promise and the number of potentially advantageous applications for nanotechnology and nanometrology has yet to be fully exploited. This presentation will discuss some of the progress made at NIST in collaboration with the manufacturing community in understanding the imaging and metrology for this new technology.

Design considerations of a real-time clinical confocal microscope

NASA Astrophysics Data System (ADS)

Masters, Barry R.

1991-06-01

A real-time clinical confocal light microscope provides the ophthalmologist with a new tool for the observation of the cornea and the ocular lens. In addition, the ciliary body, the iris, and the sclera can be observed. The real-time light microscopic images have high contrast and resolution. The transverse resolution is about one half micron and the range resolution is one micron. The following observations were made with visible light: corneal epithelial cells, wing cells, basal cells, Bowman's membrane, nerve fibers, basal lamina, fibroblast nuclei, Descemet's membrane, endothelial cells. Observation of the in situ ocular lens showed lens capsule, lens epithelium, lens fibrils, the interior of lens fibrils. The applications of the confocal microscope include: eye banking, laser refractive surgery, observation of wound healing, observation of the iris, the sciera, the ciliary body, the ocular lens, and the intraocular lens. Digital image processing can produce three-dimensional reconstructions of the cornea and the ocular lens.

Non-intrusive practitioner pupil detection for unmodified microscope oculars.

PubMed

Fuhl, Wolfgang; Santini, Thiago; Reichert, Carsten; Claus, Daniel; Herkommer, Alois; Bahmani, Hamed; Rifai, Katharina; Wahl, Siegfried; Kasneci, Enkelejda

2016-12-01

Modern microsurgery is a long and complex task requiring the surgeon to handle multiple microscope controls while performing the surgery. Eye tracking provides an additional means of interaction for the surgeon that could be used to alleviate this situation, diminishing surgeon fatigue and surgery time, thus decreasing risks of infection and human error. In this paper, we introduce a novel algorithm for pupil detection tailored for eye images acquired through an unmodified microscope ocular. The proposed approach, the Hough transform, and six state-of-the-art pupil detection algorithms were evaluated on over 4000 hand-labeled images acquired from a digital operating microscope with a non-intrusive monitoring system for the surgeon eyes integrated. Our results show that the proposed method reaches detection rates up to 71% for an error of ≈3% w.r.t the input image diagonal; none of the state-of-the-art pupil detection algorithms performed satisfactorily. The algorithm and hand-labeled data set can be downloaded at:: www.ti.uni-tuebingen.de/perception. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design of small confocal endo-microscopic probe working under multiwavelength environment

NASA Astrophysics Data System (ADS)

Kim, Young-Duk; Ahn, MyoungKi; Gweon, Dae-Gab

2010-02-01

Recently, optical imaging system is widely used in medical purpose. By using optical imaging system specific diseases can be easily diagnosed at early stage because optical imaging system has high resolution performance and various imaging method. These methods are used to get high resolution image of human body and can be used to verify whether the cell is infected by virus. Confocal microscope is one of the famous imaging systems which is used for in-vivo imaging. Because most of diseases are accompanied with cellular level changes, doctors can diagnosis at early stage by observing the cellular image of human organ. Current research is focused in the development of endo-microscope that has great advantage in accessibility to human body. In this research, I designed small probe that is connected to confocal microscope through optical fiber bundle and work as endo-microscope. And this small probe is mainly designed to correct chromatic aberration to use various laser sources for both fluorescence type and reflection type confocal images. By using two kinds of laser sources at the same time we demonstrated multi-modality confocal endo-microscope.

Simultaneous imaging of cellular morphology and multiple biomarkers using an acousto-optic tunable filter-based bright field microscope.

PubMed

Wachman, Elliot S; Geyer, Stanley J; Recht, Joel M; Ward, Jon; Zhang, Bill; Reed, Murray; Pannell, Chris

2014-05-01

An acousto-optic tunable filter (AOTF)-based multispectral imaging microscope system allows the combination of cellular morphology and multiple biomarker stainings on a single microscope slide. We describe advances in AOTF technology that have greatly improved spectral purity, field uniformity, and image quality. A multispectral imaging bright field microscope using these advances demonstrates pathology results that have great potential for clinical use.

Apertureless near-field/far-field CW two-photon microscope for biological and material imaging and spectroscopic applications.

PubMed

Nowak, Derek B; Lawrence, A J; Sánchez, Erik J

2010-12-10

We present the development of a versatile spectroscopic imaging tool to allow for imaging with single-molecule sensitivity and high spatial resolution. The microscope allows for near-field and subdiffraction-limited far-field imaging by integrating a shear-force microscope on top of a custom inverted microscope design. The instrument has the ability to image in ambient conditions with optical resolutions on the order of tens of nanometers in the near field. A single low-cost computer controls the microscope with a field programmable gate array data acquisition card. High spatial resolution imaging is achieved with an inexpensive CW multiphoton excitation source, using an apertureless probe and simplified optical pathways. The high-resolution, combined with high collection efficiency and single-molecule sensitive optical capabilities of the microscope, are demonstrated with a low-cost CW laser source as well as a mode-locked laser source.

Low-power, low-cost urinalysis system with integrated dipstick evaluation and microscopic analysis.

PubMed

Smith, Gennifer T; Li, Linkai; Zhu, Yue; Bowden, Audrey K

2018-06-21

We introduce a coupled dipstick and microscopy device for analyzing urine samples. The device is capable of accurately assessing urine dipstick results while simultaneously imaging the microscopic contents within the sample. We introduce a long working distance, cellphone-based microscope in combination with an oblique illumination scheme to accurately visualize and quantify particles within the urine sample. To facilitate accurate quantification, we couple the imaging set-up with a power-free filtration system. The proposed device is reusable, low-cost, and requires very little power. We show that results obtained with the proposed device and custom-built app are consistent with those obtained with the standard clinical protocol, suggesting the potential clinical utility of the device.

Near-field microscopy and fluorescence spectroscopy: application to chromosomes labelled with different fluorophores.

PubMed

Mahieu-Williame, L; Falgayrettes, P; Nativel, L; Gall-Borrut, P; Costa, L; Salehzada, T; Bisbal, C

2010-04-01

We have coupled a spectrophotometer with a scanning near-field optical microscope to obtain, with a single scan, simultaneously scanning near-field optical microscope fluorescence images at different wavelengths as well as topography and transmission images. Extraction of the fluorescence spectra enabled us to decompose the different wavelengths of the fluorescence signals which normally overlap. We thus obtained images of the different fluorescence emissions of acridine orange bound to single or double stranded nucleic acids in human metaphase chromosomes before and after DNAse I or RNAse A treatment. The analysis of these images allowed us to visualize some specific chromatin areas where RNA is associated with DNA showing that such a technique could be used to identify multiple components within a cell.

Dark-field imaging based on post-processed electron backscatter diffraction patterns of bulk crystalline materials in a scanning electron microscope.

PubMed

Brodusch, Nicolas; Demers, Hendrix; Gauvin, Raynald

2015-01-01

Dark-field (DF) images were acquired in the scanning electron microscope with an offline procedure based on electron backscatter diffraction (EBSD) patterns (EBSPs). These EBSD-DF images were generated by selecting a particular reflection on the electron backscatter diffraction pattern and by reporting the intensity of one or several pixels around this point at each pixel of the EBSD-DF image. Unlike previous studies, the diffraction information of the sample is the basis of the final image contrast with a pixel scale resolution at the EBSP providing DF imaging in the scanning electron microscope. The offline facility of this technique permits the selection of any diffraction condition available in the diffraction pattern and displaying the corresponding image. The high number of diffraction-based images available allows a better monitoring of deformation structures compared to electron channeling contrast imaging (ECCI) which is generally limited to a few images of the same area. This technique was applied to steel and iron specimens and showed its high capability in describing more rigorously the deformation structures around micro-hardness indents. Due to the offline relation between the reference EBSP and the EBSD-DF images, this new technique will undoubtedly greatly improve our knowledge of deformation mechanism and help to improve our understanding of the ECCI contrast mechanisms. Copyright © 2014 Elsevier B.V. All rights reserved.

Excitation-scanning hyperspectral imaging system for microscopic and endoscopic applications

NASA Astrophysics Data System (ADS)

Mayes, Sam A.; Leavesley, Silas J.; Rich, Thomas C.

2016-04-01

Current microscopic and endoscopic technologies for cancer screening utilize white-light illumination sources. Hyper-spectral imaging has been shown to improve sensitivity while retaining specificity when compared to white-light imaging in both microscopy and in vivo imaging. However, hyperspectral imaging methods have historically suffered from slow acquisition times due to the narrow bandwidth of spectral filters. Often minutes are required to gather a full image stack. We have developed a novel approach called excitation-scanning hyperspectral imaging that provides 2-3 orders of magnitude increased signal strength. This reduces acquisition times significantly, allowing for live video acquisition. Here, we describe a preliminary prototype excitation-scanning hyperspectral imaging system that can be coupled with endoscopes or microscopes for hyperspectral imaging of tissues and cells. Our system is comprised of three subsystems: illumination, transmission, and imaging. The illumination subsystem employs light-emitting diode arrays to illuminate at different wavelengths. The transmission subsystem utilizes a unique geometry of optics and a liquid light guide. Software controls allow us to interface with and control the subsystems and components. Digital and analog signals are used to coordinate wavelength intensity, cycling and camera triggering. Testing of the system shows it can cycle 16 wavelengths at as fast as 1 ms per cycle. Additionally, more than 18% of the light transmits through the system. Our setup should allow for hyperspectral imaging of tissue and cells in real time.

Image Quality Ranking Method for Microscopy

PubMed Central

Koho, Sami; Fazeli, Elnaz; Eriksson, John E.; Hänninen, Pekka E.

2016-01-01

Automated analysis of microscope images is necessitated by the increased need for high-resolution follow up of events in time. Manually finding the right images to be analyzed, or eliminated from data analysis are common day-to-day problems in microscopy research today, and the constantly growing size of image datasets does not help the matter. We propose a simple method and a software tool for sorting images within a dataset, according to their relative quality. We demonstrate the applicability of our method in finding good quality images in a STED microscope sample preparation optimization image dataset. The results are validated by comparisons to subjective opinion scores, as well as five state-of-the-art blind image quality assessment methods. We also show how our method can be applied to eliminate useless out-of-focus images in a High-Content-Screening experiment. We further evaluate the ability of our image quality ranking method to detect out-of-focus images, by extensive simulations, and by comparing its performance against previously published, well-established microscopy autofocus metrics. PMID:27364703

New deconvolution method for microscopic images based on the continuous Gaussian radial basis function interpolation model.

PubMed

Chen, Zhaoxue; Chen, Hao

2014-01-01

A deconvolution method based on the Gaussian radial basis function (GRBF) interpolation is proposed. Both the original image and Gaussian point spread function are expressed as the same continuous GRBF model, thus image degradation is simplified as convolution of two continuous Gaussian functions, and image deconvolution is converted to calculate the weighted coefficients of two-dimensional control points. Compared with Wiener filter and Lucy-Richardson algorithm, the GRBF method has an obvious advantage in the quality of restored images. In order to overcome such a defect of long-time computing, the method of graphic processing unit multithreading or increasing space interval of control points is adopted, respectively, to speed up the implementation of GRBF method. The experiments show that based on the continuous GRBF model, the image deconvolution can be efficiently implemented by the method, which also has a considerable reference value for the study of three-dimensional microscopic image deconvolution.

A Comparative Study of Microscopic Images Captured by a Box Type Digital Camera Versus a Standard Microscopic Photography Camera Unit

PubMed Central

Desai, Nandini J.; Gupta, B. D.; Patel, Pratik Narendrabhai

2014-01-01

Introduction: Obtaining images of slides viewed by a microscope can be invaluable for both diagnosis and teaching.They can be transferred among technologically-advanced hospitals for further consultation and evaluation. But a standard microscopic photography camera unit (MPCU)(MIPS-Microscopic Image projection System) is costly and not available in resource poor settings. The aim of our endeavour was to find a comparable and cheaper alternative method for photomicrography. Materials and Methods: We used a NIKON Coolpix S6150 camera (box type digital camera) with Olympus CH20i microscope and a fluorescent microscope for the purpose of this study. Results: We got comparable results for capturing images of light microscopy, but the results were not as satisfactory for fluorescent microscopy. Conclusion: A box type digital camera is a comparable, less expensive and convenient alternative to microscopic photography camera unit. PMID:25478350

Coating on Rock Beside a Young Martian Crater

NASA Image and Video Library

2010-03-24

This image from the microscopic imager on NASA Mars Exploration Rover Opportunity shows details of the coating on a rock called Chocolate Hills, which the rover found and examined at the edge of a young crater called Concepción.

Magnetic domain observation of FeCo thin films fabricated by alternate monoatomic layer deposition

NASA Astrophysics Data System (ADS)

Ohtsuki, T.; Kojima, T.; Kotsugi, M.; Ohkochi, T.; Mizuguchi, M.; Takanashi, K.

2014-01-01

FeCo thin films are fabricated by alternate monoatomic layer deposition method on a Cu3Au buffer layer, which in-plane lattice constant is very close to the predicted value to obtain a large magnetic anisotropy constant. The variation of the in-plane lattice constant during the deposition process is investigated by reflection high-energy electron diffraction. The magnetic domain images are also observed by a photoelectron emission microscope in order to microscopically understand the magnetic structure. As a result, element-specific magnetic domain images show that Fe and Co magnetic moments align parallel. A series of images obtained with various azimuth reveal that the FeCo thin films show fourfold in-plane magnetic anisotropy along ⟨110⟩ direction, and that the magnetic domain structure is composed only of 90∘ wall.

Characterizing the surface roughness of thermomechanical pulp fibers with atomic force microscopy

Treesearch

Rebecca Snell; Leslie H. Groom; Timothy G. Rials

2001-01-01

Loblolly pine, separated into mature and juvenile portions, was refined at various pressures (4, 8 and 12 bar). Fiber surfaces were investigated using a Scanning Electron Microscope (SEM) and an Atomic Force Microscope (AFM). Refiner pressure had a significant effect on the fiber surefaces. SEM images showed an apparent increase in surface roughness with increased...

DotLens smartphone microscopy for biological and biomedical applications (Conference Presentation)

NASA Astrophysics Data System (ADS)

Sung, Yu-Lung; Zhao, Fusheng; Shih, Wei-Chuan

2017-02-01

Recent advances in inkjet-printed optics have created a new class of lens fabrication technique. Lenses with a tunable geometry, magnification, and focal length can be fabricated by dispensing controlled amounts of liquid polymer onto a heated surface. This fabrication technique is highly cost-effective, and can achieve optically smooth surface finish. Dubbed DotLens, a single of which weighs less than 50 mg and occupies a volume less than 50 μL. DotLens can be attached onto any smartphone camera akin to a contact lens, and enable smartphones to obtain image resolution as fine as 1 µm. The surface curvature modifies the optical path of light to the image sensor, and enables the camera to focus as close as 2 mm. This enables microscopic imaging on a smartphone without any additional attachments, and has shown great potential in mobile point-of-care diagnostic systems, particularly for histology of tissue sections and cytology of blood cells. DotLens Smartphone Microscopy represents an innovative approach fundamentally different from other smartphone microscopes. In this paper, we describe the application and performance of DotLens smartphone microscopy in biological and biomedical research. In particular, we show recent results from images collected from pathology tissue slides with cancer features. In addition, we show performance in cytological analysis of blood smear. This tool has empowered Citizen Science investigators to collect microscopic images from various interesting objects.

Images from Phoenix's MECA Instruments

NASA Technical Reports Server (NTRS)

2008-01-01

The image on the upper left is from NASA's Phoenix Mars Lander's Optical Microscope after a sample informally called 'Sorceress' was delivered to its silicon substrate on the 38th Martian day, or sol, of the mission (July 2, 2008).

A 3D representation of the same sample is on the right, as seen by Phoenix's Atomic Force Microscope. This is 200 times greater magnification than the view from the Optical Microscope, and the most highly magnified image ever seen from another world.

The image shows four round pits, only 5 microns in depth, that were micromachined into the silicon substrate, which is the background plane shown in red. This image has been processed to reflect the levelness of the substrate.

A Martian particle only one micrometer, or one millionth of a meter, across is held in the upper left pit.

The rounded particle shown at the highest magnification ever seen from another world is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

The Optical Microscope and the Atomic Force Microscope are part of Phoenix's Microscopy, Electrochemistry and Conductivity Analyzer instrument.

The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

Grinding 'Grindstone'

NASA Technical Reports Server (NTRS)

2004-01-01

This image taken by the Mars Exploration Rover Opportunity shows a target dubbed 'Grindstone' on a rock called 'Manitoba' in 'Endurance Crater.' Opportunity dug a hole into the target with its rock abrasion tool, then captured this picture with its microscopic imager on sol 152 (June 28, 2004). The image mosaic is about 6 centimeters (2.4 inches) across.

Optical Scatter Imaging with a digital micromirror device.

PubMed

Zheng, Jing-Yi; Pasternack, Robert M; Boustany, Nada N

2009-10-26

We had developed Optical Scatter Imaging (OSI) as a method which combines light scattering spectroscopy with microscopic imaging to probe local particle size in situ. Using a variable diameter iris as a Fourier spatial filter, the technique consisted of collecting images that encoded the intensity ratio of wide-to-narrow angle scatter at each pixel in the full field of view. In this paper, we replace the variable diameter Fourier filter with a digital micromirror device (DMD) to extend our assessment of morphology to the characterization of particle shape and orientation. We describe our setup in detail and demonstrate how to eliminate aberrations associated with the placement of the DMD in a conjugate Fourier plane of our microscopic imaging system. Using bacteria and polystyrene spheres, we show how this system can be used to assess particle aspect ratio even when imaged at low resolution. We also show the feasibility of detecting alterations in organelle aspect ratio in situ within living cells. This improved OSI system could be further developed to automate morphological quantification and sorting of non-spherical particles in situ.

Scanning Microscopes Using X Rays and Microchannels

NASA Technical Reports Server (NTRS)

Wang, Yu

2003-01-01

Scanning microscopes that would be based on microchannel filters and advanced electronic image sensors and that utilize x-ray illumination have been proposed. Because the finest resolution attainable in a microscope is determined by the wavelength of the illumination, the xray illumination in the proposed microscopes would make it possible, in principle, to achieve resolutions of the order of nanometers about a thousand times as fine as the resolution of a visible-light microscope. Heretofore, it has been necessary to use scanning electron microscopes to obtain such fine resolution. In comparison with scanning electron microscopes, the proposed microscopes would likely be smaller, less massive, and less expensive. Moreover, unlike in scanning electron microscopes, it would not be necessary to place specimens under vacuum. The proposed microscopes are closely related to the ones described in several prior NASA Tech Briefs articles; namely, Miniature Microscope Without Lenses (NPO-20218), NASA Tech Briefs, Vol. 22, No. 8 (August 1998), page 43; and Reflective Variants of Miniature Microscope Without Lenses (NPO-20610), NASA Tech Briefs, Vol. 26, No. 9 (September 2002) page 6a. In all of these microscopes, the basic principle of design and operation is the same: The focusing optics of a conventional visible-light microscope are replaced by a combination of a microchannel filter and a charge-coupled-device (CCD) image detector. A microchannel plate containing parallel, microscopic-cross-section holes much longer than they are wide is placed between a specimen and an image sensor, which is typically the CCD. The microchannel plate must be made of a material that absorbs the illuminating radiation reflected or scattered from the specimen. The microchannels must be positioned and dimensioned so that each one is registered with a pixel on the image sensor. Because most of the radiation incident on the microchannel walls becomes absorbed, the radiation that reaches the image sensor consists predominantly of radiation that was launched along the longitudinal direction of the microchannels. Therefore, most of the radiation arriving at each pixel on the sensor must have traveled along a straight line from a corresponding location on the specimen. Thus, there is a one-to-one mapping from a point on a specimen to a pixel in the image sensor, so that the output of the image sensor contains image information equivalent to that from a microscope.

Emulation of anamorphic imaging on the SHARP extreme ultraviolet mask microscope

DOE PAGES

Benk, Markus P.; Wojdyla, Antoine; Chao, Weilun; ...

2016-07-12

The SHARP high-numerical aperture actinic reticle review project is a synchrotron-based, extreme ultraviolet (EUV) microscope dedicated to photomask research. SHARP emulates the illumination and imaging conditions of current EUV lithography scanners and those several generations into the future. An anamorphic imaging optic with increased mask-side numerical aperture (NA) in the horizontal and increased demagnification in the vertical direction has been proposed in this paper to overcome limitations of current multilayer coatings and extend EUV lithography beyond 0.33 NA. Zoneplate lenses with an anamorphic 4×/8× NA of 0.55 are fabricated and installed in the SHARP microscope to emulate anamorphic imaging. SHARP’smore » Fourier synthesis illuminator with a range of angles exceeding the collected solid angle of the newly designed elliptical zoneplates can produce arbitrary angular source spectra matched to anamorphic imaging. A target with anamorphic dense features down to 50-nm critical dimension is fabricated using 40 nm of nickel as the absorber. In a demonstration experiment, anamorphic imaging at 0.55 4×/8× NA and 6 deg central ray angle (CRA) is compared with conventional imaging at 0.5 4× NA and 8 deg CRA. A significant contrast loss in horizontal features is observed in the conventional images. Finally, the anamorphic images show the same image quality in the horizontal and vertical directions.« less

Emulation of anamorphic imaging on the SHARP extreme ultraviolet mask microscope

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

Benk, Markus P.; Wojdyla, Antoine; Chao, Weilun

The SHARP high-numerical aperture actinic reticle review project is a synchrotron-based, extreme ultraviolet (EUV) microscope dedicated to photomask research. SHARP emulates the illumination and imaging conditions of current EUV lithography scanners and those several generations into the future. An anamorphic imaging optic with increased mask-side numerical aperture (NA) in the horizontal and increased demagnification in the vertical direction has been proposed in this paper to overcome limitations of current multilayer coatings and extend EUV lithography beyond 0.33 NA. Zoneplate lenses with an anamorphic 4×/8× NA of 0.55 are fabricated and installed in the SHARP microscope to emulate anamorphic imaging. SHARP’smore » Fourier synthesis illuminator with a range of angles exceeding the collected solid angle of the newly designed elliptical zoneplates can produce arbitrary angular source spectra matched to anamorphic imaging. A target with anamorphic dense features down to 50-nm critical dimension is fabricated using 40 nm of nickel as the absorber. In a demonstration experiment, anamorphic imaging at 0.55 4×/8× NA and 6 deg central ray angle (CRA) is compared with conventional imaging at 0.5 4× NA and 8 deg CRA. A significant contrast loss in horizontal features is observed in the conventional images. Finally, the anamorphic images show the same image quality in the horizontal and vertical directions.« less

Design of a normal incidence multilayer imaging X-ray microscope

NASA Astrophysics Data System (ADS)

Shealy, David L.; Gabardi, David R.; Hoover, Richard B.; Walker, Arthur B. C., Jr.; Lindblom, Joakim F.

Normal incidence multilayer Cassegrain X-ray telescopes were flown on the Stanford/MSFC Rocket X-ray Spectroheliograph. These instruments produced high spatial resolution images of the sun and conclusively demonstrated that doubly reflecting multilayer X-ray optical systems are feasible. The images indicated that aplanatic imaging soft X-ray/EUV microscopes should be achievable using multilayer optics technology. A doubly reflecting normal incidence multilayer imaging X-ray microscope based on the Schwarzschild configuration has been designed. The design of the microscope and the results of the optical system ray trace analysis are discussed. High resolution aplanatic imaging X-ray microscopes using normal incidence multilayer X-ray mirrors should have many important applications in advanced X-ray astronomical instrumentation, X-ray lithography, biological, biomedical, metallurgical, and laser fusion research.

Method for stitching microbial images using a neural network

NASA Astrophysics Data System (ADS)

Semenishchev, E. A.; Voronin, V. V.; Marchuk, V. I.; Tolstova, I. V.

2017-05-01

Currently an analog microscope has a wide distribution in the following fields: medicine, animal husbandry, monitoring technological objects, oceanography, agriculture and others. Automatic method is preferred because it will greatly reduce the work involved. Stepper motors are used to move the microscope slide and allow to adjust the focus in semi-automatic or automatic mode view with transfer images of microbiological objects from the eyepiece of the microscope to the computer screen. Scene analysis allows to locate regions with pronounced abnormalities for focusing specialist attention. This paper considers the method for stitching microbial images, obtained of semi-automatic microscope. The method allows to keep the boundaries of objects located in the area of capturing optical systems. Objects searching are based on the analysis of the data located in the area of the camera view. We propose to use a neural network for the boundaries searching. The stitching image boundary is held of the analysis borders of the objects. To auto focus, we use the criterion of the minimum thickness of the line boundaries of object. Analysis produced the object located in the focal axis of the camera. We use method of recovery of objects borders and projective transform for the boundary of objects which are based on shifted relative to the focal axis. Several examples considered in this paper show the effectiveness of the proposed approach on several test images.

Variable-focus microscopy and UV surface dissolution imaging as complementary techniques in intrinsic dissolution rate determination.

PubMed

Ward, Adam; Walton, Karl; Box, Karl; Østergaard, Jesper; Gillie, Lisa J; Conway, Barbara R; Asare-Addo, Kofi

2017-09-15

This work reports a novel approach to the assessment of the surface properties of compacts used in Surface Dissolution Imaging (SDI). SDI is useful for determining intrinsic dissolution rate (IDR), an important parameter in early stage drug development. Surface topography, post-compaction and post-SDI run, have been measured using a non-contact, optical, three-dimensional microscope based on focus variation, the Alicona Infinite Focus Microscope, with the aim of correlating the IDRs to the surface properties. Ibuprofen (IBU) was used as a model poorly-soluble drug. DSC and XRD were used to monitor possible polymorphic changes that may have occurred post-compaction and post-SDI run. IBUs IDR decreased from 0.033mg/min/cm 2 to 0.022mg/min/cm 2 from 10 to 20min, respectively, during the experiment. XRD and DSC showed no form changes during the SDI run. The surface topography images showed that a distinct imprint was embossed on the surfaces of some compacts which could affect IDRs. Surface parameter values were associated with the SDI experiments which showed strong correlations with the IDR values. The variable-focus microscope can be used as a complimentary tool in the determination of IDR values from the SDI. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Automatic Focus Adjustment of a Microscope

NASA Technical Reports Server (NTRS)

Huntsberger, Terrance

2005-01-01

AUTOFOCUS is a computer program for use in a control system that automatically adjusts the position of an instrument arm that carries a microscope equipped with an electronic camera. In the original intended application of AUTOFOCUS, the imaging microscope would be carried by an exploratory robotic vehicle on a remote planet, but AUTOFOCUS could also be adapted to similar applications on Earth. Initially control software other than AUTOFOCUS brings the microscope to a position above a target to be imaged. Then the instrument arm is moved to lower the microscope toward the target: nominally, the target is approached from a starting distance of 3 cm in 10 steps of 3 mm each. After each step, the image in the camera is subjected to a wavelet transform, which is used to evaluate the texture in the image at multiple scales to determine whether and by how much the microscope is approaching focus. A focus measure is derived from the transform and used to guide the arm to bring the microscope to the focal height. When the analysis reveals that the microscope is in focus, image data are recorded and transmitted.

Segmentation of White Blood Cells From Microscopic Images Using a Novel Combination of K-Means Clustering and Modified Watershed Algorithm.

PubMed

Ghane, Narjes; Vard, Alireza; Talebi, Ardeshir; Nematollahy, Pardis

2017-01-01

Recognition of white blood cells (WBCs) is the first step to diagnose some particular diseases such as acquired immune deficiency syndrome, leukemia, and other blood-related diseases that are usually done by pathologists using an optical microscope. This process is time-consuming, extremely tedious, and expensive and needs experienced experts in this field. Thus, a computer-aided diagnosis system that assists pathologists in the diagnostic process can be so effective. Segmentation of WBCs is usually a first step in developing a computer-aided diagnosis system. The main purpose of this paper is to segment WBCs from microscopic images. For this purpose, we present a novel combination of thresholding, k-means clustering, and modified watershed algorithms in three stages including (1) segmentation of WBCs from a microscopic image, (2) extraction of nuclei from cell's image, and (3) separation of overlapping cells and nuclei. The evaluation results of the proposed method show that similarity measures, precision, and sensitivity respectively were 92.07, 96.07, and 94.30% for nucleus segmentation and 92.93, 97.41, and 93.78% for cell segmentation. In addition, statistical analysis presents high similarity between manual segmentation and the results obtained by the proposed method.

Smartphone adapters for digital photomicrography.

PubMed

Roy, Somak; Pantanowitz, Liron; Amin, Milon; Seethala, Raja R; Ishtiaque, Ahmed; Yousem, Samuel A; Parwani, Anil V; Cucoranu, Ioan; Hartman, Douglas J

2014-01-01

Photomicrographs in Anatomic Pathology provide a means of quickly sharing information from a glass slide for consultation, education, documentation and publication. While static image acquisition historically involved the use of a permanently mounted camera unit on a microscope, such cameras may be expensive, need to be connected to a computer, and often require proprietary software to acquire and process images. Another novel approach for capturing digital microscopic images is to use smartphones coupled with the eyepiece of a microscope. Recently, several smartphone adapters have emerged that allow users to attach mobile phones to the microscope. The aim of this study was to test the utility of these various smartphone adapters. We surveyed the market for adapters to attach smartphones to the ocular lens of a conventional light microscope. Three adapters (Magnifi, Skylight and Snapzoom) were tested. We assessed the designs of these adapters and their effectiveness at acquiring static microscopic digital images. All adapters facilitated the acquisition of digital microscopic images with a smartphone. The optimal adapter was dependent on the type of phone used. The Magnifi adapters for iPhone were incompatible when using a protective case. The Snapzoom adapter was easiest to use with iPhones and other smartphones even with protective cases. Smartphone adapters are inexpensive and easy to use for acquiring digital microscopic images. However, they require some adjustment by the user in order to optimize focus and obtain good quality images. Smartphone microscope adapters provide an economically feasible method of acquiring and sharing digital pathology photomicrographs.

A light field microscope imaging spectrometer based on the microlens array

NASA Astrophysics Data System (ADS)

Yao, Yu-jia; Xu, Feng; Xia, Yin-xiang

2017-10-01

A new light field spectrometry microscope imaging system, which was composed by microscope objective, microlens array and spectrometry system was designed in this paper. 5-D information (4-D light field and 1-D spectrometer) of the sample could be captured by the snapshot system in only one exposure, avoiding the motion blur and aberration caused by the scanning imaging process of the traditional imaging spectrometry. Microscope objective had been used as the former group while microlens array used as the posterior group. The optical design of the system was simulated by Zemax, the parameter matching condition between microscope objective and microlens array was discussed significantly during the simulation process. The result simulated in the image plane was analyzed and discussed.

Region-based multifocus image fusion for the precise acquisition of Pap smear images.

PubMed

Tello-Mijares, Santiago; Bescós, Jesús

2018-05-01

A multifocus image fusion method to obtain a single focused image from a sequence of microscopic high-magnification Papanicolau source (Pap smear) images is presented. These images, captured each in a different position of the microscope lens, frequently show partially focused cells or parts of cells, which makes them unpractical for the direct application of image analysis techniques. The proposed method obtains a focused image with a high preservation of original pixels information while achieving a negligible visibility of the fusion artifacts. The method starts by identifying the best-focused image of the sequence; then, it performs a mean-shift segmentation over this image; the focus level of the segmented regions is evaluated in all the images of the sequence, and best-focused regions are merged in a single combined image; finally, this image is processed with an adaptive artifact removal process. The combination of a region-oriented approach, instead of block-based approaches, and a minimum modification of the value of focused pixels in the original images achieve a highly contrasted image with no visible artifacts, which makes this method especially convenient for the medical imaging domain. The proposed method is compared with several state-of-the-art alternatives over a representative dataset. The experimental results show that our proposal obtains the best and more stable quality indicators. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

4D microscope-integrated OCT improves accuracy of ophthalmic surgical maneuvers

NASA Astrophysics Data System (ADS)

Carrasco-Zevallos, Oscar; Keller, Brenton; Viehland, Christian; Shen, Liangbo; Todorich, Bozho; Shieh, Christine; Kuo, Anthony; Toth, Cynthia; Izatt, Joseph A.

2016-03-01

Ophthalmic surgeons manipulate micron-scale tissues using stereopsis through an operating microscope and instrument shadowing for depth perception. While ophthalmic microsurgery has benefitted from rapid advances in instrumentation and techniques, the basic principles of the stereo operating microscope have not changed since the 1930's. Optical Coherence Tomography (OCT) has revolutionized ophthalmic imaging and is now the gold standard for preoperative and postoperative evaluation of most retinal and many corneal procedures. We and others have developed initial microscope-integrated OCT (MIOCT) systems for concurrent OCT and operating microscope imaging, but these are limited to 2D real-time imaging and require offline post-processing for 3D rendering and visualization. Our previously presented 4D MIOCT system can record and display the 3D surgical field stereoscopically through the microscope oculars using a dual-channel heads-up display (HUD) at up to 10 micron-scale volumes per second. In this work, we show that 4D MIOCT guidance improves the accuracy of depth-based microsurgical maneuvers (with statistical significance) in mock surgery trials in a wet lab environment. Additionally, 4D MIOCT was successfully performed in 38/45 (84%) posterior and 14/14 (100%) anterior eye human surgeries, and revealed previously unrecognized lesions that were invisible through the operating microscope. These lesions, such as residual and potentially damaging retinal deformation during pathologic membrane peeling, were visualized in real-time by the surgeon. Our integrated system provides an enhanced 4D surgical visualization platform that can improve current ophthalmic surgical practice and may help develop and refine future microsurgical techniques.

Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials

DOE PAGES

Du, Ming; Jacobsen, Chris

2017-10-07

Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zeromore » loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 mu m (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Lastly, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.« less

Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials

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

Du, Ming; Jacobsen, Chris

Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zeromore » loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 mu m (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Lastly, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified.« less

Eight-channel Kirkpatrick-Baez microscope for multiframe x-ray imaging diagnostics in laser plasma experiments.

PubMed

Yi, Shengzhen; Zhang, Zhe; Huang, Qiushi; Zhang, Zhong; Mu, Baozhong; Wang, Zhanshan; Fang, Zhiheng; Wang, Wei; Fu, Sizu

2016-10-01

Because grazing-incidence Kirkpatrick-Baez (KB) microscopes have better resolution and collection efficiency than pinhole cameras, they have been widely used for x-ray imaging diagnostics of laser inertial confinement fusion. The assembly and adjustment of a multichannel KB microscope must meet stringent requirements for image resolution and reproducible alignment. In the present study, an eight-channel KB microscope was developed for diagnostics by imaging self-emission x-rays with a framing camera at the Shenguang-II Update (SGII-Update) laser facility. A consistent object field of view is ensured in the eight channels using an assembly method based on conical reference cones, which also allow the intervals between the eight images to be tuned to couple with the microstrips of the x-ray framing camera. The eight-channel KB microscope was adjusted via real-time x-ray imaging experiments in the laboratory. This paper describes the details of the eight-channel KB microscope, its optical and multilayer design, the assembly and alignment methods, and results of imaging in the laboratory and at the SGII-Update.

Microscope-integrated optical coherence tomography for image-aided positioning of glaucoma surgery

NASA Astrophysics Data System (ADS)

Li, Xiqi; Wei, Ling; Dong, Xuechuan; Huang, Ping; Zhang, Chun; He, Yi; Shi, Guohua; Zhang, Yudong

2015-07-01

Most glaucoma surgeries involve creating new aqueous outflow pathways with the use of a small surgical instrument. This article reported a microscope-integrated, real-time, high-speed, swept-source optical coherence tomography system (SS-OCT) with a 1310-nm light source for glaucoma surgery. A special mechanism was designed to produce an adjustable system suitable for use in surgery. A two-graphic processing unit architecture was used to speed up the data processing and real-time volumetric rendering. The position of the surgical instrument can be monitored and measured using the microscope and a grid-inserted image of the SS-OCT. Finally, experiments were simulated to assess the effectiveness of this integrated system. Experimental results show that this system is a suitable positioning tool for glaucoma surgery.

Flexible conformable hydrophobized surfaces for turbulent flow drag reduction

NASA Astrophysics Data System (ADS)

Brennan, Joseph C.; Geraldi, Nicasio R.; Morris, Robert H.; Fairhurst, David J.; McHale, Glen; Newton, Michael I.

2015-05-01

In recent years extensive work has been focused onto using superhydrophobic surfaces for drag reduction applications. Superhydrophobic surfaces retain a gas layer, called a plastron, when submerged underwater in the Cassie-Baxter state with water in contact with the tops of surface roughness features. In this state the plastron allows slip to occur across the surface which results in a drag reduction. In this work we report flexible and relatively large area superhydrophobic surfaces produced using two different methods: Large roughness features were created by electrodeposition on copper meshes; Small roughness features were created by embedding carbon nanoparticles (soot) into Polydimethylsiloxane (PDMS). Both samples were made into cylinders with a diameter under 12 mm. To characterize the samples, scanning electron microscope (SEM) images and confocal microscope images were taken. The confocal microscope images were taken with each sample submerged in water to show the extent of the plastron. The hydrophobized electrodeposited copper mesh cylinders showed drag reductions of up to 32% when comparing the superhydrophobic state with a wetted out state. The soot covered cylinders achieved a 30% drag reduction when comparing the superhydrophobic state to a plain cylinder. These results were obtained for turbulent flows with Reynolds numbers 10,000 to 32,500.

Imaging properties and its improvements of scanning/imaging x-ray microscope

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

Takeuchi, Akihisa, E-mail: take@spring8.or.jp; Uesugi, Kentaro; Suzuki, Yoshio

A scanning / imaging X-ray microscope (SIXM) system has been developed at SPring-8. The SIXM consists of a scanning X-ray microscope with a one-dimensional (1D) X-ray focusing device and an imaging (full-field) X-ray microscope with a 1D X-ray objective. The motivation of the SIXM system is to realize a quantitative and highly-sensitive multimodal 3D X-ray tomography by taking advantages of both the scanning X-ray microscope using multi-pixel detector and the imaging X-ray microscope. Data acquisition process of a 2D image is completely different between in the horizontal direction and in the vertical direction; a 1D signal is obtained with themore » linear-scanning while the other dimensional signal is obtained with the imaging optics. Such condition have caused a serious problem on the imaging properties that the imaging quality in the vertical direction has been much worse than that in the horizontal direction. In this paper, two approaches to solve this problem will be presented. One is introducing a Fourier transform method for phase retrieval from one phase derivative image, and the other to develop and employ a 1D diffuser to produce an asymmetrical coherent illumination.« less

New decision support tool for acute lymphoblastic leukemia classification

NASA Astrophysics Data System (ADS)

Madhukar, Monica; Agaian, Sos; Chronopoulos, Anthony T.

2012-03-01

In this paper, we build up a new decision support tool to improve treatment intensity choice in childhood ALL. The developed system includes different methods to accurately measure furthermore cell properties in microscope blood film images. The blood images are exposed to series of pre-processing steps which include color correlation, and contrast enhancement. By performing K-means clustering on the resultant images, the nuclei of the cells under consideration are obtained. Shape features and texture features are then extracted for classification. The system is further tested on the classification of spectra measured from the cell nuclei in blood samples in order to distinguish normal cells from those affected by Acute Lymphoblastic Leukemia. The results show that the proposed system robustly segments and classifies acute lymphoblastic leukemia based on complete microscopic blood images.

Photonic-crystal membranes for optical detection of single nano-particles, designed for biosensor application.

PubMed

Grepstad, Jon Olav; Kaspar, Peter; Solgaard, Olav; Johansen, Ib-Rune; Sudbø, Aasmund S

2012-03-26

A sensor designed to detect bio-molecules is presented. The sensor exploits a planar 2D photonic crystal (PC) membrane with sub-micron thickness and through holes, to induce high optical fields that allow detection of nano-particles smaller than the diffraction limit of an optical microscope. We report on our design and fabrication of a PC membrane with a nano-particle trapped inside. We have also designed and built an imaging system where an optical microscope and a CCD camera are used to take images of the PC membrane. Results show how the trapped nano-particle appears as a bright spot in the image. In a first experimental realization of the imaging system, single particles with a radius of 75 nm can be detected.

Hyperspectral microscope imaging methods to classify gram-positive and gram-negative foodborne pathogenic bacteria

USDA-ARS?s Scientific Manuscript database

An acousto-optic tunable filter-based hyperspectral microscope imaging method has potential for identification of foodborne pathogenic bacteria from microcolony rapidly with a single cell level. We have successfully developed the method to acquire quality hyperspectral microscopic images from variou...

Optical design and system characterization of an imaging microscope at 121.6 nm

NASA Astrophysics Data System (ADS)

Gao, Weichuan; Finan, Emily; Kim, Geon-Hee; Kim, Youngsik; Milster, Thomas D.

2018-03-01

We present the optical design and system characterization of an imaging microscope prototype at 121.6 nm. System engineering processes are demonstrated through the construction of a Schwarzschild microscope objective, including tolerance analysis, fabrication, alignment, and testing. Further improvements on the as-built system with a correction phase plate are proposed and analyzed. Finally, the microscope assembly and the imaging properties of the prototype are demonstrated.

Practical three color live cell imaging by widefield microscopy

PubMed Central

Xia, Jianrun; Kim, Song Hon H.; Macmillan, Susan

2006-01-01

Live cell fluorescence microscopy using fluorescent protein tags derived from jellyfish and coral species has been a successful tool to image proteins and dynamics in many species. Multi-colored aequorea fluorescent protein (AFP) derivatives allow investigators to observe multiple proteins simultaneously, but overlapping spectral properties sometimes require the use of sophisticated and expensive microscopes. Here, we show that the aequorea coerulescens fluorescent protein derivative, PS-CFP2 has excellent practical properties as a blue fluorophore that are distinct from green or red fluorescent proteins and can be imaged with standard filter sets on a widefield microscope. We also find that by widefield illumination in live cells, that PS-CFP2 is very photostable. When fused to proteins that form concentrated puncta in either the cytoplasm or nucleus, PSCFP2 fusions do not artifactually interact with other AFP fusion proteins, even at very high levels of over-expression. PSCFP2 is therefore a good blue fluorophore for distinct three color imaging along with eGFP and mRFP using a relatively simple and inexpensive microscope. PMID:16909160

Biocompatible near-infrared fluorescent nanoparticles for macro and microscopic in vivo functional bioimaging

PubMed Central

Chu, Liliang; Wang, Shaowei; Li, Kanghui; Xi, Wang; Zhao, Xinyuan; Qian, Jun

2014-01-01

Near-infrared (NIR) imaging technology has been widely used for biomedical research and applications, since it can achieve deep penetration in biological tissues due to less absorption and scattering of NIR light. In our research, polymer nanoparticles with NIR fluorophores doped were synthesized. The morphology, absorption/emission features and chemical stability of the fluorescent nanoparticles were characterized, separately. NIR fluorescent nanoparticles were then utilized as bright optical probes for macro in vivo imaging of mice, including sentinel lymph node (SLN) mapping, as well as distribution and excretion monitoring of nanoparticles in animal body. Furthermore, we applied the NIR fluorescent nanoparticles in in vivo microscopic bioimaging via a confocal microscope. Under the 635 nm-CW excitation, the blood vessel architecture in the ear and the brain of mice, which were administered with nanoparticles, was visualized very clearly. The imaging depth of our one-photon microscopy, which was assisted with NIR fluorescent nanoprobes, can reach as deep as 500 μm. Our experiments show that NIR fluorescent nanoparticles have great potentials in various deep-tissue imaging applications. PMID:25426331

Magnetic domain observation of FeCo thin films fabricated by alternate monoatomic layer deposition

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

Ohtsuki, T., E-mail: ohtsuki@spring8.or.jp; Kotsugi, M.; Ohkochi, T.

2014-01-28

FeCo thin films are fabricated by alternate monoatomic layer deposition method on a Cu{sub 3}Au buffer layer, which in-plane lattice constant is very close to the predicted value to obtain a large magnetic anisotropy constant. The variation of the in-plane lattice constant during the deposition process is investigated by reflection high-energy electron diffraction. The magnetic domain images are also observed by a photoelectron emission microscope in order to microscopically understand the magnetic structure. As a result, element-specific magnetic domain images show that Fe and Co magnetic moments align parallel. A series of images obtained with various azimuth reveal that themore » FeCo thin films show fourfold in-plane magnetic anisotropy along 〈110〉 direction, and that the magnetic domain structure is composed only of 90∘ wall.« less

Scanning electron microscope observation of dislocations in semiconductor and metal materials.

PubMed

Kuwano, Noriyuki; Itakura, Masaru; Nagatomo, Yoshiyuki; Tachibana, Shigeaki

2010-08-01

Scanning electron microscope (SEM) image contrasts have been investigated for dislocations in semiconductor and metal materials. It is revealed that single dislocations can be observed in a high contrast in SEM images formed by backscattered electrons (BSE) under the condition of a normal configuration of SEM. The BSE images of dislocations were compared with those of the transmission electron microscope and scanning transmission electron microscope (STEM) and the dependence of BSE image contrast on the tilting of specimen was examined to discuss the origin of image contrast. From the experimental results, it is concluded that the BSE images of single dislocations are attributed to the diffraction effect and related with high-angle dark-field images of STEM.

CHAMP (Camera, Handlens, and Microscope Probe)

NASA Technical Reports Server (NTRS)

Mungas, Greg S.; Boynton, John E.; Balzer, Mark A.; Beegle, Luther; Sobel, Harold R.; Fisher, Ted; Klein, Dan; Deans, Matthew; Lee, Pascal; Sepulveda, Cesar A.

2005-01-01

CHAMP (Camera, Handlens And Microscope Probe)is a novel field microscope capable of color imaging with continuously variable spatial resolution from infinity imaging down to diffraction-limited microscopy (3 micron/pixel). As a robotic arm-mounted imager, CHAMP supports stereo imaging with variable baselines, can continuously image targets at an increasing magnification during an arm approach, can provide precision rangefinding estimates to targets, and can accommodate microscopic imaging of rough surfaces through a image filtering process called z-stacking. CHAMP was originally developed through the Mars Instrument Development Program (MIDP) in support of robotic field investigations, but may also find application in new areas such as robotic in-orbit servicing and maintenance operations associated with spacecraft and human operations. We overview CHAMP'S instrument performance and basic design considerations below.

Alterations of the cytoskeleton in human cells in space proved by life-cell imaging.

PubMed

Corydon, Thomas J; Kopp, Sascha; Wehland, Markus; Braun, Markus; Schütte, Andreas; Mayer, Tobias; Hülsing, Thomas; Oltmann, Hergen; Schmitz, Burkhard; Hemmersbach, Ruth; Grimm, Daniela

2016-01-28

Microgravity induces changes in the cytoskeleton. This might have an impact on cells and organs of humans in space. Unfortunately, studies of cytoskeletal changes in microgravity reported so far are obligatorily based on the analysis of fixed cells exposed to microgravity during a parabolic flight campaign (PFC). This study focuses on the development of a compact fluorescence microscope (FLUMIAS) for fast live-cell imaging under real microgravity. It demonstrates the application of the instrument for on-board analysis of cytoskeletal changes in FTC-133 cancer cells expressing the Lifeact-GFP marker protein for the visualization of F-actin during the 24(th) DLR PFC and TEXUS 52 rocket mission. Although vibration is an inevitable part of parabolic flight maneuvers, we successfully for the first time report life-cell cytoskeleton imaging during microgravity, and gene expression analysis after the 31(st) parabola showing a clear up-regulation of cytoskeletal genes. Notably, during the rocket flight the FLUMIAS microscope reveals significant alterations of the cytoskeleton related to microgravity. Our findings clearly demonstrate the applicability of the FLUMIAS microscope for life-cell imaging during microgravity, rendering it an important technological advance in live-cell imaging when dissecting protein localization.

Alterations of the cytoskeleton in human cells in space proved by life-cell imaging

PubMed Central

Corydon, Thomas J.; Kopp, Sascha; Wehland, Markus; Braun, Markus; Schütte, Andreas; Mayer, Tobias; Hülsing, Thomas; Oltmann, Hergen; Schmitz, Burkhard; Hemmersbach, Ruth; Grimm, Daniela

2016-01-01

Microgravity induces changes in the cytoskeleton. This might have an impact on cells and organs of humans in space. Unfortunately, studies of cytoskeletal changes in microgravity reported so far are obligatorily based on the analysis of fixed cells exposed to microgravity during a parabolic flight campaign (PFC). This study focuses on the development of a compact fluorescence microscope (FLUMIAS) for fast live-cell imaging under real microgravity. It demonstrates the application of the instrument for on-board analysis of cytoskeletal changes in FTC-133 cancer cells expressing the Lifeact-GFP marker protein for the visualization of F-actin during the 24th DLR PFC and TEXUS 52 rocket mission. Although vibration is an inevitable part of parabolic flight maneuvers, we successfully for the first time report life-cell cytoskeleton imaging during microgravity, and gene expression analysis after the 31st parabola showing a clear up-regulation of cytoskeletal genes. Notably, during the rocket flight the FLUMIAS microscope reveals significant alterations of the cytoskeleton related to microgravity. Our findings clearly demonstrate the applicability of the FLUMIAS microscope for life-cell imaging during microgravity, rendering it an important technological advance in live-cell imaging when dissecting protein localization. PMID:26818711

Atomic force-multi-optical imaging integrated microscope for monitoring molecular dynamics in live cells.

PubMed

Trache, Andreea; Meininger, Gerald A

2005-01-01

A novel hybrid imaging system is constructed integrating atomic force microscopy (AFM) with a combination of optical imaging techniques that offer high spatial resolution. The main application of this instrument (the NanoFluor microscope) is the study of mechanotransduction with an emphasis on extracellular matrix-integrin-cytoskeletal interactions and their role in the cellular responses to changes in external chemical and mechanical factors. The AFM allows the quantitative assessment of cytoskeletal changes, binding probability, adhesion forces, and micromechanical properties of the cells, while the optical imaging applications allow thin sectioning of the cell body at the coverslip-cell interface, permitting the study of focal adhesions using total internal reflection fluorescence (TIRF) and internal reflection microscopy (IRM). Combined AFM-optical imaging experiments show that mechanical stimulation at the apical surface of cells induces a force-generating cytoskeletal response, resulting in focal contact reorganization on the basal surface that can be monitored in real time. The NanoFluor system is also equipped with a novel mechanically aligned dual camera acquisition system for synthesized Forster resonance energy transfer (FRET). The integrated NanoFluor microscope system is described, including its characteristics, applications, and limitations.

Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging

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

Kovarik, Libor; Stevens, Andrew J.; Liyu, Andrey V.

Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce themore » electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. As a result, the use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO 3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.« less

Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging

DOE PAGES

Kovarik, Libor; Stevens, Andrew J.; Liyu, Andrey V.; ...

2016-10-17

Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce themore » electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.« less

Design of a normal incidence multilayer imaging x-ray microscope.

PubMed

Shealy, D L; Gabardi, D R; Hoover, R B; Walker, A B; Lindblom, J F; Barbee, T W

1989-01-01

Normal incidence multilayer Cassegrain x-ray telescopes were flown on the Stanford/MSFC Rocket X-Ray Spectroheliograph. These instruments produced high spatial resolution images of the Sun and conclusively demonstrated that doubly reflecting multilayer x-ray optical systems are feasible. The images indicated that aplanatic imaging soft x-ray /EUV microscopes should be achievable using multilayer optics technology. We have designed a doubly reflecting normal incidence multilayer imaging x-ray microscope based on the Schwarzschild configuration. The Schwarzschild microscope utilizes two spherical mirrors with concentric radii of curvature which are chosen such that the third-order spherical aberration and coma are minimized. We discuss the design of the microscope and the results of the optical system ray trace analysis which indicates that diffraction-limited performance with 600 Å spatial resolution should be obtainable over a 1 mm field of view at a wavelength of 100 Å. Fabrication of several imaging soft x-ray microscopes based upon these designs, for use in conjunction with x-ray telescopes and laser fusion research, is now in progress. High resolution aplanatic imaging x-ray microscopes using normal incidence multilayer x-ray mirrors should have many important applications in advanced x-ray astronomical instrumentation, x-ray lithography, biological, biomedical, metallurgical, and laser fusion research.

Mars Life? - Microscopic Tubular Structures

NASA Technical Reports Server (NTRS)

1996-01-01

This electron microscope image shows extremely tiny tubular structures that are possible microscopic fossils of bacteria-like organisms that may have lived on Mars more than 3.6 billion years ago. A two-year investigation by a NASA research team found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller. The fossil-like structures were found in carbonate minerals formed along pre-existing fractures in the meteorite in a fashion similar to the way fossils occur in limestone on Earth, although on a microscopic scale.

Smartphone adapters for digital photomicrography

PubMed Central

Roy, Somak; Pantanowitz, Liron; Amin, Milon; Seethala, Raja R.; Ishtiaque, Ahmed; Yousem, Samuel A.; Parwani, Anil V.; Cucoranu, Ioan; Hartman, Douglas J.

2014-01-01

Background: Photomicrographs in Anatomic Pathology provide a means of quickly sharing information from a glass slide for consultation, education, documentation and publication. While static image acquisition historically involved the use of a permanently mounted camera unit on a microscope, such cameras may be expensive, need to be connected to a computer, and often require proprietary software to acquire and process images. Another novel approach for capturing digital microscopic images is to use smartphones coupled with the eyepiece of a microscope. Recently, several smartphone adapters have emerged that allow users to attach mobile phones to the microscope. The aim of this study was to test the utility of these various smartphone adapters. Materials and Methods: We surveyed the market for adapters to attach smartphones to the ocular lens of a conventional light microscope. Three adapters (Magnifi, Skylight and Snapzoom) were tested. We assessed the designs of these adapters and their effectiveness at acquiring static microscopic digital images. Results: All adapters facilitated the acquisition of digital microscopic images with a smartphone. The optimal adapter was dependent on the type of phone used. The Magnifi adapters for iPhone were incompatible when using a protective case. The Snapzoom adapter was easiest to use with iPhones and other smartphones even with protective cases. Conclusions: Smartphone adapters are inexpensive and easy to use for acquiring digital microscopic images. However, they require some adjustment by the user in order to optimize focus and obtain good quality images. Smartphone microscope adapters provide an economically feasible method of acquiring and sharing digital pathology photomicrographs. PMID:25191623

Adaptive optical microscope for brain imaging in vivo

NASA Astrophysics Data System (ADS)

Wang, Kai

2017-04-01

The optical heterogeneity of biological tissue imposes a major limitation to acquire detailed structural and functional information deep in the biological specimens using conventional microscopes. To restore optimal imaging performance, we developed an adaptive optical microscope based on direct wavefront sensing technique. This microscope can reliably measure and correct biological samples induced aberration. We demonstrated its performance and application in structural and functional brain imaging in various animal models, including fruit fly, zebrafish and mouse.

Volumetric Light-field Encryption at the Microscopic Scale

PubMed Central

Li, Haoyu; Guo, Changliang; Muniraj, Inbarasan; Schroeder, Bryce C.; Sheridan, John T.; Jia, Shu

2017-01-01

We report a light-field based method that allows the optical encryption of three-dimensional (3D) volumetric information at the microscopic scale in a single 2D light-field image. The system consists of a microlens array and an array of random phase/amplitude masks. The method utilizes a wave optics model to account for the dominant diffraction effect at this new scale, and the system point-spread function (PSF) serves as the key for encryption and decryption. We successfully developed and demonstrated a deconvolution algorithm to retrieve both spatially multiplexed discrete data and continuous volumetric data from 2D light-field images. Showing that the method is practical for data transmission and storage, we obtained a faithful reconstruction of the 3D volumetric information from a digital copy of the encrypted light-field image. The method represents a new level of optical encryption, paving the way for broad industrial and biomedical applications in processing and securing 3D data at the microscopic scale. PMID:28059149

Volumetric Light-field Encryption at the Microscopic Scale

NASA Astrophysics Data System (ADS)

Li, Haoyu; Guo, Changliang; Muniraj, Inbarasan; Schroeder, Bryce C.; Sheridan, John T.; Jia, Shu

2017-01-01

We report a light-field based method that allows the optical encryption of three-dimensional (3D) volumetric information at the microscopic scale in a single 2D light-field image. The system consists of a microlens array and an array of random phase/amplitude masks. The method utilizes a wave optics model to account for the dominant diffraction effect at this new scale, and the system point-spread function (PSF) serves as the key for encryption and decryption. We successfully developed and demonstrated a deconvolution algorithm to retrieve both spatially multiplexed discrete data and continuous volumetric data from 2D light-field images. Showing that the method is practical for data transmission and storage, we obtained a faithful reconstruction of the 3D volumetric information from a digital copy of the encrypted light-field image. The method represents a new level of optical encryption, paving the way for broad industrial and biomedical applications in processing and securing 3D data at the microscopic scale.

Visible-to-visible four-photon ultrahigh resolution microscopic imaging with 730-nm diode laser excited nanocrystals.

PubMed

Wang, Baoju; Zhan, Qiuqiang; Zhao, Yuxiang; Wu, Ruitao; Liu, Jing; He, Sailing

2016-01-25

Further development of multiphoton microscopic imaging is confronted with a number of limitations, including high-cost, high complexity and relatively low spatial resolution due to the long excitation wavelength. To overcome these problems, for the first time, we propose visible-to-visible four-photon ultrahigh resolution microscopic imaging by using a common cost-effective 730-nm laser diode to excite the prepared Nd(3+)-sensitized upconversion nanoparticles (Nd(3+)-UCNPs). An ordinary multiphoton scanning microscope system was built using a visible CW diode laser and the lateral imaging resolution as high as 161-nm was achieved via the four-photon upconversion process. The demonstrated large saturation excitation power for Nd(3+)-UCNPs would be more practical and facilitate the four-photon imaging in the application. A sample with fine structure was imaged to demonstrate the advantages of visible-to-visible four-photon ultrahigh resolution microscopic imaging with 730-nm diode laser excited nanocrystals. Combining the uniqueness of UCNPs, the proposed visible-to-visible four-photon imaging would be highly promising and attractive in the field of multiphoton imaging.

Proper alignment of the microscope.

PubMed

Rottenfusser, Rudi

2013-01-01

The light microscope is merely the first element of an imaging system in a research facility. Such a system may include high-speed and/or high-resolution image acquisition capabilities, confocal technologies, and super-resolution methods of various types. Yet more than ever, the proverb "garbage in-garbage out" remains a fact. Image manipulations may be used to conceal a suboptimal microscope setup, but an artifact-free image can only be obtained when the microscope is optimally aligned, both mechanically and optically. Something else is often overlooked in the quest to get the best image out of the microscope: Proper sample preparation! The microscope optics can only do its job when its design criteria are matched to the specimen or vice versa. The specimen itself, the mounting medium, the cover slip, and the type of immersion medium (if applicable) are all part of the total optical makeup. To get the best results out of a microscope, understanding the functions of all of its variable components is important. Only then one knows how to optimize these components for the intended application. Different approaches might be chosen to discuss all of the microscope's components. We decided to follow the light path which starts with the light source and ends at the camera or the eyepieces. To add more transparency to this sequence, the section up to the microscope stage was called the "Illuminating Section", to be followed by the "Imaging Section" which starts with the microscope objective. After understanding the various components, we can start "working with the microscope." To get the best resolution and contrast from the microscope, the practice of "Koehler Illumination" should be understood and followed by every serious microscopist. Step-by-step instructions as well as illustrations of the beam path in an upright and inverted microscope are included in this chapter. A few practical considerations are listed in Section 3. Copyright © 2013 Elsevier Inc. All rights reserved.

Apparatus and methods for controlling electron microscope stages

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

Duden, Thomas

Methods and apparatus for generating an image of a specimen with a microscope (e.g., TEM) are disclosed. In one aspect, the microscope may generally include a beam generator, a stage, a detector, and an image generator. A plurality of crystal parameters, which describe a plurality of properties of a crystal sample, are received. In a display associated with the microscope, an interactive control sphere based at least in part on the received crystal parameters and that is rotatable by a user to different sphere orientations is presented. The sphere includes a plurality of stage coordinates that correspond to a pluralitymore » of positions of the stage and a plurality of crystallographic pole coordinates that correspond to a plurality of polar orientations of the crystal sample. Movement of the sphere causes movement of the stage, wherein the stage coordinates move in conjunction with the crystallographic coordinates represented by pole positions so as to show a relationship between stage positions and the pole positions.« less

FPscope: a field-portable high-resolution microscope using a cellphone lens.

PubMed

Dong, Siyuan; Guo, Kaikai; Nanda, Pariksheet; Shiradkar, Radhika; Zheng, Guoan

2014-10-01

The large consumer market has made cellphone lens modules available at low-cost and in high-quality. In a conventional cellphone camera, the lens module is used to demagnify the scene onto the image plane of the camera, where image sensor is located. In this work, we report a 3D-printed high-resolution Fourier ptychographic microscope, termed FPscope, which uses a cellphone lens in a reverse manner. In our platform, we replace the image sensor with sample specimens, and use the cellphone lens to project the magnified image to the detector. To supersede the diffraction limit of the lens module, we use an LED array to illuminate the sample from different incident angles and synthesize the acquired images using the Fourier ptychographic algorithm. As a demonstration, we use the reported platform to acquire high-resolution images of resolution target and biological specimens, with a maximum synthetic numerical aperture (NA) of 0.5. We also show that, the depth-of-focus of the reported platform is about 0.1 mm, orders of magnitude longer than that of a conventional microscope objective with a similar NA. The reported platform may enable healthcare accesses in low-resource settings. It can also be used to demonstrate the concept of computational optics for educational purposes.

COMPACT NON-CONTACT TOTAL EMISSION DETECTION FOR IN-VIVO MULTI-PHOTON EXCITATION MICROSCOPY

PubMed Central

Glancy, Brian; Karamzadeh, Nader S.; Gandjbakhche, Amir H.; Redford, Glen; Kilborn, Karl; Knutson, Jay R.; Balaban, Robert S.

2014-01-01

Summary We describe a compact, non-contact design for a Total Emission Detection (c-TED) system for intra-vital multi-photon imaging. To conform to a standard upright two-photon microscope design, this system uses a parabolic mirror surrounding a standard microscope objective in concert with an optical path that does not interfere with normal microscope operation. The non-contact design of this device allows for maximal light collection without disrupting the physiology of the specimen being examined. Tests were conducted on exposed tissues in live animals to examine the emission collection enhancement of the c-TED device compared to heavily optimized objective-based emission collection. The best light collection enhancement was seen from murine fat (5×-2× gains as a function of depth), while murine skeletal muscle and rat kidney showed gains of over two and just under two-fold near the surface, respectively. Gains decreased with imaging depth (particularly in the kidney). Zebrafish imaging on a reflective substrate showed close to a two-fold gain throughout the entire volume of an intact embryo (approximately 150 μm deep). Direct measurement of bleaching rates confirmed that the lower laser powers (enabled by greater light collection efficiency) yielded reduced photobleaching in vivo. The potential benefits of increased light collection in terms of speed of imaging and reduced photo-damage, as well as the applicability of this device to other multi-photon imaging methods is discussed. PMID:24251437

Ordered Structure Formed by Biologically Related Molecules

NASA Astrophysics Data System (ADS)

Hatta, Ichiro; Nishino, Junichiro; Sumi, Akinori; Hibino, Masahiro

1995-07-01

The two-dimensional arrangement of biologically related molecules was studied by means of scanning probe microscopy. For monolayers of fatty acid molecules with a saturated hydrocarbon chain adsorbed on a graphite substrate, in the scanning tunneling microscope image, the position associated with the carbon atoms was clearly distinguished. In addition, based on the image for fatty acid molecules with an unsaturated hydrocarbon chain, at the position of a double bond, local electrical conductance was found to increase. Based on the images, it was pointed out that not the position of each carbon but the interaction between a graphite substrate and an alkyl chain plays an important role in imaging. On the other hand, for the surface of Langmuir-Blodgett films composed of phosphatidic acids with cations, the scanning force microscope image shows, for the first time, evidence of the methyl ends in the arrangement of phospholipid molecules.

High resolution imaging of latent fingerprints by localized corrosion on brass surfaces.

PubMed

Goddard, Alex J; Hillman, A Robert; Bond, John W

2010-01-01

The Atomic Force Microscope (AFM) is capable of imaging fingerprint ridges on polished brass substrates at an unprecedented level of detail. While exposure to elevated humidity at ambient or slightly raised temperatures does not change the image appreciably, subsequent brief heating in a flame results in complete loss of the sweat deposit and the appearance of pits and trenches. Localized elemental analysis (using EDAX, coupled with SEM imaging) shows the presence of the constituents of salt in the initial deposits. Together with water and atmospheric oxygen--and with thermal enhancement--these are capable of driving a surface corrosion process. This process is sufficiently localized that it has the potential to generate a durable negative topographical image of the fingerprint. AFM examination of surface regions between ridges revealed small deposits (probably microscopic "spatter" of sweat components or transferred particulates) that may ultimately limit the level of ridge detail analysis.

Remote Histology Learning from Static versus Dynamic Microscopic Images

ERIC Educational Resources Information Center

Mione, Sylvia; Valcke, Martin; Cornelissen, Maria

2016-01-01

Histology is the study of microscopic structures in normal tissue sections. Curriculum redesign in medicine has led to a decrease in the use of optical microscopes during practical classes. Other imaging solutions have been implemented to facilitate remote learning. With advancements in imaging technologies, learning material can now be digitized.…

A frameless stereotaxic operating microscope for neurosurgery.

PubMed

Friets, E M; Strohbehn, J W; Hatch, J F; Roberts, D W

1989-06-01

A new system, which we call the frameless stereotaxic operating microscope, is discussed. Its purpose is to display CT or other image data in the operating microscope in the correct scale, orientation, and position without the use of a stereotaxic frame. A nonimaging ultrasonic rangefinder allows the position of the operating microscope and the position of the patient to be determined. Discrete fiducial points on the patient's external anatomy are located in both image space and operating room space, linking the image data and the operating room. Physician-selected image information, e.g., tumor contours or guidance to predetermined targets, is projected through the optics of the operating microscope using a miniature cathode ray tube and a beam splitter. Projected images superpose the surgical field, reconstructed from image data to match the focal plane of the operating microscope. The algorithms on which the system is based are described, and the sources and effects of errors are discussed. The system's performance is simulated, providing an estimate of accuracy. Two phantoms are used to measure accuracy experimentally. Clinical results and observations are given.

Automatic analysis for neuron by confocal laser scanning microscope

NASA Astrophysics Data System (ADS)

Satou, Kouhei; Aoki, Yoshimitsu; Mataga, Nobuko; Hensh, Takao K.; Taki, Katuhiko

2005-12-01

The aim of this study is to develop a system that recognizes both the macro- and microscopic configurations of nerve cells and automatically performs the necessary 3-D measurements and functional classification of spines. The acquisition of 3-D images of cranial nerves has been enabled by the use of a confocal laser scanning microscope, although the highly accurate 3-D measurements of the microscopic structures of cranial nerves and their classification based on their configurations have not yet been accomplished. In this study, in order to obtain highly accurate measurements of the microscopic structures of cranial nerves, existing positions of spines were predicted by the 2-D image processing of tomographic images. Next, based on the positions that were predicted on the 2-D images, the positions and configurations of the spines were determined more accurately by 3-D image processing of the volume data. We report the successful construction of an automatic analysis system that uses a coarse-to-fine technique to analyze the microscopic structures of cranial nerves with high speed and accuracy by combining 2-D and 3-D image analyses.

Assessment of a liquid lens enabled in vivo optical coherence microscope.

PubMed

Murali, Supraja; Meemon, Panomsak; Lee, Kye-Sung; Kuhn, William P; Thompson, Kevin P; Rolland, Jannick P

2010-06-01

The optical aberrations induced by imaging through skin can be predicted using formulas for Seidel aberrations of a plane-parallel plate. Knowledge of these aberrations helps to guide the choice of numerical aperture (NA) of the optics we can use in an implementation of Gabor domain optical coherence microscopy (GD-OCM), where the focus is the only aberration adjustment made through depth. On this basis, a custom-designed, liquid-lens enabled dynamic focusing optical coherence microscope operating at 0.2 NA is analyzed and validated experimentally. As part of the analysis, we show that the full width at half-maximum metric, as a characteristic descriptor for the point spread function, while commonly used, is not a useful metric for quantifying resolution in non-diffraction-limited systems. Modulation transfer function (MTF) measurements quantify that the liquid lens performance is as predicted by design, even when accounting for the effect of gravity. MTF measurements in a skinlike scattering medium also quantify the performance of the microscope in its potential applications. To guide the fusion of images across the various focus positions of the microscope, as required in GD-OCM, we present depth of focus measurements that can be used to determine the effective number of focusing zones required for a given goal resolution. Subcellular resolution in an onion sample, and high-definition in vivo imaging in human skin are demonstrated with the custom-designed and built microscope.

Comparison of the manual, semiautomatic, and automatic selection and leveling of hot spots in whole slide images for Ki-67 quantification in meningiomas.

PubMed

Swiderska, Zaneta; Korzynska, Anna; Markiewicz, Tomasz; Lorent, Malgorzata; Zak, Jakub; Wesolowska, Anna; Roszkowiak, Lukasz; Slodkowska, Janina; Grala, Bartlomiej

2015-01-01

Background. This paper presents the study concerning hot-spot selection in the assessment of whole slide images of tissue sections collected from meningioma patients. The samples were immunohistochemically stained to determine the Ki-67/MIB-1 proliferation index used for prognosis and treatment planning. Objective. The observer performance was examined by comparing results of the proposed method of automatic hot-spot selection in whole slide images, results of traditional scoring under a microscope, and results of a pathologist's manual hot-spot selection. Methods. The results of scoring the Ki-67 index using optical scoring under a microscope, software for Ki-67 index quantification based on hot spots selected by two pathologists (resp., once and three times), and the same software but on hot spots selected by proposed automatic methods were compared using Kendall's tau-b statistics. Results. Results show intra- and interobserver agreement. The agreement between Ki-67 scoring with manual and automatic hot-spot selection is high, while agreement between Ki-67 index scoring results in whole slide images and traditional microscopic examination is lower. Conclusions. The agreement observed for the three scoring methods shows that automation of area selection is an effective tool in supporting physicians and in increasing the reliability of Ki-67 scoring in meningioma.

A photoelastic modulator-based birefringence imaging microscope for measuring biological specimens

NASA Astrophysics Data System (ADS)

Freudenthal, John; Leadbetter, Andy; Wolf, Jacob; Wang, Baoliang; Segal, Solomon

2014-11-01

The photoelastic modulator (PEM) has been applied to a variety of polarimetric measurements. However, nearly all such applications use point-measurements where each point (spot) on the sample is measured one at a time. The main challenge for employing the PEM in a camera-based imaging instrument is that the PEM modulates too fast for typical cameras. The PEM modulates at tens of KHz. To capture the specific polarization information that is carried on the modulation frequency of the PEM, the camera needs to be at least ten times faster. However, the typical frame rates of common cameras are only in the tens or hundreds frames per second. In this paper, we report a PEM-camera birefringence imaging microscope. We use the so-called stroboscopic illumination method to overcome the incompatibility of the high frequency of the PEM to the relatively slow frame rate of a camera. We trigger the LED light source using a field-programmable gate array (FPGA) in synchrony with the modulation of the PEM. We show the measurement results of several standard birefringent samples as a part of the instrument calibration. Furthermore, we show results observed in two birefringent biological specimens, a human skin tissue that contains collagen and a slice of mouse brain that contains bundles of myelinated axonal fibers. Novel applications of this PEM-based birefringence imaging microscope to both research communities and industrial applications are being tested.

Comparison of the Manual, Semiautomatic, and Automatic Selection and Leveling of Hot Spots in Whole Slide Images for Ki-67 Quantification in Meningiomas

PubMed Central

Swiderska, Zaneta; Korzynska, Anna; Markiewicz, Tomasz; Lorent, Malgorzata; Zak, Jakub; Wesolowska, Anna; Roszkowiak, Lukasz; Slodkowska, Janina; Grala, Bartlomiej

2015-01-01

Background. This paper presents the study concerning hot-spot selection in the assessment of whole slide images of tissue sections collected from meningioma patients. The samples were immunohistochemically stained to determine the Ki-67/MIB-1 proliferation index used for prognosis and treatment planning. Objective. The observer performance was examined by comparing results of the proposed method of automatic hot-spot selection in whole slide images, results of traditional scoring under a microscope, and results of a pathologist's manual hot-spot selection. Methods. The results of scoring the Ki-67 index using optical scoring under a microscope, software for Ki-67 index quantification based on hot spots selected by two pathologists (resp., once and three times), and the same software but on hot spots selected by proposed automatic methods were compared using Kendall's tau-b statistics. Results. Results show intra- and interobserver agreement. The agreement between Ki-67 scoring with manual and automatic hot-spot selection is high, while agreement between Ki-67 index scoring results in whole slide images and traditional microscopic examination is lower. Conclusions. The agreement observed for the three scoring methods shows that automation of area selection is an effective tool in supporting physicians and in increasing the reliability of Ki-67 scoring in meningioma. PMID:26240787

Field-Portable Pixel Super-Resolution Colour Microscope

PubMed Central

Greenbaum, Alon; Akbari, Najva; Feizi, Alborz; Luo, Wei; Ozcan, Aydogan

2013-01-01

Based on partially-coherent digital in-line holography, we report a field-portable microscope that can render lensfree colour images over a wide field-of-view of e.g., >20 mm2. This computational holographic microscope weighs less than 145 grams with dimensions smaller than 17×6×5 cm, making it especially suitable for field settings and point-of-care use. In this lensfree imaging design, we merged a colorization algorithm with a source shifting based multi-height pixel super-resolution technique to mitigate ‘rainbow’ like colour artefacts that are typical in holographic imaging. This image processing scheme is based on transforming the colour components of an RGB image into YUV colour space, which separates colour information from brightness component of an image. The resolution of our super-resolution colour microscope was characterized using a USAF test chart to confirm sub-micron spatial resolution, even for reconstructions that employ multi-height phase recovery to handle dense and connected objects. To further demonstrate the performance of this colour microscope Papanicolaou (Pap) smears were also successfully imaged. This field-portable and wide-field computational colour microscope could be useful for tele-medicine applications in resource poor settings. PMID:24086742

Field-portable pixel super-resolution colour microscope.

PubMed

Greenbaum, Alon; Akbari, Najva; Feizi, Alborz; Luo, Wei; Ozcan, Aydogan

2013-01-01

Based on partially-coherent digital in-line holography, we report a field-portable microscope that can render lensfree colour images over a wide field-of-view of e.g., >20 mm(2). This computational holographic microscope weighs less than 145 grams with dimensions smaller than 17×6×5 cm, making it especially suitable for field settings and point-of-care use. In this lensfree imaging design, we merged a colorization algorithm with a source shifting based multi-height pixel super-resolution technique to mitigate 'rainbow' like colour artefacts that are typical in holographic imaging. This image processing scheme is based on transforming the colour components of an RGB image into YUV colour space, which separates colour information from brightness component of an image. The resolution of our super-resolution colour microscope was characterized using a USAF test chart to confirm sub-micron spatial resolution, even for reconstructions that employ multi-height phase recovery to handle dense and connected objects. To further demonstrate the performance of this colour microscope Papanicolaou (Pap) smears were also successfully imaged. This field-portable and wide-field computational colour microscope could be useful for tele-medicine applications in resource poor settings.

Nanoimaging using soft X-ray and EUV laser-plasma sources

NASA Astrophysics Data System (ADS)

Wachulak, Przemyslaw; Torrisi, Alfio; Ayele, Mesfin; Bartnik, Andrzej; Czwartos, Joanna; Węgrzyński, Łukasz; Fok, Tomasz; Fiedorowicz, Henryk

2018-01-01

In this work we present three experimental, compact desk-top imaging systems: SXR and EUV full field microscopes and the SXR contact microscope. The systems are based on laser-plasma EUV and SXR sources based on a double stream gas puff target. The EUV and SXR full field microscopes, operating at 13.8 nm and 2.88 nm wavelengths are capable of imaging nanostructures with a sub-50 nm spatial resolution and short (seconds) exposure times. The SXR contact microscope operates in the "water-window" spectral range and produces an imprint of the internal structure of the imaged sample in a thin layer of SXR sensitive photoresist. Applications of such desk-top EUV and SXR microscopes, mostly for biological samples (CT26 fibroblast cells and Keratinocytes) are also presented. Details about the sources, the microscopes as well as the imaging results for various objects will be presented and discussed. The development of such compact imaging systems may be important to the new research related to biological, material science and nanotechnology applications.

A wide field-of-view microscope based on holographic focus grid

NASA Astrophysics Data System (ADS)

Wu, Jigang; Cui, Xiquan; Zheng, Guoan; Lee, Lap Man; Yang, Changhuei

2010-02-01

We have developed a novel microscope technique that can achieve wide field-of-view (FOV) imaging and yet possess resolution that is comparable to conventional microscope. The principle of wide FOV microscope system breaks the link between resolution and FOV magnitude of traditional microscopes. Furthermore, by eliminating bulky optical elements from its design and utilizing holographic optical elements, the wide FOV microscope system is more cost-effective. In our system, a hologram was made to focus incoming collimated beam into a focus grid. The sample is put in the focal plane and the transmissions of the focuses are detected by an imaging sensor. By scanning the incident angle of the incoming beam, the focus grid will scan across the sample and the time-varying transmission can be detected. We can then reconstruct the transmission image of the sample. The resolution of microscopic image is limited by the size of the focus formed by the hologram. The scanning area of each focus spot is determined by the separation of the focus spots and can be made small for fast imaging speed. We have fabricated a prototype system with a 2.4-mm FOV and 1-μm resolution. The prototype system was used to image onion skin cells for a demonstration. The preliminary experiments prove the feasibility of the wide FOV microscope technique, and the possibility of a wider FOV system with better resolution.

Modular Scanning Confocal Microscope with Digital Image Processing.

PubMed

Ye, Xianjun; McCluskey, Matthew D

2016-01-01

In conventional confocal microscopy, a physical pinhole is placed at the image plane prior to the detector to limit the observation volume. In this work, we present a modular design of a scanning confocal microscope which uses a CCD camera to replace the physical pinhole for materials science applications. Experimental scans were performed on a microscope resolution target, a semiconductor chip carrier, and a piece of etched silicon wafer. The data collected by the CCD were processed to yield images of the specimen. By selecting effective pixels in the recorded CCD images, a virtual pinhole is created. By analyzing the image moments of the imaging data, a lateral resolution enhancement is achieved by using a 20 × / NA = 0.4 microscope objective at 532 nm laser wavelength.

On-line transmission electron microscopic image analysis of chromatin texture for differentiation of thyroid gland tumors.

PubMed

Kriete, A; Schäffer, R; Harms, H; Aus, H M

1987-06-01

Nuclei of the cells from the thyroid gland were analyzed in a transmission electron microscope by direct TV scanning and on-line image processing. The method uses the advantages of a visual-perception model to detect structures in noisy and low-contrast images. The features analyzed include area, a form factor and texture parameters from the second derivative stage. Three tumor-free thyroid tissues, three follicular adenomas, three follicular carcinomas and three papillary carcinomas were studied. The computer-aided cytophotometric method showed that the most significant differences were the statistics of the chromatin texture features of homogeneity and regularity. These findings document the possibility of an automated differentiation of tumors at the ultrastructural level.

A sub-sampled approach to extremely low-dose STEM

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

Stevens, A.; Luzi, L.; Yang, H.

The inpainting of randomly sub-sampled images acquired by scanning transmission electron microscopy (STEM) is an attractive method for imaging under low-dose conditions (≤ 1 e -Å 2) without changing either the operation of the microscope or the physics of the imaging process. We show that 1) adaptive sub-sampling increases acquisition speed, resolution, and sensitivity; and 2) random (non-adaptive) sub-sampling is equivalent, but faster than, traditional low-dose techniques. Adaptive sub-sampling opens numerous possibilities for the analysis of beam sensitive materials and in-situ dynamic processes at the resolution limit of the aberration corrected microscope and is demonstrated here for the analysis ofmore » the node distribution in metal-organic frameworks (MOFs).« less

CHAMP - Camera, Handlens, and Microscope Probe

NASA Technical Reports Server (NTRS)

Mungas, G. S.; Beegle, L. W.; Boynton, J.; Sepulveda, C. A.; Balzer, M. A.; Sobel, H. R.; Fisher, T. A.; Deans, M.; Lee, P.

2005-01-01

CHAMP (Camera, Handlens And Microscope Probe) is a novel field microscope capable of color imaging with continuously variable spatial resolution from infinity imaging down to diffraction-limited microscopy (3 micron/pixel). As an arm-mounted imager, CHAMP supports stereo-imaging with variable baselines, can continuously image targets at an increasing magnification during an arm approach, can provide precision range-finding estimates to targets, and can accommodate microscopic imaging of rough surfaces through a image filtering process called z-stacking. Currently designed with a filter wheel with 4 different filters, so that color and black and white images can be obtained over the entire Field-of-View, future designs will increase the number of filter positions to include 8 different filters. Finally, CHAMP incorporates controlled white and UV illumination so that images can be obtained regardless of sun position, and any potential fluorescent species can be identified so the most astrobiologically interesting samples can be identified.

X-ray imaging and controlled solidification of Al-Cu alloys toward microstructures by design

DOE PAGES

Clarke, Amy J.; Tourret, Damien; Imhoff, Seth D.; ...

2015-01-30

X-ray imaging, which permits the microscopic visualization of metal alloy solidification dynamics, can be coupled with controlled solidification to create microstructures by design. In this study, this x-ray image shows a process-derived composite microstructure being made from a eutectic Al-17.1 at.%Cu alloy by successive solidification and remelting steps.

Micro axial tomography: A miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy

NASA Astrophysics Data System (ADS)

Staier, Florian; Eipel, Heinz; Matula, Petr; Evsikov, Alexei V.; Kozubek, Michal; Cremer, Christoph; Hausmann, Michael

2011-09-01

With the development of novel fluorescence techniques, high resolution light microscopy has become a challenging technique for investigations of the three-dimensional (3D) micro-cosmos in cells and sub-cellular components. So far, all fluorescence microscopes applied for 3D imaging in biosciences show a spatially anisotropic point spread function resulting in an anisotropic optical resolution or point localization precision. To overcome this shortcoming, micro axial tomography was suggested which allows object tilting on the microscopic stage and leads to an improvement in localization precision and spatial resolution. Here, we present a miniaturized device which can be implemented in a motor driven microscope stage. The footprint of this device corresponds to a standard microscope slide. A special glass fiber can manually be adjusted in the object space of the microscope lens. A stepwise fiber rotation can be controlled by a miniaturized stepping motor incorporated into the device. By means of a special mounting device, test particles were fixed onto glass fibers, optically localized with high precision, and automatically rotated to obtain views from different perspective angles under which distances of corresponding pairs of objects were determined. From these angle dependent distance values, the real 3D distance was calculated with a precision in the ten nanometer range (corresponding here to an optical resolution of 10-30 nm) using standard microscopic equipment. As a proof of concept, the spindle apparatus of a mature mouse oocyte was imaged during metaphase II meiotic arrest under different perspectives. Only very few images registered under different rotation angles are sufficient for full 3D reconstruction. The results indicate the principal advantage of the micro axial tomography approach for many microscopic setups therein and also those of improved resolutions as obtained by high precision localization determination.

Moessbauer Nose Print

NASA Technical Reports Server (NTRS)

2004-01-01

This image was taken by the microscopic imager, an instrument located on the Mars Exploration Rover Opportunity 's instrument deployment device, or 'arm.' The image shows the imprint of the donut-shaped plate on the rover's Moessbauer spectrometer instrument, also located on the 'arm.' The Moessbauer spectrometer was deployed within the trench to investigate the fine-grained soil for iron-bearing minerals. The area in this image measures approximately 3 centimeters (1.2 inches) across.

'Berries' on the Ground

NASA Technical Reports Server (NTRS)

2004-01-01

This mosaic image shows an extreme close-up of round, blueberry-shaped formations in the martian soil near a part of the rock outcrop at Meridiani Planum called Stone Mountain. Scientists are studying these curious formations for clues about the area's past environmental conditions. The image, one of the highest resolution images ever taken by the microscopic imager, an instrument located on the Mars Exploration Rover Opportunity's instrument deployment device or 'arm.'

A portable fluorescence microscopic imaging system for cholecystectomy

NASA Astrophysics Data System (ADS)

Ye, Jian; Yang, Chaoyu; Gan, Qi; Ma, Rong; Zhang, Zeshu; Chang, Shufang; Shao, Pengfei; Zhang, Shiwu; Liu, Chenhai; Xu, Ronald

2016-03-01

In this paper we proposed a portable fluorescence microscopic imaging system to prevent iatrogenic biliary injuries from occurring during cholecystectomy due to misidentification of the cystic structures. The system consisted of a light source module, a CMOS camera, a Raspberry Pi computer and a 5 inch HDMI LCD. Specifically, the light source module was composed of 690 nm and 850 nm LEDs, allowing the CMOS camera to simultaneously acquire both fluorescence and background images. The system was controlled by Raspberry Pi using Python programming with the OpenCV library under Linux. We chose Indocyanine green(ICG) as a fluorescent contrast agent and then tested fluorescence intensities of the ICG aqueous solution at different concentration levels by our fluorescence microscopic system compared with the commercial Xenogen IVIS system. The spatial resolution of the proposed fluorescence microscopic imaging system was measured by a 1951 USAF resolution target and the dynamic response was evaluated quantitatively with an automatic displacement platform. Finally, we verified the technical feasibility of the proposed system in mouse models of bile duct, performing both correct and incorrect gallbladder resection. Our experiments showed that the proposed system can provide clear visualization of the confluence between the cystic duct and common bile duct or common hepatic duct, suggesting that this is a potential method for guiding cholecystectomy. The proposed portable system only cost a total of $300, potentially promoting its use in resource-limited settings.

Local dynamic range compensation for scanning electron microscope imaging system by sub-blocking multiple peak HE with convolution.

PubMed

Sim, K S; Teh, V; Tey, Y C; Kho, T K

2016-11-01

This paper introduces new development technique to improve the Scanning Electron Microscope (SEM) image quality and we name it as sub-blocking multiple peak histogram equalization (SUB-B-MPHE) with convolution operator. By using this new proposed technique, it shows that the new modified MPHE performs better than original MPHE. In addition, the sub-blocking method consists of convolution operator which can help to remove the blocking effect for SEM images after applying this new developed technique. Hence, by using the convolution operator, it effectively removes the blocking effect by properly distributing the suitable pixel value for the whole image. Overall, the SUB-B-MPHE with convolution outperforms the rest of methods. SCANNING 38:492-501, 2016. © 2015 Wiley Periodicals, Inc. © Wiley Periodicals, Inc.

A new algorithm to reduce noise in microscopy images implemented with a simple program in python.

PubMed

Papini, Alessio

2012-03-01

All microscopical images contain noise, increasing when (e.g., transmission electron microscope or light microscope) approaching the resolution limit. Many methods are available to reduce noise. One of the most commonly used is image averaging. We propose here to use the mode of pixel values. Simple Python programs process a given number of images, recorded consecutively from the same subject. The programs calculate the mode of the pixel values in a given position (a, b). The result is a new image containing in (a, b) the mode of the values. Therefore, the final pixel value corresponds to that read in at least two of the pixels in position (a, b). The application of the program on a set of images obtained by applying salt and pepper noise and GIMP hurl noise with 10-90% standard deviation showed that the mode performs better than averaging with three-eight images. The data suggest that the mode would be more efficient (in the sense of a lower number of recorded images to process to reduce noise below a given limit) for lower number of total noisy pixels and high standard deviation (as impulse noise and salt and pepper noise), while averaging would be more efficient when the number of varying pixels is high, and the standard deviation is low, as in many cases of Gaussian noise affected images. The two methods may be used serially. Copyright © 2011 Wiley Periodicals, Inc.

Relative merits and limiting factors for x-ray and electron microscopy of thick, hydrated organic materials.

PubMed

Du, Ming; Jacobsen, Chris

2018-01-01

Electron and x-ray microscopes allow one to image the entire, unlabeled structure of hydrated materials at a resolution well beyond what visible light microscopes can achieve. However, both approaches involve ionizing radiation, so that radiation damage must be considered as one of the limits to imaging. Drawing upon earlier work, we describe here a unified approach to estimating the image contrast (and thus the required exposure and corresponding radiation dose) in both x-ray and electron microscopy. This approach accounts for factors such as plural and inelastic scattering, and (in electron microscopy) the use of energy filters to obtain so-called "zero loss" images. As expected, it shows that electron microscopy offers lower dose for specimens thinner than about 1 µm (such as for studies of macromolecules, viruses, bacteria and archaebacteria, and thin sectioned material), while x-ray microscopy offers superior characteristics for imaging thicker specimen such as whole eukaryotic cells, thick-sectioned tissues, and organs. The required radiation dose scales strongly as a function of the desired spatial resolution, allowing one to understand the limits of live and frozen hydrated specimen imaging. Finally, we consider the factors limiting x-ray microscopy of thicker materials, suggesting that specimens as thick as a whole mouse brain can be imaged with x-ray microscopes without significant image degradation should appropriate image reconstruction methods be identified. Copyright © 2017 Elsevier B.V. All rights reserved.

Blueberries Inside Popcorn

NASA Image and Video Library

2004-08-18

This view from the microscopic imager on NASA Mars Exploration Rover Opportunity shows a type of light-colored, rough-textured spherules scientists call popcorn in contrast to the darker, smoother spherules called blueberries.

Applications of virtual reality technology in pathology.

PubMed

Grimes, G J; McClellan, S A; Goldman, J; Vaughn, G L; Conner, D A; Kujawski, E; McDonald, J; Winokur, T; Fleming, W

1997-01-01

TelePath(SM) a telerobotic system utilizing virtual microscope concepts based on high quality still digital imaging and aimed at real-time support for surgery by remote diagnosis of frozen sections. Many hospitals and clinics have an application for the remote practice of pathology, particularly in the area of reading frozen sections in support of surgery, commonly called anatomic pathology. The goal is to project the expertise of the pathologist into the remote setting by giving the pathologist access to the microscope slides with an image quality and human interface comparable to what the pathologist would experience at a real rather than a virtual microscope. A working prototype of a virtual microscope has been defined and constructed which has the needed performance in both the image quality and human interface areas for a pathologist to work remotely. This is accomplished through the use of telerobotics and an image quality which provides the virtual microscope the same diagnostic capabilities as a real microscope. The examination of frozen sections is performed a two-dimensional world. The remote pathologist is in a virtual world with the same capabilities as a "real" microscope, but response times may be slower depending on the specific computing and telecommunication environments. The TelePath system has capabilities far beyond a normal biological microscope, such as the ability to create a low power image of the entire sample using multiple images digitally matched together; the ability to digitally retrace a viewing trajectory; and the ability to archive images using CD ROM and other mass storage devices.

High-resolution, high-throughput imaging with a multibeam scanning electron microscope.

PubMed

Eberle, A L; Mikula, S; Schalek, R; Lichtman, J; Knothe Tate, M L; Zeidler, D

2015-08-01

Electron-electron interactions and detector bandwidth limit the maximal imaging speed of single-beam scanning electron microscopes. We use multiple electron beams in a single column and detect secondary electrons in parallel to increase the imaging speed by close to two orders of magnitude and demonstrate imaging for a variety of samples ranging from biological brain tissue to semiconductor wafers. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Comprehensive optical and data management infrastructure for high-throughput light-sheet microscopy of whole mouse brains.

PubMed

Müllenbroich, M Caroline; Silvestri, Ludovico; Onofri, Leonardo; Costantini, Irene; Hoff, Marcel Van't; Sacconi, Leonardo; Iannello, Giulio; Pavone, Francesco S

2015-10-01

Comprehensive mapping and quantification of neuronal projections in the central nervous system requires high-throughput imaging of large volumes with microscopic resolution. To this end, we have developed a confocal light-sheet microscope that has been optimized for three-dimensional (3-D) imaging of structurally intact clarified whole-mount mouse brains. We describe the optical and electromechanical arrangement of the microscope and give details on the organization of the microscope management software. The software orchestrates all components of the microscope, coordinates critical timing and synchronization, and has been written in a versatile and modular structure using the LabVIEW language. It can easily be adapted and integrated to other microscope systems and has been made freely available to the light-sheet community. The tremendous amount of data routinely generated by light-sheet microscopy further requires novel strategies for data handling and storage. To complete the full imaging pipeline of our high-throughput microscope, we further elaborate on big data management from streaming of raw images up to stitching of 3-D datasets. The mesoscale neuroanatomy imaged at micron-scale resolution in those datasets allows characterization and quantification of neuronal projections in unsectioned mouse brains.

Scanning Miniature Microscopes without Lenses

NASA Technical Reports Server (NTRS)

Wang, Yu

2009-01-01

The figure schematically depicts some alternative designs of proposed compact, lightweight optoelectronic microscopes that would contain no lenses and would generate magnified video images of specimens. Microscopes of this type were described previously in Miniature Microscope Without Lenses (NPO - 20218), NASA Tech Briefs, Vol. 22, No. 8 (August 1998), page 43 and Reflective Variants of Miniature Microscope Without Lenses (NPO 20610), NASA Tech Briefs, Vol. 26, No. 9 (September 1999), page 6a. To recapitulate: In the design and construction of a microscope of this type, the focusing optics of a conventional microscope are replaced by a combination of a microchannel filter and a charge-coupled-device (CCD) image detector. Elimination of focusing optics reduces the size and weight of the instrument and eliminates the need for the time-consuming focusing operation. The microscopes described in the cited prior articles contained two-dimensional CCDs registered with two-dimensional arrays of microchannels and, as such, were designed to produce full two-dimensional images, without need for scanning. The microscopes of the present proposal would contain one-dimensional (line image) CCDs registered with linear arrays of microchannels. In the operation of such a microscope, one would scan a specimen along a line perpendicular to the array axis (in other words, one would scan in pushbroom fashion). One could then synthesize a full two-dimensional image of the specimen from the line-image data acquired at one-pixel increments of position along the scan. In one of the proposed microscopes, a beam of unpolarized light for illuminating the specimen would enter from the side. This light would be reflected down onto the specimen by a nonpolarizing beam splitter attached to the microchannels at their lower ends. A portion of the light incident on the specimen would be reflected upward, through the beam splitter and along the microchannels, to form an image on the CCD. If the nonpolarizing beam splitter were replaced by a polarizing one, then the specimen would be illuminated by s-polarized light. Upon reflection from the specimen, some of the s-polarized light would become p-polarized. Only the p-polarized light would contribute to the image on the CCD; in other words, the image would contain information on the polarization rotating characteristic of the specimen.

Modular Scanning Confocal Microscope with Digital Image Processing

PubMed Central

McCluskey, Matthew D.

2016-01-01

In conventional confocal microscopy, a physical pinhole is placed at the image plane prior to the detector to limit the observation volume. In this work, we present a modular design of a scanning confocal microscope which uses a CCD camera to replace the physical pinhole for materials science applications. Experimental scans were performed on a microscope resolution target, a semiconductor chip carrier, and a piece of etched silicon wafer. The data collected by the CCD were processed to yield images of the specimen. By selecting effective pixels in the recorded CCD images, a virtual pinhole is created. By analyzing the image moments of the imaging data, a lateral resolution enhancement is achieved by using a 20 × / NA = 0.4 microscope objective at 532 nm laser wavelength. PMID:27829052

A simple water-immersion condenser for imaging living brain slices on an inverted microscope.

PubMed

Prusky, G T

1997-09-05

Due to some physical limitations of conventional condensers, inverted compound microscopes are not optimally suited for imaging living brain slices with transmitted light. Herein is described a simple device that converts an inverted microscope into an effective tool for this application by utilizing an objective as a condenser. The device is mounted on a microscope in place of the condenser, is threaded to accept a water immersion objective, and has a slot for a differential interference contrast (DIC) slider. When combined with infrared video techniques, this device allows an inverted microscope to effectively image living cells within thick brain slices in an open perfusion chamber.

ImSyn: photonic image synthesis applied to synthetic aperture radar, microscopy, and ultrasound imaging

NASA Astrophysics Data System (ADS)

Turpin, Terry M.; Lafuse, James L.

1993-02-01

ImSynTM is an image synthesis technology, developed and patented by Essex Corporation. ImSynTM can provide compact, low cost, and low power solutions to some of the most difficult image synthesis problems existing today. The inherent simplicity of ImSynTM enables the manufacture of low cost and reliable photonic systems for imaging applications ranging from airborne reconnaissance to doctor's office ultrasound. The initial application of ImSynTM technology has been to SAR processing; however, it has a wide range of applications such as: image correlation, image compression, acoustic imaging, x-ray tomographic (CAT, PET, SPECT), magnetic resonance imaging (MRI), microscopy, range- doppler mapping (extended TDOA/FDOA). This paper describes ImSynTM in terms of synthetic aperture microscopy and then shows how the technology can be extended to ultrasound and synthetic aperture radar. The synthetic aperture microscope (SAM) enables high resolution three dimensional microscopy with greater dynamic range than real aperture microscopes. SAM produces complex image data, enabling the use of coherent image processing techniques. Most importantly SAM produces the image data in a form that is easily manipulated by a digital image processing workstation.

An Innovative Method for Obtaining Consistent Images and Quantification of Histochemically Stained Specimens

PubMed Central

Sedgewick, Gerald J.; Ericson, Marna

2015-01-01

Obtaining digital images of color brightfield microscopy is an important aspect of biomedical research and the clinical practice of diagnostic pathology. Although the field of digital pathology has had tremendous advances in whole-slide imaging systems, little effort has been directed toward standardizing color brightfield digital imaging to maintain image-to-image consistency and tonal linearity. Using a single camera and microscope to obtain digital images of three stains, we show that microscope and camera systems inherently produce image-to-image variation. Moreover, we demonstrate that post-processing with a widely used raster graphics editor software program does not completely correct for session-to-session inconsistency. We introduce a reliable method for creating consistent images with a hardware/software solution (ChromaCal™; Datacolor Inc., NJ) along with its features for creating color standardization, preserving linear tonal levels, providing automated white balancing and setting automated brightness to consistent levels. The resulting image consistency using this method will also streamline mean density and morphometry measurements, as images are easily segmented and single thresholds can be used. We suggest that this is a superior method for color brightfield imaging, which can be used for quantification and can be readily incorporated into workflows. PMID:25575568

Preclinical evaluation and intraoperative human retinal imaging with a high-resolution microscope-integrated spectral domain optical coherence tomography device.

PubMed

Hahn, Paul; Migacz, Justin; O'Donnell, Rachelle; Day, Shelley; Lee, Annie; Lin, Phoebe; Vann, Robin; Kuo, Anthony; Fekrat, Sharon; Mruthyunjaya, Prithvi; Postel, Eric A; Izatt, Joseph A; Toth, Cynthia A

2013-01-01

The authors have recently developed a high-resolution microscope-integrated spectral domain optical coherence tomography (MIOCT) device designed to enable OCT acquisition simultaneous with surgical maneuvers. The purpose of this report is to describe translation of this device from preclinical testing into human intraoperative imaging. Before human imaging, surgical conditions were fully simulated for extensive preclinical MIOCT evaluation in a custom model eye system. Microscope-integrated spectral domain OCT images were then acquired in normal human volunteers and during vitreoretinal surgery in patients who consented to participate in a prospective institutional review board-approved study. Microscope-integrated spectral domain OCT images were obtained before and at pauses in surgical maneuvers and were compared based on predetermined diagnostic criteria to images obtained with a high-resolution spectral domain research handheld OCT system (HHOCT; Bioptigen, Inc) at the same time point. Cohorts of five consecutive patients were imaged. Successful end points were predefined, including ≥80% correlation in identification of pathology between MIOCT and HHOCT in ≥80% of the patients. Microscope-integrated spectral domain OCT was favorably evaluated by study surgeons and scrub nurses, all of whom responded that they would consider participating in human intraoperative imaging trials. The preclinical evaluation identified significant improvements that were made before MIOCT use during human surgery. The MIOCT transition into clinical human research was smooth. Microscope-integrated spectral domain OCT imaging in normal human volunteers demonstrated high resolution comparable to tabletop scanners. In the operating room, after an initial learning curve, surgeons successfully acquired human macular MIOCT images before and after surgical maneuvers. Microscope-integrated spectral domain OCT imaging confirmed preoperative diagnoses, such as full-thickness macular hole and vitreomacular traction, and demonstrated postsurgical changes in retinal morphology. Two cohorts of five patients were imaged. In the second cohort, the predefined end points were exceeded with ≥80% correlation between microscope-mounted OCT and HHOCT imaging in 100% of the patients. This report describes high-resolution MIOCT imaging using the prototype device in human eyes during vitreoretinal surgery, with successful achievement of predefined end points for imaging. Further refinements and investigations will be directed toward fully integrating MIOCT with vitreoretinal and other ocular surgery to image surgical maneuvers in real time.

A mini-microscope for in situ monitoring of cells.

PubMed

Kim, Sang Bok; Koo, Kyo-in; Bae, Hojae; Dokmeci, Mehmet R; Hamilton, Geraldine A; Bahinski, Anthony; Kim, Sun Min; Ingber, Donald E; Khademhosseini, Ali

2012-10-21

A mini-microscope was developed for in situ monitoring of cells by modifying off-the-shelf components of a commercial webcam. The mini-microscope consists of a CMOS imaging module, a small plastic lens and a white LED illumination source. The CMOS imaging module was connected to a laptop computer through a USB port for image acquisition and analysis. Due to its compact size, 8 × 10 × 9 cm, the present microscope is portable and can easily fit inside a conventional incubator, and enables real-time monitoring of cellular behaviour. Moreover, the mini-microscope can be used for imaging cells in conventional cell culture flasks, such as Petri dishes and multi-well plates. To demonstrate the operation of the mini-microscope, we monitored the cellular migration of mouse 3T3 fibroblasts in a scratch assay in medium containing three different concentrations of fetal bovine serum (5, 10, and 20%) and demonstrated differential responses depending on serum levels. In addition, we seeded embryonic stem cells inside poly(ethylene glycol) microwells and monitored the formation of stem cell aggregates in real time using the mini-microscope. Furthermore, we also combined a lab-on-a-chip microfluidic device for microdroplet generation and analysis with the mini-microscope and observed the formation of droplets under different flow conditions. Given its cost effectiveness, robust imaging and portability, the presented platform may be useful for a range of applications for real-time cellular imaging using lab-on-a-chip devices at low cost.

A mini-microscope for in situ monitoring of cells†‡

PubMed Central

Kim, Sang Bok; Koo, Kyo-in; Bae, Hojae; Dokmeci, Mehmet R.; Hamilton, Geraldine A.; Bahinski, Anthony; Kim, Sun Min; Ingber, Donald E.

2013-01-01

A mini-microscope was developed for in situ monitoring of cells by modifying off-the-shelf components of a commercial webcam. The mini-microscope consists of a CMOS imaging module, a small plastic lens and a white LED illumination source. The CMOS imaging module was connected to a laptop computer through a USB port for image acquisition and analysis. Due to its compact size, 8 × 10 × 9 cm, the present microscope is portable and can easily fit inside a conventional incubator, and enables real-time monitoring of cellular behaviour. Moreover, the mini-microscope can be used for imaging cells in conventional cell culture flasks, such as Petri dishes and multi-well plates. To demonstrate the operation of the mini-microscope, we monitored the cellular migration of mouse 3T3 fibroblasts in a scratch assay in medium containing three different concentrations of fetal bovine serum (5, 10, and 20%) and demonstrated differential responses depending on serum levels. In addition, we seeded embryonic stem cells inside poly(ethylene glycol) microwells and monitored the formation of stem cell aggregates in real time using the mini-microscope. Furthermore, we also combined a lab-on-a-chip microfluidic device for microdroplet generation and analysis with the mini-microscope and observed the formation of droplets under different flow conditions. Given its cost effectiveness, robust imaging and portability, the presented platform may be useful for a range of applications for real-time cellular imaging using lab-on-a-chip devices at low cost. PMID:22911426

[Scanning electron microscope observation and image quantitative analysis of Hippocampi].

PubMed

Zhang, Z; Pu, Z; Xu, L; Xu, G; Wang, Q; Xu, G; Wu, L; Chen, J

1998-12-01

The "scale-like projects" on the derma of 3 species of Hippocampi, H. kuda Bleerer, H. trimaculatus Leach and H. japonicus Kaup were observed by scanning electron microscope (SEM). Results showed that some characteristics such us size, shape and type of arrangement of the "scale-like projects" can be considered as the evidence for microanalysis. Image quantitative analysis of the "scale-like project" was carried out on 45 pieces of photograph using area, long diameter, short diameter and shape factor as parameters. No difference among the different parts of the same species was observed, but significant differences were found among the above 3 species.

Red Blood Cell Count Automation Using Microscopic Hyperspectral Imaging Technology.

PubMed

Li, Qingli; Zhou, Mei; Liu, Hongying; Wang, Yiting; Guo, Fangmin

2015-12-01

Red blood cell counts have been proven to be one of the most frequently performed blood tests and are valuable for early diagnosis of some diseases. This paper describes an automated red blood cell counting method based on microscopic hyperspectral imaging technology. Unlike the light microscopy-based red blood count methods, a combined spatial and spectral algorithm is proposed to identify red blood cells by integrating active contour models and automated two-dimensional k-means with spectral angle mapper algorithm. Experimental results show that the proposed algorithm has better performance than spatial based algorithm because the new algorithm can jointly use the spatial and spectral information of blood cells.

Extreme ultraviolet patterned mask inspection performance of advanced projection electron microscope system for 11nm half-pitch generation

NASA Astrophysics Data System (ADS)

Hirano, Ryoichi; Iida, Susumu; Amano, Tsuyoshi; Watanabe, Hidehiro; Hatakeyama, Masahiro; Murakami, Takeshi; Suematsu, Kenichi; Terao, Kenji

2016-03-01

Novel projection electron microscope optics have been developed and integrated into a new inspection system named EBEYE-V30 ("Model EBEYE" is an EBARA's model code) , and the resulting system shows promise for application to half-pitch (hp) 16-nm node extreme ultraviolet lithography (EUVL) patterned mask inspection. To improve the system's inspection throughput for 11-nm hp generation defect detection, a new electron-sensitive area image sensor with a high-speed data processing unit, a bright and stable electron source, and an image capture area deflector that operates simultaneously with the mask scanning motion have been developed. A learning system has been used for the mask inspection tool to meet the requirements of hp 11-nm node EUV patterned mask inspection. Defects are identified by the projection electron microscope system using the "defectivity" from the characteristics of the acquired image. The learning system has been developed to reduce the labor and costs associated with adjustment of the detection capability to cope with newly-defined mask defects. We describe the integration of the developed elements into the inspection tool and the verification of the designed specification. We have also verified the effectiveness of the learning system, which shows enhanced detection capability for the hp 11-nm node.

Flexible conformable hydrophobized surfaces for turbulent flow drag reduction

PubMed Central

Brennan, Joseph C; Geraldi, Nicasio R; Morris, Robert H; Fairhurst, David J; McHale, Glen; Newton, Michael I

2015-01-01

In recent years extensive work has been focused onto using superhydrophobic surfaces for drag reduction applications. Superhydrophobic surfaces retain a gas layer, called a plastron, when submerged underwater in the Cassie-Baxter state with water in contact with the tops of surface roughness features. In this state the plastron allows slip to occur across the surface which results in a drag reduction. In this work we report flexible and relatively large area superhydrophobic surfaces produced using two different methods: Large roughness features were created by electrodeposition on copper meshes; Small roughness features were created by embedding carbon nanoparticles (soot) into Polydimethylsiloxane (PDMS). Both samples were made into cylinders with a diameter under 12 mm. To characterize the samples, scanning electron microscope (SEM) images and confocal microscope images were taken. The confocal microscope images were taken with each sample submerged in water to show the extent of the plastron. The hydrophobized electrodeposited copper mesh cylinders showed drag reductions of up to 32% when comparing the superhydrophobic state with a wetted out state. The soot covered cylinders achieved a 30% drag reduction when comparing the superhydrophobic state to a plain cylinder. These results were obtained for turbulent flows with Reynolds numbers 10,000 to 32,500. PMID:25975704

Calcified miliary brain metastases with mitochondrial inclusion bodies.

PubMed Central

Yamazaki, T; Harigaya, Y; Noguchi, O; Okamoto, K; Hirai, S

1993-01-01

A patient with calcified miliary brain metastases from lung adenocarcinoma is reported. Electron microscopic study of the metastatic tumour cells showed membranous inclusion bodies in mitochondria. Images PMID:8429312

Microscope-on-Chip Using Micro-Channel and Solid State Image Sensors

NASA Technical Reports Server (NTRS)

Wang, Yu

2000-01-01

Recently, Jet Propulsion Laboratory has invented and developed a miniature optical microscope, microscope-on-chip using micro-channel and solid state image sensors. It is lightweight, low-power, fast speed instrument, it has no image lens, does not need focus adjustment, and the total mass is less than 100g. A prototype has been built and demonstrated at JPL.

Cryotomography x-ray microscopy state

DOEpatents

Le Gros, Mark; Larabell, Carolyn A.

2010-10-26

An x-ray microscope stage enables alignment of a sample about a rotation axis to enable three dimensional tomographic imaging of the sample using an x-ray microscope. A heat exchanger assembly provides cooled gas to a sample during x-ray microscopic imaging.

Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications

NASA Astrophysics Data System (ADS)

Zhang, Yu Shrike; Chang, Jae-Byum; Alvarez, Mario Moisés; Trujillo-de Santiago, Grissel; Aleman, Julio; Batzaya, Byambaa; Krishnadoss, Vaishali; Ramanujam, Aishwarya Aravamudhan; Kazemzadeh-Narbat, Mehdi; Chen, Fei; Tillberg, Paul W.; Dokmeci, Mehmet Remzi; Boyden, Edward S.; Khademhosseini, Ali

2016-03-01

To date, much effort has been expended on making high-performance microscopes through better instrumentation. Recently, it was discovered that physical magnification of specimens was possible, through a technique called expansion microscopy (ExM), raising the question of whether physical magnification, coupled to inexpensive optics, could together match the performance of high-end optical equipment, at a tiny fraction of the price. Here we show that such “hybrid microscopy” methods—combining physical and optical magnifications—can indeed achieve high performance at low cost. By physically magnifying objects, then imaging them on cheap miniature fluorescence microscopes (“mini-microscopes”), it is possible to image at a resolution comparable to that previously attainable only with benchtop microscopes that present costs orders of magnitude higher. We believe that this unprecedented hybrid technology that combines expansion microscopy, based on physical magnification, and mini-microscopy, relying on conventional optics—a process we refer to as Expansion Mini-Microscopy (ExMM)—is a highly promising alternative method for performing cost-effective, high-resolution imaging of biological samples. With further advancement of the technology, we believe that ExMM will find widespread applications for high-resolution imaging particularly in research and healthcare scenarios in undeveloped countries or remote places.

Time-resolved molecular imaging

NASA Astrophysics Data System (ADS)

Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

2016-06-01

Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

Augmented microscopy with near-infrared fluorescence detection

NASA Astrophysics Data System (ADS)

Watson, Jeffrey R.; Martirosyan, Nikolay; Skoch, Jesse; Lemole, G. Michael; Anton, Rein; Romanowski, Marek

2015-03-01

Near-infrared (NIR) fluorescence has become a frequently used intraoperative technique for image-guided surgical interventions. In procedures such as cerebral angiography, surgeons use the optical surgical microscope for the color view of the surgical field, and then switch to an electronic display for the NIR fluorescence images. However, the lack of stereoscopic, real-time, and on-site coregistration adds time and uncertainty to image-guided surgical procedures. To address these limitations, we developed the augmented microscope, whereby the electronically processed NIR fluorescence image is overlaid with the anatomical optical image in real-time within the optical path of the microscope. In vitro, the augmented microscope can detect and display indocyanine green (ICG) concentrations down to 94.5 nM, overlaid with the anatomical color image. We prepared polyacrylamide tissue phantoms with embedded polystyrene beads, yielding scattering properties similar to brain matter. In this model, 194 μM solution of ICG was detectable up to depths of 5 mm. ICG angiography was then performed in anesthetized rats. A dynamic process of ICG distribution in the vascular system overlaid with anatomical color images was observed and recorded. In summary, the augmented microscope demonstrates NIR fluorescence detection with superior real-time coregistration displayed within the ocular of the stereomicroscope. In comparison to other techniques, the augmented microscope retains full stereoscopic vision and optical controls including magnification and focus, camera capture, and multiuser access. Augmented microscopy may find application in surgeries where the use of traditional microscopes can be enhanced by contrast agents and image guided delivery of therapeutics, including oncology, neurosurgery, and ophthalmology.

Optical path difference microscopy with a Shack-Hartmann wavefront sensor.

PubMed

Gong, Hai; Agbana, Temitope E; Pozzi, Paolo; Soloviev, Oleg; Verhaegen, Michel; Vdovin, Gleb

2017-06-01

In this Letter, we show that a Shack-Hartmann wavefront sensor can be used for the quantitative measurement of the specimen optical path difference (OPD) in an ordinary incoherent optical microscope, if the spatial coherence of the illumination light in the plane of the specimen is larger than the microscope resolution. To satisfy this condition, the illumination numerical aperture should be smaller than the numerical aperture of the imaging lens. This principle has been successfully applied to build a high-resolution reference-free instrument for the characterization of the OPD of micro-optical components and microscopic biological samples.

Laser shock wave assisted patterning on NiTi shape memory alloy surfaces

NASA Astrophysics Data System (ADS)

Seyitliyev, Dovletgeldi; Li, Peizhen; Kholikov, Khomidkhodza; Grant, Byron; Karaca, Haluk E.; Er, Ali O.

2017-02-01

An advanced direct imprinting method with low cost, quick, and less environmental impact to create thermally controllable surface pattern using the laser pulses is reported. Patterned micro indents were generated on Ni50Ti50 shape memory alloys (SMA) using an Nd:YAG laser operating at 1064 nm combined with suitable transparent overlay, a sacrificial layer of graphite, and copper grid. Laser pulses at different energy densities which generates pressure pulses up to 10 GPa on the surface was focused through the confinement medium, ablating the copper grid to create plasma and transferring the grid pattern onto the NiTi surface. Scanning electron microscope (SEM) and optical microscope images of square pattern with different sizes were studied. One dimensional profile analysis shows that the depth of the patterned sample initially increase linearly with the laser energy until 125 mJ/pulse where the plasma further absorbs and reflects the laser beam. In addition, light the microscope image show that the surface of NiTi alloy was damaged due to the high power laser energy which removes the graphite layer.

Video-Rate Confocal Microscopy for Single-Molecule Imaging in Live Cells and Superresolution Fluorescence Imaging

PubMed Central

Lee, Jinwoo; Miyanaga, Yukihiro; Ueda, Masahiro; Hohng, Sungchul

2012-01-01

There is no confocal microscope optimized for single-molecule imaging in live cells and superresolution fluorescence imaging. By combining the swiftness of the line-scanning method and the high sensitivity of wide-field detection, we have developed a, to our knowledge, novel confocal fluorescence microscope with a good optical-sectioning capability (1.0 μm), fast frame rates (<33 fps), and superior fluorescence detection efficiency. Full compatibility of the microscope with conventional cell-imaging techniques allowed us to do single-molecule imaging with a great ease at arbitrary depths of live cells. With the new microscope, we monitored diffusion motion of fluorescently labeled cAMP receptors of Dictyostelium discoideum at both the basal and apical surfaces and obtained superresolution fluorescence images of microtubules of COS-7 cells at depths in the range 0–85 μm from the surface of a coverglass. PMID:23083712

Imaging nanoclusters in the constant height mode of the dynamic SFM.

PubMed

Barth, Clemens; Pakarinen, Olli H; Foster, Adam S; Henry, Claude R

2006-04-14

For the first time, high quality images of metal nanoclusters which were recorded in the constant height mode of a dynamic scanning force microscope (dynamic SFM) are shown. Surfaces of highly ordered pyrolytic graphite (HOPG) were used as a test substrate since metal nanoclusters with well defined and symmetric shapes can be created by epitaxial growth. We performed imaging of gold clusters with sizes between 5 and 15 nm in both scanning modes, constant Δf mode and constant height mode, and compared the image contrast. We notice that clusters in constant height images appear much sharper, and exhibit more reasonable lateral shapes and sizes in comparison to images recorded in the constant Δf mode. With the help of numerical simulations we show that only a microscopically small part of the tip apex (nanotip) is probably the main contributor for the image contrast formation. In principle, the constant height mode can be used for imaging surfaces of any material, e.g. ionic crystals, as shown for the system Au/NaCl(001).

Hyperspectral Imaging and Spectroscopy of Fluorescently Coupled Acyl-CoA: Cholesterol Acyltransferase in Insect Cells

NASA Technical Reports Server (NTRS)

Malak, H.; Mahtani, H.; Herman, P.; Vecer, J.; Lu, X.; Chang, T. Y.; Richmond, Robert C.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

A high-performance hyperspectral imaging module with high throughput of light suitable for low-intensity fluorescence microscopic imaging and subsequent analysis, including single-pixel-defined emission spectroscopy, was tested on Sf21 insect cells expressing green fluorescence associated with recombinant green fluorescent protein linked or not with the membrane protein acyl-CoA:cholesterol acyltransferase. The imager utilized the phenomenon of optical activity as a new technique providing information over a spectral range of 220-1400 nm, and was inserted between the microscope and an 8-bit CCD video-rate camera. The resulting fluorescence image did not introduce observable image aberrations. The images provided parallel acquisition of well resolved concurrent spatial and spectral information such that fluorescence associated with green fluorescent protein alone was demonstrated to be diffuse within the Sf21 insect cell, and that green fluorescence associated with the membrane protein was shown to be specifically concentrated within regions of the cell cytoplasm. Emission spectra analyzed from different regions of the fluorescence image showed blue shift specific for the regions of concentration associated with the membrane protein.

Biological tissue imaging with a position and time sensitive pixelated detector.

PubMed

Jungmann, Julia H; Smith, Donald F; MacAleese, Luke; Klinkert, Ivo; Visser, Jan; Heeren, Ron M A

2012-10-01

We demonstrate the capabilities of a highly parallel, active pixel detector for large-area, mass spectrometric imaging of biological tissue sections. A bare Timepix assembly (512 × 512 pixels) is combined with chevron microchannel plates on an ion microscope matrix-assisted laser desorption time-of-flight mass spectrometer (MALDI TOF-MS). The detector assembly registers position- and time-resolved images of multiple m/z species in every measurement frame. We prove the applicability of the detection system to biomolecular mass spectrometry imaging on biologically relevant samples by mass-resolved images from Timepix measurements of a peptide-grid benchmark sample and mouse testis tissue slices. Mass-spectral and localization information of analytes at physiologic concentrations are measured in MALDI-TOF-MS imaging experiments. We show a high spatial resolution (pixel size down to 740 × 740 nm(2) on the sample surface) and a spatial resolving power of 6 μm with a microscope mode laser field of view of 100-335 μm. Automated, large-area imaging is demonstrated and the Timepix' potential for fast, large-area image acquisition is highlighted.

Hard x-ray phase contrastmicroscopy - techniques and applications

NASA Astrophysics Data System (ADS)

Holzner, Christian

In 1918, Einstein provided the first description of the nature of the refractive index for X-rays, showing that phase contrast effects are significant. A century later, most x-ray microscopy and nearly all medical imaging remains based on absorption contrast, even though phase contrast offers orders of magnitude improvements in contrast and reduced radiation exposure at multi-keV x-ray energies. The work presented is concerned with developing practical and quantitative methods of phase contrast for x-ray microscopy. A theoretical framework for imaging in phase contrast is put forward; this is used to obtain quantitative images in a scanning microscope using a segmented detector, and to correct for artifacts in a commercial phase contrast x-ray nano-tomography system. The principle of reciprocity between scanning and full-field microscopes is then used to arrive at a novel solution: Zernike contrast in a scanning microscope. These approaches are compared on a theoretical and experimental basis in direct connection with applications using multi-keV x-ray microscopes at the Advanced Photon Source at Argonne National Laboratory. Phase contrast provides the best means to image mass and ultrastructure of light elements that mainly constitute biological matter, while stimulated x-ray fluorescence provides high sensitivity for studies of the distribution of heavier trace elements, such as metals. These approaches are combined in a complementary way to yield quantitative maps of elemental concentration from 2D images, with elements placed in their ultrastructural context. The combination of x-ray fluorescence and phase contrast poses an ideal match for routine, high resolution tomographic imaging of biological samples in the future. The presented techniques and demonstration experiments will help pave the way for this development.

Thermal-Wave Microscope

NASA Technical Reports Server (NTRS)

Jones, Robert E.; Kramarchuk, Ihor; Williams, Wallace D.; Pouch, John J.; Gilbert, Percy

1989-01-01

Computer-controlled thermal-wave microscope developed to investigate III-V compound semiconductor devices and materials. Is nondestructive technique providing information on subsurface thermal features of solid samples. Furthermore, because this is subsurface technique, three-dimensional imaging also possible. Microscope uses intensity-modulated electron beam of modified scanning electron microscope to generate thermal waves in sample. Acoustic waves generated by thermal waves received by transducer and processed in computer to form images displayed on video display of microscope or recorded on magnetic disk.

Mark of the Moessbauer

NASA Technical Reports Server (NTRS)

2004-01-01

This image, taken by an instrument called the microscopic imager on the Mars Exploration Rover Spirit, reveals an imprint left by another instrument, the Moessbauer spectrometer. The imprint is at a location within the rover wheel track named 'Middle of Road.' Both instruments are located on the rover's instrument deployment device, or 'arm.'

Not only was the Moessbauer spectrometer able to gain important mineralogical information about this site, it also aided in the placement of the microscopic imager. On hard rocks, the microscopic imager uses its tiny metal sensor to determine proper placement for best possible focus. However, on the soft martian soil this guide would sink, prohibiting proper placement of the microscopic imager. After the Moessbauer spectrometer's much larger, donut-shaped plate touches the surface, Spirit can correctly calculate where to position the microscopic imager.

Scientists find this image particularly interesting because of the compacted nature of the soil that was underneath the Moessbauer spectrometer plate. Also of interest are the embedded, round grains and the fractured appearance of the material disturbed within the hole. The material appears to be slightly cohesive. The field of view in this image, taken on Sol 43 (February 16, 2004), measures approximately 3 centimeters (1.2 inches) across.

Visualizing individual microtubules by bright field microscopy

NASA Astrophysics Data System (ADS)

Gutiérrez-Medina, Braulio; Block, Steven M.

2010-11-01

Microtubules are slender (˜25 nm diameter), filamentous polymers involved in cellular structure and organization. Individual microtubules have been visualized via fluorescence imaging of dye-labeled tubulin subunits and by video-enhanced, differential interference-contrast microscopy of unlabeled polymers using sensitive CCD cameras. We demonstrate the imaging of unstained microtubules using a microscope with conventional bright field optics in conjunction with a webcam-type camera and a light-emitting diode illuminator. The light scattered by microtubules is image-processed to remove the background, reduce noise, and enhance contrast. The setup is based on a commercial microscope with a minimal set of inexpensive components, suitable for implementation in a student laboratory. We show how this approach can be used in a demonstration motility assay, tracking the gliding motions of microtubules driven by the motor protein kinesin.

Multimodal Nonlinear Optical Microscopy

PubMed Central

Yue, Shuhua; Slipchenko, Mikhail N.; Cheng, Ji-Xin

2013-01-01

Because each nonlinear optical (NLO) imaging modality is sensitive to specific molecules or structures, multimodal NLO imaging capitalizes the potential of NLO microscopy for studies of complex biological tissues. The coupling of multiphoton fluorescence, second harmonic generation, and coherent anti-Stokes Raman scattering (CARS) has allowed investigation of a broad range of biological questions concerning lipid metabolism, cancer development, cardiovascular disease, and skin biology. Moreover, recent research shows the great potential of using CARS microscope as a platform to develop more advanced NLO modalities such as electronic-resonance-enhanced four-wave mixing, stimulated Raman scattering, and pump-probe microscopy. This article reviews the various approaches developed for realization of multimodal NLO imaging as well as developments of new NLO modalities on a CARS microscope. Applications to various aspects of biological and biomedical research are discussed. PMID:24353747

To boldly glow ... applications of laser scanning confocal microscopy in developmental biology.

PubMed

Paddock, S W

1994-05-01

The laser scanning confocal microscope (LSCM) is now established as an invaluable tool in developmental biology for improved light microscope imaging of fluorescently labelled eggs, embryos and developing tissues. The universal application of the LSCM in biomedical research has stimulated improvements to the microscopes themselves and the synthesis of novel probes for imaging biological structures and physiological processes. Moreover the ability of the LSCM to produce an optical series in perfect register has made computer 3-D reconstruction and analysis of light microscope images a practical option.

Remote microscopy and volumetric imaging on the surface of icy satellites

NASA Astrophysics Data System (ADS)

Soto, Alejandro; Nowicki, Keith; Howett, Carly; Feldkhun, Daniel; Retherford, Kurt D.

2017-10-01

With NASA PIDDP support we have applied recent advancements in Fourier-domain microscopy to develop an instrument capable of microscopic imaging from meter-scale distances for use on a planetary lander on the surface of an icy satellite or other planetary bodies. Without moving parts, our instrument projects dynamic patterns of laser light onto a distant target using a lightweight large-aperture reflector, which then collects the light scattered or fluoresced by the target on a fast photon-bucket detector. Using Fourier Transform based techniques, we reconstruct an image from the detected light. The remote microscope has been demonstrated to produce 2D images with better than 15 micron lateral resolution for targets at a distance of 5 meters and is capable of linearly proportionally higher resolution at shorter distances. The remote microscope is also capable of providing three-dimensional (3D) microscopic imaging capabilities, allowing future surface scientists to explore the morphology of microscopic features in surface ices, for example. The instrument enables microscopic in-situ imaging during day or night without the use of a robotic arm, greatly facilitating the surface operations for a lander or rover while expanding the area of investigation near a landing site for improved science targeting. We are developing this remote microscope for in-situ planetary exploration as a collaboration between the Southwest Research Institute, LambdaMetrics, and the University of Colorado.

New implementation of a shear-force microscope suitable to study topographical features over wide areas

NASA Astrophysics Data System (ADS)

Ustione, A.; Cricenti, A.; Piacentini, M.; Felici, A. C.

2006-09-01

A new implementation of a shear-force microscope is described that uses a shear-force detection system to perform topographical imaging of large areas (˜1×1mm2). This implementation finds very interesting application in the study of archeological or artistic samples. Three dc motors are used to move a sample during a scan, allowing the probe tip to follow the surface and to face height differences of several tens of micrometers. This large-area topographical imaging mode exploits new subroutines that were added to the existing homemade software; these subroutines were created in Microsoft VISUAL BASIC 6.0 programming language. With this new feature our shear-force microscope can be used to study topographical details over large areas of archaeological samples in a nondestructive way. We show results detecting worn reliefs over a coin.

Time-lapse microscopy using smartphone with augmented reality markers.

PubMed

Baek, Dongyoub; Cho, Sungmin; Yun, Kyungwon; Youn, Keehong; Bang, Hyunwoo

2014-04-01

A prototype system that replaces the conventional time-lapse imaging in microscopic inspection for use with smartphones is presented. Existing time-lapse imaging requires a video data feed between a microscope and a computer that varies depending on the type of image grabber. Even with proper hardware setups, a series of tedious and repetitive tasks is still required to relocate to the region-of-interest (ROI) of the specimens. In order to simplify the system and improve the efficiency of time-lapse imaging tasks, a smartphone-based platform utilizing microscopic augmented reality (μ-AR) markers is proposed. To evaluate the feasibility and efficiency of the proposed system, a user test was designed and performed, measuring the elapse time for a trial of the task starting from the execution of the application software to the completion of restoring and imaging of an ROI saved in advance. The results of the user test showed that the average elapse time was 65.3 ± 15.2 s with 6.86 ± 3.61 μm of position error and 0.08 ± 0.40 degrees of angle error. This indicates that the time-lapse imaging task was accomplished rapidly with a high level of accuracy. Thus, simplification of both the system and the task was achieved via our proposed system. Copyright © 2014 Wiley Periodicals, Inc.

Failure Analysis of Heavy-Ion-Irradiated Schottky Diodes

NASA Technical Reports Server (NTRS)

Casey, Megan C.; Lauenstein, Jean-Marie; Wilcox, Edward P.; Topper, Alyson D.; Campola, Michael J.; Label, Kenneth A.

2017-01-01

In this work, we use high- and low-magnitude optical microscope images, infrared camera images, and scanning electron microscope images to identify and describe the failure locations in heavy-ion-irradiated Schottky diodes.

Imaging Schwarzschild multilayer X-ray microscope

NASA Technical Reports Server (NTRS)

Hoover, Richard B.; Baker, Phillip C.; Shealy, David L.; Core, David B.; Walker, Arthur B. C., Jr.; Barbee, Troy W., Jr.; Kerstetter, Ted

1993-01-01

We have designed, analyzed, fabricated, and tested Schwarzschild multilayer X-ray microscopes. These instruments use flow-polished Zerodur mirror substrates which have been coated with multilayers optimized for maximum reflectivity at normal incidence at 135 A. They are being developed as prototypes for the Water Window Imaging X-Ray Microscope. Ultrasmooth mirror sets of hemlite grade sapphire have been fabricated and they are now being coated with multilayers to reflect soft X-rays at 38 A, within the biologically important 'water window'. In this paper, we discuss the fabrication of the microscope optics and structural components as well as the mounting of the optics and assembly of the microscopes. We also describe the optical alignment, interferometric and visible light testing of the microscopes, present interferometrically measured performance data, and provide the first results of optical imaging tests.

Design, Fabrication and Testing of Multilayer Coated X-Ray Optics for the Water Window Imaging X-Ray Microscope

NASA Technical Reports Server (NTRS)

Spencer, Dwight C.

1996-01-01

Hoover et. al. built and tested two imaging Schwarzschild multilayer microscopes. These instruments were constructed as prototypes for the "Water Window Imaging X-Ray Microscope," which is a doubly reflecting, multilayer x-ray microscope configured to operate within the "water window." The "water window" is the narrow region of the x-ray spectrum between the K absorption edges of oxygen (lamda = 23.3 Angstroms) and of carbon (lamda = 43.62 Angstroms), where water is relatively highly transmissive and carbon is highly absorptive. This property of these materials, thus permits the use of high resolution multilayer x-ray microscopes for producing high contrast images of carbon-based structures within the aqueous physiological environments of living cells. We report the design, fabrication and testing of multilayer optics that operate in this regime.

Tip localization of an atomic force microscope in transmission microscopy with nanoscale precision

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

Baumann, Fabian; Pippig, Diana A., E-mail: diana.pippig@physik.uni-muenchen.de; Gaub, Hermann E.

Since the atomic force microscope (AFM) has evolved into a general purpose platform for mechanical experiments at the nanoscale, the need for a simple and generally applicable localization of the AFM cantilever in the reference frame of an optical microscope has grown. Molecular manipulations like in single molecule cut and paste or force spectroscopy as well as tip mediated nanolithography are prominent examples for the broad variety of applications implemented to date. In contrast to the different kinds of superresolution microscopy where fluorescence is used to localize the emitter, we, here, employ the absorbance of the tip to localize itsmore » position in transmission microscopy. We show that in a low aperture illumination, the tip causes a significant reduction of the intensity in the image plane of the microscope objective when it is closer than a few hundred nm. By independently varying the z-position of the sample slide, we could verify that this diffraction limited image of the tip is not caused by a near field effect but is rather caused by the absorbance of the transmitted light in the low apex needle-like tip. We localized the centroid position of this tip image with a precision of better than 6 nm and used it in a feedback loop to position the tip into nano-apertures of 110 nm radius. Single-molecule force spectroscopy traces on the unfolding of individual green fluorescent proteins within the nano-apertures showed that their center positions were repeatedly approached with very high fidelity leaving the specific handle chemistry on the tip’s surface unimpaired.« less

Blind restoration method of three-dimensional microscope image based on RL algorithm

NASA Astrophysics Data System (ADS)

Yao, Jin-li; Tian, Si; Wang, Xiang-rong; Wang, Jing-li

2013-08-01

Thin specimens of biological tissue appear three dimensional transparent under a microscope. The optic slice images can be captured by moving the focal planes at the different locations of the specimen. The captured image has low resolution due to the influence of the out-of-focus information comes from the planes adjacent to the local plane. Using traditional methods can remove the blur in the images at a certain degree, but it needs to know the point spread function (PSF) of the imaging system accurately. The accuracy degree of PSF influences the restoration result greatly. In fact, it is difficult to obtain the accurate PSF of the imaging system. In order to restore the original appearance of the specimen under the conditions of the imaging system parameters are unknown or there is noise and spherical aberration in the system, a blind restoration methods of three-dimensional microscope based on the R-L algorithm is proposed in this paper. On the basis of the exhaustive study of the two-dimension R-L algorithm, according to the theory of the microscopy imaging and the wavelet transform denoising pretreatment, we expand the R-L algorithm to three-dimension space. It is a nonlinear restoration method with the maximum entropy constraint. The method doesn't need to know the PSF of the microscopy imaging system precisely to recover the blur image. The image and PSF converge to the optimum solutions by many alterative iterations and corrections. The matlab simulation and experiments results show that the expansion algorithm is better in visual indicators, peak signal to noise ratio and improved signal to noise ratio when compared with the PML algorithm, and the proposed algorithm can suppress noise, restore more details of target, increase image resolution.

Adaptive optics plug-and-play setup for high-resolution microscopes with multi-actuator adaptive lens

NASA Astrophysics Data System (ADS)

Quintavalla, M.; Pozzi, P.; Verhaegen, Michelle; Bijlsma, Hielke; Verstraete, Hans; Bonora, S.

2018-02-01

Adaptive Optics (AO) has revealed as a very promising technique for high-resolution microscopy, where the presence of optical aberrations can easily compromise the image quality. Typical AO systems however, are almost impossible to implement on commercial microscopes. We propose a simple approach by using a Multi-actuator Adaptive Lens (MAL) that can be inserted right after the objective and works in conjunction with an image optimization software allowing for a wavefront sensorless correction. We presented the results obtained on several commercial microscopes among which a confocal microscope, a fluorescence microscope, a light sheet microscope and a multiphoton microscope.

In vivo study of rat cortical hemodynamics using a stereotaxic-apparatus-compatible photoacoustic microscope.

PubMed

Guo, Heng; Chen, Qian; Qi, Weizhi; Chen, Xingxing; Xi, Lei

2018-04-19

Brain imaging is an important technique in cognitive neuroscience. In this article, we designed a stereotaxic-apparatus-compatible photoacoustic microscope for the studies of rat cortical hemodynamics. Compared with existing optical resolution photoacoustic microscopy (ORPAM) systems, the probe owns feature of fast, light and miniature. In this microscope, we integrated a miniaturized ultrasound transducer with a center frequency of 10 MHz to detect photoacoustic signals and a 2-dimensional (2D) microelectromechanical system (MEMS) scanner to achieve raster scanning of the optical focus. Based on phantom evaluation, this imaging probe has a high lateral resolution of 3.8 μm and an effective imaging domain of 2 × 2 mm 2 . Different from conventional ORPAMs, combining with standard stereotaxic apparatus enables broad studies of rodent brains without any motion artifact. To show its capability, we successfully captured red blood cell flow in the capillary, monitored the vascular changes during bleeding and blood infusion and visualized cortical hemodynamics induced by middle cerebral artery occlusion. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fourier transform infrared spectroscopy microscopic imaging classification based on spatial-spectral features

NASA Astrophysics Data System (ADS)

Liu, Lian; Yang, Xiukun; Zhong, Mingliang; Liu, Yao; Jing, Xiaojun; Yang, Qin

2018-04-01

The discrete fractional Brownian incremental random (DFBIR) field is used to describe the irregular, random, and highly complex shapes of natural objects such as coastlines and biological tissues, for which traditional Euclidean geometry cannot be used. In this paper, an anisotropic variable window (AVW) directional operator based on the DFBIR field model is proposed for extracting spatial characteristics of Fourier transform infrared spectroscopy (FTIR) microscopic imaging. Probabilistic principal component analysis first extracts spectral features, and then the spatial features of the proposed AVW directional operator are combined with the former to construct a spatial-spectral structure, which increases feature-related information and helps a support vector machine classifier to obtain more efficient distribution-related information. Compared to Haralick’s grey-level co-occurrence matrix, Gabor filters, and local binary patterns (e.g. uniform LBPs, rotation-invariant LBPs, uniform rotation-invariant LBPs), experiments on three FTIR spectroscopy microscopic imaging datasets show that the proposed AVW directional operator is more advantageous in terms of classification accuracy, particularly for low-dimensional spaces of spatial characteristics.

Extracellular vesicles of calcifying turkey leg tendon characterized by immunocytochemistry and high voltage electron microscopic tomography and 3-D graphic image reconstruction

NASA Technical Reports Server (NTRS)

Landis, W. J.; Hodgens, K. J.; McKee, M. D.; Nanci, A.; Song, M. J.; Kiyonaga, S.; Arena, J.; McEwen, B.

1992-01-01

To gain insight into the structure and possible function of extracellular vesicles in certain calcifying vertebrate tissues, normally mineralizing leg tendons from the domestic turkey, Meleagris gallopavo, have been studied in two separate investigations, one concerning the electron microscopic immunolocalization of the 66 kDa phosphoprotein, osteopontin, and the other detailing the organization and distribution of mineral crystals associated with the vesicles as determined by high voltage microscopic tomography and 3-D graphic image reconstruction. Immunolabeling shows that osteopontin is related to extracellular vesicles of the tendon in the sense that its initial presence appears coincident with the development of mineral associated with the vesicle loci. By high voltage electron microscopy and 3-D imaging techniques, mineral crystals are found to consist of small irregularly shaped particles somewhat randomly oriented throughout individual vesicles sites. Their appearance is different from that found for the mineral observed within calcifying tendon collagen, and their 3-D disposition is not regularly ordered. Possible spatial and temporal relationships of vesicles, osteopontin, mineral, and collagen are being examined further by these approaches.

An open source, wireless capable miniature microscope system

NASA Astrophysics Data System (ADS)

Liberti, William A., III; Perkins, L. Nathan; Leman, Daniel P.; Gardner, Timothy J.

2017-08-01

Objective. Fluorescence imaging through head-mounted microscopes in freely behaving animals is becoming a standard method to study neural circuit function. Flexible, open-source designs are needed to spur evolution of the method. Approach. We describe a miniature microscope for single-photon fluorescence imaging in freely behaving animals. The device is made from 3D printed parts and off-the-shelf components. These microscopes weigh less than 1.8 g, can be configured to image a variety of fluorophores, and can be used wirelessly or in conjunction with active commutators. Microscope control software, based in Swift for macOS, provides low-latency image processing capabilities for closed-loop, or BMI, experiments. Main results. Miniature microscopes were deployed in the songbird premotor region HVC (used as a proper name), in singing zebra finches. Individual neurons yield temporally precise patterns of calcium activity that are consistent over repeated renditions of song. Several cells were tracked over timescales of weeks and months, providing an opportunity to study learning related changes in HVC. Significance. 3D printed miniature microscopes, composed completely of consumer grade components, are a cost-effective, modular option for head-mounting imaging. These easily constructed and customizable tools provide access to cell-type specific neural ensembles over timescales of weeks.

Smartphone confocal microscopy for imaging cellular structures in human skin in vivo.

PubMed

Freeman, Esther E; Semeere, Aggrey; Osman, Hany; Peterson, Gary; Rajadhyaksha, Milind; González, Salvador; Martin, Jeffery N; Anderson, R Rox; Tearney, Guillermo J; Kang, Dongkyun

2018-04-01

We report development of a low-cost smartphone confocal microscope and its first demonstration of in vivo human skin imaging. The smartphone confocal microscope uses a slit aperture and diffraction grating to conduct two-dimensional confocal imaging without using any beam scanning devices. Lateral and axial resolutions of the smartphone confocal microscope were measured as 2 and 5 µm, respectively. In vivo confocal images of human skin revealed characteristic cellular structures, including spinous and basal keratinocytes and papillary dermis. Results suggest that the smartphone confocal microscope has a potential to examine cellular details in vivo and may help disease diagnosis in resource-poor settings, where conducting standard histopathologic analysis is challenging.

Smartphone confocal microscopy for imaging cellular structures in human skin in vivo

PubMed Central

Freeman, Esther E.; Semeere, Aggrey; Osman, Hany; Peterson, Gary; Rajadhyaksha, Milind; González, Salvador; Martin, Jeffery N.; Anderson, R. Rox; Tearney, Guillermo J.; Kang, Dongkyun

2018-01-01

We report development of a low-cost smartphone confocal microscope and its first demonstration of in vivo human skin imaging. The smartphone confocal microscope uses a slit aperture and diffraction grating to conduct two-dimensional confocal imaging without using any beam scanning devices. Lateral and axial resolutions of the smartphone confocal microscope were measured as 2 and 5 µm, respectively. In vivo confocal images of human skin revealed characteristic cellular structures, including spinous and basal keratinocytes and papillary dermis. Results suggest that the smartphone confocal microscope has a potential to examine cellular details in vivo and may help disease diagnosis in resource-poor settings, where conducting standard histopathologic analysis is challenging. PMID:29675328

Scanning evanescent electro-magnetic microscope

DOEpatents

Xiang, Xiao-Dong; Gao, Chen; Schultz, Peter G.; Wei, Tao

2003-01-01

A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

Scanning evanescent electro-magnetic microscope

DOEpatents

Xiang, Xiao-Dong; Gao, Chen

2001-01-01

A novel scanning microscope is described that uses near-field evanescent electromagnetic waves to probe sample properties. The novel microscope is capable of high resolution imaging and quantitative measurements of the electrical properties of the sample. The inventive scanning evanescent wave electromagnetic microscope (SEMM) can map dielectric constant, tangent loss, conductivity, complex electrical impedance, and other electrical parameters of materials. The quantitative map corresponds to the imaged detail. The novel microscope can be used to measure electrical properties of both dielectric and electrically conducting materials.

Comprehensive study of unexpected microscope condensers formed in sample arrangements commonly used in optical microscopy.

PubMed

Desai, Darshan B; Aldawsari, Mabkhoot Mudith S; Alharbi, Bandar Mohammed H; Sen, Sanchari; Grave de Peralta, Luis

2015-09-01

We show that various setups for optical microscopy which are commonly used in biomedical laboratories behave like efficient microscope condensers that are responsible for observed subwavelength resolution. We present a series of experiments and simulations that reveal how inclined illumination from such unexpected condensers occurs when the sample is perpendicularly illuminated by a microscope's built-in white-light source. In addition, we demonstrate an inexpensive add-on optical module that serves as an efficient and lightweight microscope condenser. Using such add-on optical module in combination with a low-numerical-aperture objective lens and Fourier plane imaging microscopy technique, we demonstrate detection of photonic crystals with a period nearly eight times smaller than the Rayleigh resolution limit.

"Berries" on the Ground

NASA Image and Video Library

2004-02-12

This mosaic image shows an extreme close-up of round, blueberry-shaped formations in the martian soil near a part of the rock outcrop at Meridiani Planum called Stone Mountain. Scientists are studying these curious formations for clues about the area's past environmental conditions. The image, one of the highest resolution images ever taken by the microscopic imager, an instrument located on the Mars Exploration Rover Opportunity's instrument deployment device or "arm." http://photojournal.jpl.nasa.gov/catalog/PIA05273

Stimulated penetrating keratoplasty using real-time virtual intraoperative surgical optical coherence tomography

PubMed Central

Lee, Changho; Kim, Kyungun; Han, Seunghoon; Kim, Sehui; Lee, Jun Hoon; Kim, Hong kyun; Kim, Chulhong; Jung, Woonggyu; Kim, Jeehyun

2014-01-01

Abstract. An intraoperative surgical microscope is an essential tool in a neuro- or ophthalmological surgical environment. Yet, it has an inherent limitation to classify subsurface information because it only provides the surface images. To compensate for and assist in this problem, combining the surgical microscope with optical coherence tomography (OCT) has been adapted. We developed a real-time virtual intraoperative surgical OCT (VISOCT) system by adapting a spectral-domain OCT scanner with a commercial surgical microscope. Thanks to our custom-made beam splitting and image display subsystems, the OCT images and microscopic images are simultaneously visualized through an ocular lens or the eyepiece of the microscope. This improvement helps surgeons to focus on the operation without distraction to view OCT images on another separate display. Moreover, displaying the OCT live images on the eyepiece helps surgeon’s depth perception during the surgeries. Finally, we successfully processed stimulated penetrating keratoplasty in live rabbits. We believe that these technical achievements are crucial to enhance the usability of the VISOCT system in a real surgical operating condition. PMID:24604471

Mars Rock Formation Poses Mystery

NASA Technical Reports Server (NTRS)

2004-01-01

This sharp, close-up image taken by the microscopic imager on the Mars Exploration Rover Opportunity's instrument deployment device, or 'arm,' shows a rock target dubbed 'Robert E,' located on the rock outcrop at Meridiani Planum, Mars. Scientists are studying this area for clues about the rock outcrop's composition. This image measures 3 centimeters (1.2 inches) across and was taken on the 15th day of Opportunity's journey (Feb. 8, 2004).

Image analysis for the automated estimation of clonal growth and its application to the growth of smooth muscle cells.

PubMed

Gavino, V C; Milo, G E; Cornwell, D G

1982-03-01

Image analysis was used for the automated measurement of colony frequency (f) and colony diameter (d) in cultures of smooth muscle cells, Initial studies with the inverted microscope showed that number of cells (N) in a colony varied directly with d: log N = 1.98 log d - 3.469 Image analysis generated the complement of a cumulative distribution for f as a function of d. The number of cells in each segment of the distribution function was calculated by multiplying f and the average N for the segment. These data were displayed as a cumulative distribution function. The total number of colonies (fT) and the total number of cells (NT) were used to calculate the average colony size (NA). Population doublings (PD) were then expressed as log2 NA. Image analysis confirmed previous studies in which colonies were sized and counted with an inverted microscope. Thus, image analysis is a rapid and automated technique for the measurement of clonal growth.

Seamless stitching of tile scan microscope images.

PubMed

Legesse, F B; Chernavskaia, O; Heuke, S; Bocklitz, T; Meyer, T; Popp, J; Heintzmann, R

2015-06-01

For diagnostic purposes, optical imaging techniques need to obtain high-resolution images of extended biological specimens in reasonable time. The field of view of an objective lens, however, is often smaller than the sample size. To image the whole sample, laser scanning microscopes acquire tile scans that are stitched into larger mosaics. The appearance of such image mosaics is affected by visible edge artefacts that arise from various optical aberrations which manifest in grey level jumps across tile boundaries. In this contribution, a technique for stitching tiles into a seamless mosaic is presented. The stitching algorithm operates by equilibrating neighbouring edges and forcing the brightness at corners to a common value. The corrected image mosaics appear to be free from stitching artefacts and are, therefore, suited for further image analysis procedures. The contribution presents a novel method to seamlessly stitch tiles captured by a laser scanning microscope into a large mosaic. The motivation for the work is the failure of currently existing methods for stitching nonlinear, multimodal images captured by our microscopic setups. Our method eliminates the visible edge artefacts that appear between neighbouring tiles by taking into account the overall illumination differences among tiles in such mosaics. The algorithm first corrects the nonuniform brightness that exists within each of the tiles. It then compensates for grey level differences across tile boundaries by equilibrating neighbouring edges and forcing the brightness at the corners to a common value. After these artefacts have been removed further image analysis procedures can be applied on the microscopic images. Even though the solution presented here is tailored for the aforementioned specific case, it could be easily adapted to other contexts where image tiles are assembled into mosaics such as in astronomical or satellite photos. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Evaluation of breast tissue with confocal strip-mosaicking microscopy: a test approach emulating pathology-like examination

PubMed Central

Abeytunge, Sanjee; Larson, Bjorg; Peterson, Gary; Morrow, Monica; Rajadhyaksha, Milind

2017-01-01

Abstract. Confocal microscopy is an emerging technology for rapid imaging of freshly excised tissue without the need for frozen- or fixed-section processing. Initial studies have described imaging of breast tissue using fluorescence confocal microscopy with small regions of interest, typically 750×750  μm2. We present exploration with a microscope, termed confocal strip-mosaicking microscope (CSM microscope), which images an area of 2×2  cm2 of tissue with cellular-level resolution in 10 min of excision. Using the CSM microscope, we imaged 34 fresh, human, large breast tissue specimens from 18 patients, blindly analyzed by a board-certified pathologist and subsequently correlated with the corresponding standard fixed histopathology. Invasive tumors and benign tissue were clearly identified in CSM strip-mosaic images. Thirty specimens were concordant for image-to-histopathology correlation while four were discordant. PMID:28327961

Remote histology learning from static versus dynamic microscopic images.

PubMed

Mione, Sylvia; Valcke, Martin; Cornelissen, Maria

2016-05-06

Histology is the study of microscopic structures in normal tissue sections. Curriculum redesign in medicine has led to a decrease in the use of optical microscopes during practical classes. Other imaging solutions have been implemented to facilitate remote learning. With advancements in imaging technologies, learning material can now be digitized. Digitized microscopy images can be presented in either a static or dynamic format. This study of remote histology education identifies whether dynamic pictures are superior to static images for the acquisition of histological knowledge. Test results of two cohorts of second-year Bachelor in Medicine students at Ghent University were analyzed in two consecutive academic years: Cohort 1 (n = 190) and Cohort 2 (n = 174). Students in Cohort 1 worked with static images whereas students in Cohort 2 were presented with dynamic images. ANCOVA was applied to study differences in microscopy performance scores between the two cohorts, taking into account any possible initial differences in prior knowledge. The results show that practical histology scores are significantly higher with dynamic images as compared to static images (F (1,361) = 15.14, P < 0.01), regardless of student's gender and performance level. Several reasons for this finding can be explained in accordance with cognitivist learning theory. Since the findings suggest that knowledge construction with dynamic pictures is stronger as compared to static images, dynamic images should be introduced in a remote setting for microscopy education. Further implementation within a larger electronic learning management system needs to be explored in future research. Anat Sci Educ 9: 222-230. © 2015 American Association of Anatomists. © 2015 American Association of Anatomists.

Assessing various Infrared (IR) microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains.

PubMed

Woess, Claudia; Unterberger, Seraphin Hubert; Roider, Clemens; Ritsch-Marte, Monika; Pemberger, Nadin; Cemper-Kiesslich, Jan; Hatzer-Grubwieser, Petra; Parson, Walther; Pallua, Johannes Dominikus

2017-01-01

Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization) was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies) between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43-at 450 cm-1 and ν4PO43- from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio decreases with time. Cluster-analyses of data from Raman microscopic imaging reconstructed histo-anatomical features in comparison to the light microscopic image and finally, by application of principal component analyses (PCA), it was possible to see a clear distinction between forensic and archaeological bone samples. Hence, the spectral characterization of inorganic and organic compounds by the afore mentioned techniques, followed by analyses such as multivariate imaging analysis (MIAs) and principal component analyses (PCA), appear to be suitable for the post mortem interval (PMI) estimation of human skeletal remains.

Assessing various Infrared (IR) microscopic imaging techniques for post-mortem interval evaluation of human skeletal remains

PubMed Central

Roider, Clemens; Ritsch-Marte, Monika; Pemberger, Nadin; Cemper-Kiesslich, Jan; Hatzer-Grubwieser, Petra; Parson, Walther; Pallua, Johannes Dominikus

2017-01-01

Due to the influence of many environmental processes, a precise determination of the post-mortem interval (PMI) of skeletal remains is known to be very complicated. Although methods for the investigation of the PMI exist, there still remains much room for improvement. In this study the applicability of infrared (IR) microscopic imaging techniques such as reflection-, ATR- and Raman- microscopic imaging for the estimation of the PMI of human skeletal remains was tested. PMI specific features were identified and visualized by overlaying IR imaging data with morphological tissue structures obtained using light microscopy to differentiate between forensic and archaeological bone samples. ATR and reflection spectra revealed that a more prominent peak at 1042 cm-1 (an indicator for bone mineralization) was observable in archeological bone material when compared with forensic samples. Moreover, in the case of the archaeological bone material, a reduction in the levels of phospholipids, proteins, nucleic acid sugars, complex carbohydrates as well as amorphous or fully hydrated sugars was detectable at (reciprocal wavelengths/energies) between 3000 cm-1 to 2800 cm-1. Raman spectra illustrated a similar picture with less ν2PO43−at 450 cm-1 and ν4PO43− from 590 cm-1 to 584 cm-1, amide III at 1272 cm-1 and protein CH2 deformation at 1446 cm-1 in archeological bone material/samples/sources. A semi-quantitative determination of various distributions of biomolecules by chemi-maps of reflection- and ATR- methods revealed that there were less carbohydrates and complex carbohydrates as well as amorphous or fully hydrated sugars in archaeological samples compared with forensic bone samples. Raman- microscopic imaging data showed a reduction in B-type carbonate and protein α-helices after a PMI of 3 years. The calculated mineral content ratio and the organic to mineral ratio displayed that the mineral content ratio increases, while the organic to mineral ratio decreases with time. Cluster-analyses of data from Raman microscopic imaging reconstructed histo-anatomical features in comparison to the light microscopic image and finally, by application of principal component analyses (PCA), it was possible to see a clear distinction between forensic and archaeological bone samples. Hence, the spectral characterization of inorganic and organic compounds by the afore mentioned techniques, followed by analyses such as multivariate imaging analysis (MIAs) and principal component analyses (PCA), appear to be suitable for the post mortem interval (PMI) estimation of human skeletal remains. PMID:28334006

DIY: "Do Imaging Yourself" - Conventional microscopes as powerful tools for in vivo investigation.

PubMed

Antunes, Maísa Mota; Carvalho, Érika de; Menezes, Gustavo Batista

2018-01-01

Intravital imaging has been increasingly employed in cell biology studies and it is becoming one of the most powerful tools for in vivo investigation. Although some protocols can be extremely complex, most intravital imaging procedures can be performed using basic surgery and animal maintenance techniques. More importantly, regular confocal microscopes - the same that are used for imaging immunofluorescence slides - can also acquire high quality intravital images and movies after minor adaptations. Here we propose minimal adaptations in stock microscopes that allow major improvements in different fields of scientific investigation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microscope mode secondary ion mass spectrometry imaging with a Timepix detector.

PubMed

Kiss, Andras; Jungmann, Julia H; Smith, Donald F; Heeren, Ron M A

2013-01-01

In-vacuum active pixel detectors enable high sensitivity, highly parallel time- and space-resolved detection of ions from complex surfaces. For the first time, a Timepix detector assembly was combined with a secondary ion mass spectrometer for microscope mode secondary ion mass spectrometry (SIMS) imaging. Time resolved images from various benchmark samples demonstrate the imaging capabilities of the detector system. The main advantages of the active pixel detector are the higher signal-to-noise ratio and parallel acquisition of arrival time and position. Microscope mode SIMS imaging of biomolecules is demonstrated from tissue sections with the Timepix detector.

Martian Microscope

NASA Technical Reports Server (NTRS)

2004-01-01

The microscopic imager (circular device in center) is in clear view above the surface at Meridiani Planum, Mars, in this approximate true-color image taken by the panoramic camera on the Mars Exploration Rover Opportunity. The image was taken on the 9th sol of the rover's journey. The microscopic imager is located on the rover's instrument deployment device, or arm. The arrow is pointing to the lens of the instrument. Note the dust cover, which flips out to the left of the lens, is open. This approximated color image was created using the camera's violet and infrared filters as blue and red.

Predictive value of magnetic resonance imaging determined tumor contact length for extracapsular extension of prostate cancer.

PubMed

Baco, Eduard; Rud, Erik; Vlatkovic, Ljiljana; Svindland, Aud; Eggesbø, Heidi B; Hung, Andrew J; Matsugasumi, Toru; Bernhard, Jean-Christophe; Gill, Inderbir S; Ukimura, Osamu

2015-02-01

Tumor contact length is defined as the amount of prostate cancer in contact with the prostatic capsule. We evaluated the ability of magnetic resonance imaging determined tumor contact length to predict microscopic extracapsular extension compared to existing predictors of extracapsular extension. We retrospectively analyzed the records of 111 consecutive patients with magnetic resonance imaging/ultrasound fusion targeted, biopsy proven prostate cancer who underwent radical prostatectomy from January 2010 to July 2013. Median patient age was 64 years and median prostate specific antigen was 8.9 ng/ml. Clinical stage was cT1 in 93 cases (84%) and cT2 in 18 (16%). Postoperative pathological analysis confirmed pT2 in 71 patients (64%) and pT3 in 40 (36%). We evaluated 1) in the radical prostatectomy specimen the correlation of microscopic extracapsular extension with pathological cancer volume, pathological tumor contact length and Gleason score, 2) the correlation between microscopic extracapsular extension and magnetic resonance imaging tumor contact length, and 3) the ability of preoperative variables to predict microscopic extracapsular extension. Logistic regression analysis revealed that pathological tumor contact length correlated better with microscopic extracapsular extension than the predictive power of pathological cancer volume (0.821 vs 0.685). The Spearman correlation between pathological and magnetic resonance imaging tumor contact length was r = 0.839 (p <0.0001). ROC AUC analysis revealed that magnetic resonance imaging tumor contact length outperformed cancer core involvement on targeted biopsy and the Partin tables to predict microscopic extracapsular extension (0.88 vs 0.70 and 0.63, respectively). At a magnetic resonance imaging tumor contact length threshold of 20 mm the accuracy for diagnosing microscopic extracapsular extension was superior to that of conventional magnetic resonance imaging criteria (82% vs 67%, p = 0.015). We developed a predicted probability plot curve of extracapsular extension according to magnetic resonance imaging tumor contact length. Magnetic resonance imaging determined tumor contact length could be a promising quantitative predictor of microscopic extracapsular extension. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Surface imaging microscope

NASA Astrophysics Data System (ADS)

Rogala, Eric W.; Bankman, Isaac N.

2008-04-01

The three-dimensional shapes of microscopic objects are becoming increasingly important for battlespace CBRNE sensing. Potential applications of microscopic 3D shape observations include characterization of biological weapon particles and manufacturing of micromechanical components. Aerosol signatures of stand-off lidar systems, using elastic backscatter or polarization, are dictated by the aerosol particle shapes and sizes that must be well characterized in the lab. A low-cost, fast instrument for 3D surface shape microscopy will be a valuable point sensor for biological particle sensing applications. Both the cost and imaging durations of traditional techniques such as confocal microscopes, atomic force microscopes, and electron scanning microscopes are too high. We investigated the feasibility of a low-cost, fast interferometric technique for imaging the 3D surface shape of microscopic objects at frame rates limited only by the camera in the system. The system operates at two laser wavelengths producing two fringe images collected simultaneously by a digital camera, and a specialized algorithm we developed reconstructs the surface map of the microscopic object. The current implementation assembled to test the concept and develop the new 3D reconstruction algorithm has 0.25 micron resolution in the x and y directions, and about 0.1 micron accuracy in the z direction, as tested on a microscopic glass test object manufactured with etching techniques. We describe the interferometric instrument, present the reconstruction algorithm, and discuss further development.

Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method

NASA Astrophysics Data System (ADS)

Huynh, Toan; Daddysman, Matthew K.; Bao, Ying; Selewa, Alan; Kuznetsov, Andrey; Philipson, Louis H.; Scherer, Norbert F.

2017-05-01

Imaging specific regions of interest (ROIs) of nanomaterials or biological samples with different imaging modalities (e.g., light and electron microscopy) or at subsequent time points (e.g., before and after off-microscope procedures) requires relocating the ROIs. Unfortunately, relocation is typically difficult and very time consuming to achieve. Previously developed techniques involve the fabrication of arrays of features, the procedures for which are complex, and the added features can interfere with imaging the ROIs. We report the Fast and Accurate Relocation of Microscopic Experimental Regions (FARMER) method, which only requires determining the coordinates of 3 (or more) conspicuous reference points (REFs) and employs an algorithm based on geometric operators to relocate ROIs in subsequent imaging sessions. The 3 REFs can be quickly added to various regions of a sample using simple tools (e.g., permanent markers or conductive pens) and do not interfere with the ROIs. The coordinates of the REFs and the ROIs are obtained in the first imaging session (on a particular microscope platform) using an accurate and precise encoded motorized stage. In subsequent imaging sessions, the FARMER algorithm finds the new coordinates of the ROIs (on the same or different platforms), using the coordinates of the manually located REFs and the previously recorded coordinates. FARMER is convenient, fast (3-15 min/session, at least 10-fold faster than manual searches), accurate (4.4 μm average error on a microscope with a 100x objective), and precise (almost all errors are <8 μm), even with deliberate rotating and tilting of the sample well beyond normal repositioning accuracy. We demonstrate this versatility by imaging and re-imaging a diverse set of samples and imaging methods: live mammalian cells at different time points; fixed bacterial cells on two microscopes with different imaging modalities; and nanostructures on optical and electron microscopes. FARMER can be readily adapted to any imaging system with an encoded motorized stage and can facilitate multi-session and multi-platform imaging experiments in biology, materials science, photonics, and nanoscience.

Ultrafast superresolution fluorescence imaging with spinning disk confocal microscope optics.

PubMed

Hayashi, Shinichi; Okada, Yasushi

2015-05-01

Most current superresolution (SR) microscope techniques surpass the diffraction limit at the expense of temporal resolution, compromising their applications to live-cell imaging. Here we describe a new SR fluorescence microscope based on confocal microscope optics, which we name the spinning disk superresolution microscope (SDSRM). Theoretically, the SDSRM is equivalent to a structured illumination microscope (SIM) and achieves a spatial resolution of 120 nm, double that of the diffraction limit of wide-field fluorescence microscopy. However, the SDSRM is 10 times faster than a conventional SIM because SR signals are recovered by optical demodulation through the stripe pattern of the disk. Therefore a single SR image requires only a single averaged image through the rotating disk. On the basis of this theory, we modified a commercial spinning disk confocal microscope. The improved resolution around 120 nm was confirmed with biological samples. The rapid dynamics of micro-tubules, mitochondria, lysosomes, and endosomes were observed with temporal resolutions of 30-100 frames/s. Because our method requires only small optical modifications, it will enable an easy upgrade from an existing spinning disk confocal to a SR microscope for live-cell imaging. © 2015 Hayashi and Okada. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Mars Under the Microscope

NASA Technical Reports Server (NTRS)

2004-01-01

This magnified look at the martian soil near the Mars Exploration Rover Opportunity's landing site, Meridiani Planum, shows coarse grains sprinkled over a fine layer of sand. The image was captured by the rover's microscopic imager on the 10th day, or sol, of its mission. Scientists are intrigued by the spherical rocks, which can be formed by a variety of geologic processes, including cooling of molten lava droplets and accretion of concentric layers of material around a particle or 'seed.'

The examined patch of soil is 3 centimeters (1.2 inches) across. The circular grain in the lower left corner is approximately 3 millimeters (.12 inches) across, or about the size of a sunflower seed.

Enhancement of graphene visibility on transparent substrates by refractive index optimization.

PubMed

Gonçalves, Hugo; Alves, Luís; Moura, Cacilda; Belsley, Michael; Stauber, Tobias; Schellenberg, Peter

2013-05-20

Optical reflection microscopy is one of the main imaging tools to visualize graphene microstructures. Here is reported a novel method that employs refractive index optimization in an optical reflection microscope, which greatly improves the visibility of graphene flakes. To this end, an immersion liquid with a refractive index that is close to that of the glass support is used in-between the microscope lens and the support improving the contrast and resolution of the sample image. Results show that the contrast of single and few layer graphene crystals and structures can be enhanced by a factor of 4 compared to values commonly achieved with transparent substrates using optical reflection microscopy lacking refractive index optimization.

Morphometric information to reduce the semantic gap in the characterization of microscopic images of thyroid nodules.

PubMed

Macedo, Alessandra A; Pessotti, Hugo C; Almansa, Luciana F; Felipe, Joaquim C; Kimura, Edna T

2016-07-01

The analyses of several systems for medical-imaging processing typically support the extraction of image attributes, but do not comprise some information that characterizes images. For example, morphometry can be applied to find new information about the visual content of an image. The extension of information may result in knowledge. Subsequently, results of mappings can be applied to recognize exam patterns, thus improving the accuracy of image retrieval and allowing a better interpretation of exam results. Although successfully applied in breast lesion images, the morphometric approach is still poorly explored in thyroid lesions due to the high subjectivity thyroid examinations. This paper presents a theoretical-practical study, considering Computer Aided Diagnosis (CAD) and Morphometry, to reduce the semantic discontinuity between medical image features and human interpretation of image content. The proposed method aggregates the content of microscopic images characterized by morphometric information and other image attributes extracted by traditional object extraction algorithms. This method carries out segmentation, feature extraction, image labeling and classification. Morphometric analysis was included as an object extraction method in order to verify the improvement of its accuracy for automatic classification of microscopic images. To validate this proposal and verify the utility of morphometric information to characterize thyroid images, a CAD system was created to classify real thyroid image-exams into Papillary Cancer, Goiter and Non-Cancer. Results showed that morphometric information can improve the accuracy and precision of image retrieval and the interpretation of results in computer-aided diagnosis. For example, in the scenario where all the extractors are combined with the morphometric information, the CAD system had its best performance (70% of precision in Papillary cases). Results signalized a positive use of morphometric information from images to reduce semantic discontinuity between human interpretation and image characterization. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Soft x-ray imaging with incoherent sources

NASA Astrophysics Data System (ADS)

Wachulak, P.; Torrisi, A.; Ayele, M.; Bartnik, A.; Czwartos, J.; Wegrzyński, Ł.; Fok, T.; Parkman, T.; Vondrová, Š.; Turnová, J.; Odstrcil, M.; Fiedorowicz, H.

2017-05-01

In this work we present experimental, compact desk-top SXR microscope, the EUV microscope which is at this stage a technology demonstrator, and finally, the SXR contact microscope. The systems are based on laser-plasma EUV and SXR sources, employing a double stream gas puff target. The EUV and SXR full field microscopes, operating at 13.8 nm and 2.88 nm wavelengths, respectively, are capable of imaging nanostructures with a sub-50 nm spatial resolution with relatively short (seconds) exposure times. The SXR contact microscope operates in the "water-window" spectral range, to produce an imprint of the internal structure of the sample in a thin layer of SXR light sensitive photoresist. Applications of such desk-top EUV and SXR microscopes for studies of variety of different samples - test objects for resolution assessment and other objects such as carbon membranes, DNA plasmid samples, organic and inorganic thin layers, diatoms, algae and carcinoma cells, are also presented. Details about the sources, the microscopes as well as the imaging results for various objects will be presented and discussed. The development of such compact imaging systems may be important to the new research related to biological, material science and nanotechnology applications.

Water window imaging x ray microscope

NASA Technical Reports Server (NTRS)

Hoover, Richard B. (Inventor)

1992-01-01

A high resolution x ray microscope for imaging microscopic structures within biological specimens has an optical system including a highly polished primary and secondary mirror coated with identical multilayer coatings, the mirrors acting at normal incidence. The coatings have a high reflectivity in the narrow wave bandpass between 23.3 and 43.7 angstroms and have low reflectivity outside of this range. The primary mirror has a spherical concave surface and the secondary mirror has a spherical convex surface. The radii of the mirrors are concentric about a common center of curvature on the optical axis of the microscope extending from the object focal plane to the image focal plane. The primary mirror has an annular configuration with a central aperture and the secondary mirror is positioned between the primary mirror and the center of curvature for reflecting radiation through the aperture to a detector. An x ray filter is mounted at the stage end of the microscope, and film sensitive to x rays in the desired band width is mounted in a camera at the image plane of the optical system. The microscope is mounted within a vacuum chamber for minimizing the absorption of x rays in air from a source through the microscope.

SlideJ: An ImageJ plugin for automated processing of whole slide images.

PubMed

Della Mea, Vincenzo; Baroni, Giulia L; Pilutti, David; Di Loreto, Carla

2017-01-01

The digital slide, or Whole Slide Image, is a digital image, acquired with specific scanners, that represents a complete tissue sample or cytological specimen at microscopic level. While Whole Slide image analysis is recognized among the most interesting opportunities, the typical size of such images-up to Gpixels- can be very demanding in terms of memory requirements. Thus, while algorithms and tools for processing and analysis of single microscopic field images are available, Whole Slide images size makes the direct use of such tools prohibitive or impossible. In this work a plugin for ImageJ, named SlideJ, is proposed with the objective to seamlessly extend the application of image analysis algorithms implemented in ImageJ for single microscopic field images to a whole digital slide analysis. The plugin has been complemented by examples of macro in the ImageJ scripting language to demonstrate its use in concrete situations.

Video-rate confocal microscopy for single-molecule imaging in live cells and superresolution fluorescence imaging.

PubMed

Lee, Jinwoo; Miyanaga, Yukihiro; Ueda, Masahiro; Hohng, Sungchul

2012-10-17

There is no confocal microscope optimized for single-molecule imaging in live cells and superresolution fluorescence imaging. By combining the swiftness of the line-scanning method and the high sensitivity of wide-field detection, we have developed a, to our knowledge, novel confocal fluorescence microscope with a good optical-sectioning capability (1.0 μm), fast frame rates (<33 fps), and superior fluorescence detection efficiency. Full compatibility of the microscope with conventional cell-imaging techniques allowed us to do single-molecule imaging with a great ease at arbitrary depths of live cells. With the new microscope, we monitored diffusion motion of fluorescently labeled cAMP receptors of Dictyostelium discoideum at both the basal and apical surfaces and obtained superresolution fluorescence images of microtubules of COS-7 cells at depths in the range 0-85 μm from the surface of a coverglass. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

In vivo imaging of oral neoplasia using a miniaturized fiber optic confocal reflectance microscope.

PubMed

Maitland, Kristen C; Gillenwater, Ann M; Williams, Michelle D; El-Naggar, Adel K; Descour, Michael R; Richards-Kortum, Rebecca R

2008-11-01

The purpose of this study was to determine whether in vivo images of oral mucosa obtained with a fiber optic confocal reflectance microscope could be used to differentiate normal and neoplastic tissues. We imaged 20 oral sites in eight patients undergoing surgery for squamous cell carcinoma. Normal and abnormal areas within the oral cavity were identified clinically, and real-time videos of each site were obtained in vivo using a fiber optic confocal reflectance microscope. Following imaging, each site was biopsied and submitted for histopathologic examination. We identified distinct features, such as nuclear irregularity and spacing, which can be used to qualitatively differentiate between normal and abnormal tissue. Representative confocal images of normal, pre-neoplastic, and neoplastic oral tissue are presented. Previous work using much larger microscopes has demonstrated the ability of confocal reflectance microscopy to image cellular and tissue architecture in situ. New advances in technology have enabled miniaturization of imaging systems for in vivo use.

AOTF microscope for imaging with increased speed and spectral versatility.

PubMed Central

Wachman, E S; Niu, W; Farkas, D L

1997-01-01

We have developed a new fluorescence microscope that addresses the spectral and speed limitations of current light microscopy instrumentation. In the present device, interference and neutral density filters normally used for fluorescence excitation and detection are replaced by acousto-optic tunable filters (AOTFs). Improvements are described, including the use of a dispersing prism in conjunction with the imaging AOTF and an oblique-illumination excitation scheme, which together enable the AOTF microscope to produce images comparable to those obtained with conventional fluorescence instruments. The superior speed and spectral versatility of the AOTF microscope are demonstrated by a ratio image pair acquired in 3.5 ms and a micro-spectral absorbance measurement of hemoglobin through a cranial window in a living mouse. Images FIGURE 1 FIGURE 2 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 PMID:9284289

Active mask segmentation of fluorescence microscope images.

PubMed

Srinivasa, Gowri; Fickus, Matthew C; Guo, Yusong; Linstedt, Adam D; Kovacević, Jelena

2009-08-01

We propose a new active mask algorithm for the segmentation of fluorescence microscope images of punctate patterns. It combines the (a) flexibility offered by active-contour methods, (b) speed offered by multiresolution methods, (c) smoothing offered by multiscale methods, and (d) statistical modeling offered by region-growing methods into a fast and accurate segmentation tool. The framework moves from the idea of the "contour" to that of "inside and outside," or masks, allowing for easy multidimensional segmentation. It adapts to the topology of the image through the use of multiple masks. The algorithm is almost invariant under initialization, allowing for random initialization, and uses a few easily tunable parameters. Experiments show that the active mask algorithm matches the ground truth well and outperforms the algorithm widely used in fluorescence microscopy, seeded watershed, both qualitatively, as well as quantitatively.

Multi-compartment microscopic diffusion imaging

PubMed Central

Kaden, Enrico; Kelm, Nathaniel D.; Carson, Robert P.; Does, Mark D.; Alexander, Daniel C.

2017-01-01

This paper introduces a multi-compartment model for microscopic diffusion anisotropy imaging. The aim is to estimate microscopic features specific to the intra- and extra-neurite compartments in nervous tissue unconfounded by the effects of fibre crossings and orientation dispersion, which are ubiquitous in the brain. The proposed MRI method is based on the Spherical Mean Technique (SMT), which factors out the neurite orientation distribution and thus provides direct estimates of the microscopic tissue structure. This technique can be immediately used in the clinic for the assessment of various neurological conditions, as it requires only a widely available off-the-shelf sequence with two b-shells and high-angular gradient resolution achievable within clinically feasible scan times. To demonstrate the developed method, we use high-quality diffusion data acquired with a bespoke scanner system from the Human Connectome Project. This study establishes the normative values of the new biomarkers for a large cohort of healthy young adults, which may then support clinical diagnostics in patients. Moreover, we show that the microscopic diffusion indices offer direct sensitivity to pathological tissue alterations, exemplified in a preclinical animal model of Tuberous Sclerosis Complex (TSC), a genetic multi-organ disorder which impacts brain microstructure and hence may lead to neurological manifestations such as autism, epilepsy and developmental delay. PMID:27282476

A study on high NA and evanescent imaging with polarized illumination

NASA Astrophysics Data System (ADS)

Yang, Seung-Hune

Simulation techniques are developed for high NA polarized microscopy with Babinet's principle, partial coherence and vector diffraction for non-periodic geometries. A mathematical model for the Babinet approach is developed and interpreted. Simulation results of the Babinet's principle approach are compared with those of Rigorous Coupled Wave Theory (RCWT) for periodic structures to investigate the accuracy of this approach and its limitations. A microscope system using a special solid immersion lens (SIL) is introduced to image Blu-Ray (BD) optical disc samples without removing the protective cover layer. Aberration caused by the cover layer is minimized with a truncated SIL. Sub-surface imaging simulation is achieved by RCWT, partial coherence, vector diffraction and Babinet's Principle. Simulated results are compared with experimental images and atomic force microscopy (AFM) measurement. A technique for obtaining native and induced using a significant amount of evanescent energy is described for a solid immersion lens (SIL) microscope. Characteristics of native and induced polarization images for different object structures and materials are studied in detail. Experiments are conducted with a NA = 1.48 at lambda = 550nm microscope. Near-field images are simulated and analyzed with an RCWT approach. Contrast curve versus object spatial frequency calculations are compared with experimental measurements. Dependencies of contrast versus source polarization angles and air gap for native and induced polarization image profiles are evaluated. By using the relationship between induced polarization and topographical structure, an induced polarization image of an alternating phase shift mask (PSM) is converted into a topographical image, which shows very good agreement with AFM measurement. Images of other material structures include a dielectric grating, chrome-on-glass grating, silicon CPU structure, BD-R and BD-ROM.

Mars Life? - Microscopic Tubular Structures

NASA Technical Reports Server (NTRS)

1996-01-01

This electron microscope image shows tubular structures of likely Martian origin. These structures are very similar in size and shape to extremely tiny microfossils found in some Earth rocks. This photograph is part of a report by a NASA research team published in the Aug. 16, 1996, issue of the journal Science. A two-year investigation by the team found organic molecules, mineral features characteristic of biological activity and possible microscopic fossils such as these inside of an ancient Martian rock that fell to Earth as a meteorite. The largest possible fossils are less than 1/100th the diameter of a human hair in size while most are ten times smaller.

Image Montaging for Creating a Virtual Pathology Slide: An Innovative and Economical Tool to Obtain a Whole Slide Image

PubMed Central

Pandurangappa, Rohit; Annavajjula, Saileela; Rajashekaraiah, Premalatha Bidadi

2016-01-01

Background. Microscopes are omnipresent throughout the field of biological research. With microscopes one can see in detail what is going on at the cellular level in tissues. Though it is a ubiquitous tool, the limitation is that with high magnification there is a small field of view. It is often advantageous to see an entire sample at high magnification. Over the years technological advancements in optics have helped to provide solutions to this limitation of microscopes by creating the so-called dedicated “slide scanners” which can provide a “whole slide digital image.” These scanners can provide seamless, large-field-of-view, high resolution image of entire tissue section. The only disadvantage of such complete slide imaging system is its outrageous cost, thereby hindering their practical use by most laboratories, especially in developing and low resource countries. Methods. In a quest for their substitute, we tried commonly used image editing software Adobe Photoshop along with a basic image capturing device attached to a trinocular microscope to create a digital pathology slide. Results. The seamless image created using Adobe Photoshop maintained its diagnostic quality. Conclusion. With time and effort photomicrographs obtained from a basic camera-microscope set up can be combined and merged in Adobe Photoshop to create a whole slide digital image of practically usable quality at a negligible cost. PMID:27747147

Image Montaging for Creating a Virtual Pathology Slide: An Innovative and Economical Tool to Obtain a Whole Slide Image.

PubMed

Banavar, Spoorthi Ravi; Chippagiri, Prashanthi; Pandurangappa, Rohit; Annavajjula, Saileela; Rajashekaraiah, Premalatha Bidadi

2016-01-01

Background . Microscopes are omnipresent throughout the field of biological research. With microscopes one can see in detail what is going on at the cellular level in tissues. Though it is a ubiquitous tool, the limitation is that with high magnification there is a small field of view. It is often advantageous to see an entire sample at high magnification. Over the years technological advancements in optics have helped to provide solutions to this limitation of microscopes by creating the so-called dedicated "slide scanners" which can provide a "whole slide digital image." These scanners can provide seamless, large-field-of-view, high resolution image of entire tissue section. The only disadvantage of such complete slide imaging system is its outrageous cost, thereby hindering their practical use by most laboratories, especially in developing and low resource countries. Methods . In a quest for their substitute, we tried commonly used image editing software Adobe Photoshop along with a basic image capturing device attached to a trinocular microscope to create a digital pathology slide. Results . The seamless image created using Adobe Photoshop maintained its diagnostic quality. Conclusion . With time and effort photomicrographs obtained from a basic camera-microscope set up can be combined and merged in Adobe Photoshop to create a whole slide digital image of practically usable quality at a negligible cost.

Mars Rock Formation Poses Mystery-2

NASA Technical Reports Server (NTRS)

2004-01-01

This sharp, close-up image taken by the microscopic imager on the Mars Exploration Rover Opportunity's instrument deployment device, or 'arm,' shows a rock target dubbed 'Robert E,' located on the rock outcrop at Meridiani Planum, Mars. Scientists are studying the spherule, or small sphere, in the center of the image that appears to be protruding from the rock formation. This image measures 3 centimeters (1.2 inches) across and was taken on the 15th day of Opportunity's journey (Feb. 8, 2004).

SlideJ: An ImageJ plugin for automated processing of whole slide images

PubMed Central

Baroni, Giulia L.; Pilutti, David; Di Loreto, Carla

2017-01-01

The digital slide, or Whole Slide Image, is a digital image, acquired with specific scanners, that represents a complete tissue sample or cytological specimen at microscopic level. While Whole Slide image analysis is recognized among the most interesting opportunities, the typical size of such images—up to Gpixels- can be very demanding in terms of memory requirements. Thus, while algorithms and tools for processing and analysis of single microscopic field images are available, Whole Slide images size makes the direct use of such tools prohibitive or impossible. In this work a plugin for ImageJ, named SlideJ, is proposed with the objective to seamlessly extend the application of image analysis algorithms implemented in ImageJ for single microscopic field images to a whole digital slide analysis. The plugin has been complemented by examples of macro in the ImageJ scripting language to demonstrate its use in concrete situations. PMID:28683129

Cryogenic immersion microscope

DOEpatents

Le Gros, Mark; Larabell, Carolyn A.

2010-12-14

A cryogenic immersion microscope whose objective lens is at least partially in contact with a liquid reservoir of a cryogenic liquid, in which reservoir a sample of interest is immersed is disclosed. When the cryogenic liquid has an index of refraction that reduces refraction at interfaces between the lens and the sample, overall resolution and image quality are improved. A combination of an immersion microscope and x-ray microscope, suitable for imaging at cryogenic temperatures is also disclosed.

Quantification of tooth wear: conventional vs new method using toolmakers microscope and a three-dimensional measuring technique.

PubMed

Al-Omiri, Mahmoud K; Harb, Rousan; Abu Hammad, Osama A; Lamey, Philip-John; Lynch, Edward; Clifford, Thomas J

2010-07-01

This study aimed to evaluate the reliability of a new CAD-CAM Laser scanning machine in detection of incisal tooth wear through a 6-month period and to compare the accuracy of using this new machine against measuring tooth wear using tool maker microscope and conventional tooth wear index. Twenty participants (11 males and 9 females, mean age=22.7 years, SD=2.0) were assessed for incisal tooth wear of lower anterior teeth using Smith and Knight clinical tooth wear index (TWI) on two occasions, the study baseline and 6 months later. Stone dies for each tooth were prepared and scanned using the CAD-CAM Laser Cercon System (Cercon Smart Ceramics, DeguDent, Germany). Scanned images were printed and examined under a toolmaker microscope (Stedall-Dowding Machine Tool Company, Optique et Mecanique de Precision, Marcel Aubert SA, Switzerland) to quantify tooth wear and then the dies were directly assessed under the microscope to measure tooth wear. The Wilcoxon Signed Ranks Test was used to analyse the data. TWI scores for incisal edges were 0, 1, and 2 and were similar at both occasions. Scores 3 and 4 were not detected. Wear values measured by directly assessing the dies under the tool maker microscope (range=517-656microm, mean=582microm, and SD=50) were significantly more than those measured from the Cercon digital machine images (range=132-193microm, mean =165microm, and SD=27) and both showed significant differences between the two occasions. Measuring images obtained with Cercon digital machine under tool maker microscope allowed detection of wear progression over the 6-month period. However, measuring the dies of worn dentition directly under the tool maker microscope enabled detection of wear progression more accurately. Conventional method was the least sensitive for tooth wear quantification and was unable to identify wear progression in most cases. Copyright 2010 Elsevier Ltd. All rights reserved.

Near-Field Acoustical Imaging using Lateral Bending Mode of Atomic Force Microscope Cantilevers

NASA Astrophysics Data System (ADS)

Caron, A.; Rabe, U.; Rödel, J.; Arnold, W.

Scanning probe microscopy techniques enable one to investigate surface properties such as contact stiffness and friction between the probe tip and a sample with nm resolution. So far the bending and the torsional eigenmodes of an atomic force microscope cantilever have been used to image variations of elasticity and shear elasticity, respectively. Such images are near-field images with the resolution given by the contact radius typically between 10 nm and 50 nm. We show that the flexural modes of a cantilever oscillating in the width direction and parallel to the sample surface can also be used for imaging. Additional to the dominant in-plane component of the oscillation, the lateral modes exhibit a vertical component as well, provided there is an asymmetry in the cross-section of the cantilever or in its suspension. The out-of-plane deflection renders the lateral modes detectable by the optical position sensors used in atomic force microscopes. We studied cracks which were generated by Vickers indents, in submicro- and nanocrystalline ZrO2. Images of the lateral contact stiffness were obtained by vibrating the cantilever close to a contact-resonance frequency. A change in contact stiffness causes a shift of the resonant frequency and hence a change of the cantilever vibration amplitude. The lateral contact-stiffness images close to the crack faces display a contrast that we attribute to altered elastic properties indicating a process zone. This could be caused by a stress-induced phase transformation during crack propagation. Using the contact mode of an atomic force microscope, we measured the crack-opening displacement as a function of distance from the crack tip, and we determined the crack-tip toughness Ktip. Furthermore, K1c was inferred from the length of radial cracks of Vickers indents that were measured using classical scanning acoustic microscopy

Images from Phoenix's MECA Instruments

NASA Technical Reports Server (NTRS)

2008-01-01

The image on the upper left is from NASA's Phoenix Mars Lander's Optical Microscope after a sample informally called 'Sorceress' was delivered to its silicon substrate on the 38th Martian day, or sol, of the mission (July 2, 2008).

A 3D representation of the same sample is on the right, as seen by Phoenix's Atomic Force Microscope. This is 100 times greater magnification than the view from the Optical Microscope, and the most highly magnified image ever seen from another world.

The Optical Microscope and the Atomic Force Microscope are part of Phoenix's Microscopy, Electrochemistry and Conductivity Analyzer instrument.

The Atomic Force Microscope was developed by a Swiss-led consortium in collaboration with Imperial College London.

The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

Navigation and Image Injection for Control of Bone Removal and Osteotomy Planes in Spine Surgery.

PubMed

Kosterhon, Michael; Gutenberg, Angelika; Kantelhardt, Sven Rainer; Archavlis, Elefterios; Giese, Alf

2017-04-01

In contrast to cranial interventions, neuronavigation in spinal surgery is used in few applications, not tapping into its full technological potential. We have developed a method to preoperatively create virtual resection planes and volumes for spinal osteotomies and export 3-D operation plans to a navigation system controlling intraoperative visualization using a surgical microscope's head-up display. The method was developed using a Sawbone ® model of the lumbar spine, demonstrating feasibility with high precision. Computer tomographic and magnetic resonance image data were imported into Amira ® , a 3-D visualization software. Resection planes were positioned, and resection volumes representing intraoperative bone removal were defined. Fused to the original Digital Imaging and Communications in Medicine data, the osteotomy planes were exported to the cranial version of a Brainlab ® navigation system. A navigated surgical microscope with video connection to the navigation system allowed intraoperative image injection to visualize the preplanned resection planes. The workflow was applied to a patient presenting with a congenital hemivertebra of the thoracolumbar spine. Dorsal instrumentation with pedicle screws and rods was followed by resection of the deformed vertebra guided by the in-view image injection of the preplanned resection planes into the optical path of a surgical microscope. Postoperatively, the patient showed no neurological deficits, and the spine was found to be restored in near physiological posture. The intraoperative visualization of resection planes in a microscope's head-up display was found to assist the surgeon during the resection of a complex-shaped bone wedge and may help to further increase accuracy and patient safety. Copyright © 2017 by the Congress of Neurological Surgeons

Scanning electron microscope fine tuning using four-bar piezoelectric actuated mechanism

NASA Astrophysics Data System (ADS)

Hatamleh, Khaled S.; Khasawneh, Qais A.; Al-Ghasem, Adnan; Jaradat, Mohammad A.; Sawaqed, Laith; Al-Shabi, Mohammad

2018-01-01

Scanning Electron Microscopes are extensively used for accurate micro/nano images exploring. Several strategies have been proposed to fine tune those microscopes in the past few years. This work presents a new fine tuning strategy of a scanning electron microscope sample table using four bar piezoelectric actuated mechanisms. The introduced paper presents an algorithm to find all possible inverse kinematics solutions of the proposed mechanism. In addition, another algorithm is presented to search for the optimal inverse kinematic solution. Both algorithms are used simultaneously by means of a simulation study to fine tune a scanning electron microscope sample table through a pre-specified circular or linear path of motion. Results of the study shows that, proposed algorithms were able to minimize the power required to drive the piezoelectric actuated mechanism by a ratio of 97.5% for all simulated paths of motion when compared to general non-optimized solution.

Optimal resolution in Fresnel incoherent correlation holographic fluorescence microscopy

PubMed Central

Brooker, Gary; Siegel, Nisan; Wang, Victor; Rosen, Joseph

2011-01-01

Fresnel Incoherent Correlation Holography (FINCH) enables holograms and 3D images to be created from incoherent light with just a camera and spatial light modulator (SLM). We previously described its application to microscopic incoherent fluorescence wherein one complex hologram contains all the 3D information in the microscope field, obviating the need for scanning or serial sectioning. We now report experiments which have led to the optimal optical, electro-optic, and computational conditions necessary to produce holograms which yield high quality 3D images from fluorescent microscopic specimens. An important improvement from our previous FINCH configurations capitalizes on the polarization sensitivity of the SLM so that the same SLM pixels which create the spherical wave simulating the microscope tube lens, also pass the plane waves from the infinity corrected microscope objective, so that interference between the two wave types at the camera creates a hologram. This advance dramatically improves the resolution of the FINCH system. Results from imaging a fluorescent USAF pattern and a pollen grain slide reveal resolution which approaches the Rayleigh limit by this simple method for 3D fluorescent microscopic imaging. PMID:21445140

Assessing delivery and quantifying efficacy of small interfering ribonucleic acid therapeutics in the skin using a dual-axis confocal microscope

NASA Astrophysics Data System (ADS)

Ra, Hyejun; Gonzalez-Gonzalez, Emilio; Smith, Bryan R.; Gambhir, Sanjiv S.; Kino, Gordon S.; Solgaard, Olav; Kaspar, Roger L.; Contag, Christopher H.

2010-05-01

Transgenic reporter mice and advances in imaging instrumentation are enabling real-time visualization of cellular mechanisms in living subjects and accelerating the development of novel therapies. Innovative confocal microscope designs are improving their utility for microscopic imaging of fluorescent reporters in living animals. We develop dual-axis confocal (DAC) microscopes for such in vivo studies and create mouse models where fluorescent proteins are expressed in the skin for the purpose of advancing skin therapeutics and transdermal delivery tools. Three-dimensional image volumes, through the different skin compartments of the epidermis and dermis, can be acquired in several seconds with the DAC microscope in living mice, and are comparable to histologic analyses of reporter protein expression patterns in skin sections. Intravital imaging with the DAC microscope further enables visualization of green fluorescent protein (GFP) reporter gene expression in the skin over time, and quantification of transdermal delivery of small interfering RNA (siRNA) and therapeutic efficacy. Visualization of transdermal delivery of nucleic acids will play an important role in the development of innovative strategies for treating skin pathologies.

On-Chip Imaging of Schistosoma haematobium Eggs in Urine for Diagnosis by Computer Vision

PubMed Central

Linder, Ewert; Grote, Anne; Varjo, Sami; Linder, Nina; Lebbad, Marianne; Lundin, Mikael; Diwan, Vinod; Hannuksela, Jari; Lundin, Johan

2013-01-01

Background Microscopy, being relatively easy to perform at low cost, is the universal diagnostic method for detection of most globally important parasitic infections. As quality control is hard to maintain, misdiagnosis is common, which affects both estimates of parasite burdens and patient care. Novel techniques for high-resolution imaging and image transfer over data networks may offer solutions to these problems through provision of education, quality assurance and diagnostics. Imaging can be done directly on image sensor chips, a technique possible to exploit commercially for the development of inexpensive “mini-microscopes”. Images can be transferred for analysis both visually and by computer vision both at point-of-care and at remote locations. Methods/Principal Findings Here we describe imaging of helminth eggs using mini-microscopes constructed from webcams and mobile phone cameras. The results show that an inexpensive webcam, stripped off its optics to allow direct application of the test sample on the exposed surface of the sensor, yields images of Schistosoma haematobium eggs, which can be identified visually. Using a highly specific image pattern recognition algorithm, 4 out of 5 eggs observed visually could be identified. Conclusions/Significance As proof of concept we show that an inexpensive imaging device, such as a webcam, may be easily modified into a microscope, for the detection of helminth eggs based on on-chip imaging. Furthermore, algorithms for helminth egg detection by machine vision can be generated for automated diagnostics. The results can be exploited for constructing simple imaging devices for low-cost diagnostics of urogenital schistosomiasis and other neglected tropical infectious diseases. PMID:24340107

Hybrid of two-photon microscopy and optical multimodality imaging for multi-scale imaging of small animals

NASA Astrophysics Data System (ADS)

Li, Tianmeng; Hui, Hui; Ma, He; Yang, Xin; Tian, Jie

2018-02-01

Non-invasive imaging technologies, such as magnetic resonance imaging (MRI) and optical multimodality imaging methods, are commonly used for diagnosing and supervising the development of inflammatory bowel disease (IBD). These in vivo imaging methods can provide morphology changes information of IBD in macro-scale. However, it is difficult to investigate the intestinal wall in molecular and cellular level. State-of-art light-sheet and two-photon microscopy have the ability to acquire the changes for IBD in micro-scale. The aim of this work is to evaluate the size of the enterocoel and the thickness of colon wall using both MRI for in vivo imaging, and light-sheet and two-photon microscope for in vitro imaging. C57BL/6 mice were received 3.5% Dextran sodium sulfate (DSS) in the drinking water for 5 days to build IBD model. Mice were imaged with MRI on days 0, 6 to observe colitis progression. After MRI imaging, the mice were sacrificed to take colons for tissue clearing. Then, light-sheet and two-photon microscopies are used for in vitro imaging of the cleared samples. The experimental group showed symptoms of bloody stools, sluggishness and weight loss. It showed that the colon wall was thicker while the enterocoel was narrower compare to control group. The more details are observed using light-sheet and two-photon microscope. It is demonstrated that hybrid of MRI in macro-scale and light-sheet and two-photon microscopy in micro-scale imaging is feasible for colon inflammation diagnosing and supervising.

Modulated electron-multiplied fluorescence lifetime imaging microscope: all-solid-state camera for fluorescence lifetime imaging.

PubMed

Zhao, Qiaole; Schelen, Ben; Schouten, Raymond; van den Oever, Rein; Leenen, René; van Kuijk, Harry; Peters, Inge; Polderdijk, Frank; Bosiers, Jan; Raspe, Marcel; Jalink, Kees; Geert Sander de Jong, Jan; van Geest, Bert; Stoop, Karel; Young, Ian Ted

2012-12-01

We have built an all-solid-state camera that is directly modulated at the pixel level for frequency-domain fluorescence lifetime imaging microscopy (FLIM) measurements. This novel camera eliminates the need for an image intensifier through the use of an application-specific charge coupled device design in a frequency-domain FLIM system. The first stage of evaluation for the camera has been carried out. Camera characteristics such as noise distribution, dark current influence, camera gain, sampling density, sensitivity, linearity of photometric response, and optical transfer function have been studied through experiments. We are able to do lifetime measurement using our modulated, electron-multiplied fluorescence lifetime imaging microscope (MEM-FLIM) camera for various objects, e.g., fluorescein solution, fixed green fluorescent protein (GFP) cells, and GFP-actin stained live cells. A detailed comparison of a conventional microchannel plate (MCP)-based FLIM system and the MEM-FLIM system is presented. The MEM-FLIM camera shows higher resolution and a better image quality. The MEM-FLIM camera provides a new opportunity for performing frequency-domain FLIM.

Sub-nanosecond time-resolved near-field scanning magneto-optical microscope.

PubMed

Rudge, J; Xu, H; Kolthammer, J; Hong, Y K; Choi, B C

2015-02-01

We report on the development of a new magnetic microscope, time-resolved near-field scanning magneto-optical microscope, which combines a near-field scanning optical microscope and magneto-optical contrast. By taking advantage of the high temporal resolution of time-resolved Kerr microscope and the sub-wavelength spatial resolution of a near-field microscope, we achieved a temporal resolution of ∼50 ps and a spatial resolution of <100 nm. In order to demonstrate the spatiotemporal magnetic imaging capability of this microscope, the magnetic field pulse induced gyrotropic vortex dynamics occurring in 1 μm diameter, 20 nm thick CoFeB circular disks has been investigated. The microscope provides sub-wavelength resolution magnetic images of the gyrotropic motion of the vortex core at a resonance frequency of ∼240 MHz.

Single-frame 3D fluorescence microscopy with ultraminiature lensless FlatScope

PubMed Central

Adams, Jesse K.; Boominathan, Vivek; Avants, Benjamin W.; Vercosa, Daniel G.; Ye, Fan; Baraniuk, Richard G.; Robinson, Jacob T.; Veeraraghavan, Ashok

2017-01-01

Modern biology increasingly relies on fluorescence microscopy, which is driving demand for smaller, lighter, and cheaper microscopes. However, traditional microscope architectures suffer from a fundamental trade-off: As lenses become smaller, they must either collect less light or image a smaller field of view. To break this fundamental trade-off between device size and performance, we present a new concept for three-dimensional (3D) fluorescence imaging that replaces lenses with an optimized amplitude mask placed a few hundred micrometers above the sensor and an efficient algorithm that can convert a single frame of captured sensor data into high-resolution 3D images. The result is FlatScope: perhaps the world’s tiniest and lightest microscope. FlatScope is a lensless microscope that is scarcely larger than an image sensor (roughly 0.2 g in weight and less than 1 mm thick) and yet able to produce micrometer-resolution, high–frame rate, 3D fluorescence movies covering a total volume of several cubic millimeters. The ability of FlatScope to reconstruct full 3D images from a single frame of captured sensor data allows us to image 3D volumes roughly 40,000 times faster than a laser scanning confocal microscope while providing comparable resolution. We envision that this new flat fluorescence microscopy paradigm will lead to implantable endoscopes that minimize tissue damage, arrays of imagers that cover large areas, and bendable, flexible microscopes that conform to complex topographies. PMID:29226243

High-resolution, high-throughput imaging with a multibeam scanning electron microscope

PubMed Central

EBERLE, AL; MIKULA, S; SCHALEK, R; LICHTMAN, J; TATE, ML KNOTHE; ZEIDLER, D

2015-01-01

Electron–electron interactions and detector bandwidth limit the maximal imaging speed of single-beam scanning electron microscopes. We use multiple electron beams in a single column and detect secondary electrons in parallel to increase the imaging speed by close to two orders of magnitude and demonstrate imaging for a variety of samples ranging from biological brain tissue to semiconductor wafers. Lay Description The composition of our world and our bodies on the very small scale has always fascinated people, making them search for ways to make this visible to the human eye. Where light microscopes reach their resolution limit at a certain magnification, electron microscopes can go beyond. But their capability of visualizing extremely small features comes at the cost of a very small field of view. Some of the questions researchers seek to answer today deal with the ultrafine structure of brains, bones or computer chips. Capturing these objects with electron microscopes takes a lot of time – maybe even exceeding the time span of a human being – or new tools that do the job much faster. A new type of scanning electron microscope scans with 61 electron beams in parallel, acquiring 61 adjacent images of the sample at the same time a conventional scanning electron microscope captures one of these images. In principle, the multibeam scanning electron microscope’s field of view is 61 times larger and therefore coverage of the sample surface can be accomplished in less time. This enables researchers to think about large-scale projects, for example in the rather new field of connectomics. A very good introduction to imaging a brain at nanometre resolution can be found within course material from Harvard University on http://www.mcb80x.org/# as featured media entitled ‘connectomics’. PMID:25627873

Detection of marginal leakage of Class V restorations in vitro by micro-computed tomography.

PubMed

Zhao, X Y; Li, S B; Gu, L J; Li, Y

2014-01-01

This in vitro study evaluated the efficacy of micro-computed tomography (CT) in marginal leakage detection of Class V restorations. Standardized Class V preparations with cervical margins in dentin and occlusal margins in enamel were made in 20 extracted human molars and restored with dental bonding agents and resin composite. All teeth were then immersed in 50% ammoniacal silver nitrate solution for 12 hours, followed by a developing solution for eight hours. Each restoration was scanned by micro-CT, the depth of marginal silver leakage in the central scanning section was measured, and the three-dimensional images of the silver leakage around each restoration were reconstructed. Afterward, all restorations were cut through the center and examined for leakage depth using a microscope. The silver leakage depth of each restoration obtained by the micro-CT and the microscope were compared for equivalency. The silver leakage depth in cervical walls observed by micro-CT and microscope showed no significant difference; however, in certain cases the judgment of leakage depth in the occlusal wall in micro-CT image was affected by adjacent enamel structure, providing less leakage depth than was observed with the microscope (p<0.01). Micro-CT displayed the three-dimensional image of the leakage around the Class V restorations with clear borders only in the dentin region. It can be concluded that micro-CT can detect nondestructively the leakage around a resin composite restoration in two and three dimensions, with accuracy comparable to that of the conventional microscope method in the dentin region but with inferior accuracy in the enamel region.

Microscopic neural image registration based on the structure of mitochondria

NASA Astrophysics Data System (ADS)

Cao, Huiwen; Han, Hua; Rao, Qiang; Xiao, Chi; Chen, Xi

2017-02-01

Microscopic image registration is a key component of the neural structure reconstruction with serial sections of neural tissue. The goal of microscopic neural image registration is to recover the 3D continuity and geometrical properties of specimen. During image registration, various distortions need to be corrected, including image rotation, translation, tissue deformation et.al, which come from the procedure of sample cutting, staining and imaging. Furthermore, there is only certain similarity between adjacent sections, and the degree of similarity depends on local structure of the tissue and the thickness of the sections. These factors make the microscopic neural image registration a challenging problem. To tackle the difficulty of corresponding landmarks extraction, we introduce a novel image registration method for Scanning Electron Microscopy (SEM) images of serial neural tissue sections based on the structure of mitochondria. The ellipsoidal shape of mitochondria ensures that the same mitochondria has similar shape between adjacent sections, and its characteristic of broad distribution in the neural tissue guarantees that landmarks based on the mitochondria distributed widely in the image. The proposed image registration method contains three parts: landmarks extraction between adjacent sections, corresponding landmarks matching and image deformation based on the correspondences. We demonstrate the performance of our method with SEM images of drosophila brain.

A high-resolution multimode digital microscope system.

PubMed

Salmon, Edward D; Shaw, Sidney L; Waters, Jennifer C; Waterman-Storer, Clare M; Maddox, Paul S; Yeh, Elaine; Bloom, Kerry

2013-01-01

This chapter describes the development of a high-resolution, multimode digital imaging system based on a wide-field epifluorescent and transmitted light microscope, and a cooled charge-coupled device (CCD) camera. The three main parts of this imaging system are Nikon FXA microscope, Hamamatsu C4880 cooled CCD camera, and MetaMorph digital imaging system. This chapter presents various design criteria for the instrument and describes the major features of the microscope components-the cooled CCD camera and the MetaMorph digital imaging system. The Nikon FXA upright microscope can produce high resolution images for both epifluorescent and transmitted light illumination without switching the objective or moving the specimen. The functional aspects of the microscope set-up can be considered in terms of the imaging optics, the epi-illumination optics, the transillumination optics, the focus control, and the vibration isolation table. This instrument is somewhat specialized for microtubule and mitosis studies, and it is also applicable to a variety of problems in cellular imaging, including tracking proteins fused to the green fluorescent protein in live cells. The instrument is also valuable for correlating the assembly dynamics of individual cytoplasmic microtubules (labeled by conjugating X-rhodamine to tubulin) with the dynamics of membranes of the endoplasmic reticulum (labeled with DiOC6) and the dynamics of the cell cortex (by differential interference contrast) in migrating vertebrate epithelial cells. This imaging system also plays an important role in the analysis of mitotic mutants in the powerful yeast genetic system Saccharomyces cerevisiae. Copyright © 1998 Elsevier Inc. All rights reserved.

Hartmann characterization of the PEEM-3 aberration-corrected X-ray photoemission electron microscope.

PubMed

Scholl, A; Marcus, M A; Doran, A; Nasiatka, J R; Young, A T; MacDowell, A A; Streubel, R; Kent, N; Feng, J; Wan, W; Padmore, H A

2018-05-01

Aberration correction by an electron mirror dramatically improves the spatial resolution and transmission of photoemission electron microscopes. We will review the performance of the recently installed aberration corrector of the X-ray Photoemission Electron Microscope PEEM-3 and show a large improvement in the efficiency of the electron optics. Hartmann testing is introduced as a quantitative method to measure the geometrical aberrations of a cathode lens electron microscope. We find that aberration correction leads to an order of magnitude reduction of the spherical aberrations, suggesting that a spatial resolution of below 100 nm is possible at 100% transmission of the optics when using x-rays. We demonstrate this improved performance by imaging test patterns employing element and magnetic contrast. Published by Elsevier B.V.

A colinear backscattering Mueller matrix microscope for reflection Muller matrix imaging

NASA Astrophysics Data System (ADS)

Chen, Zhenhua; Yao, Yue; Zhu, Yuanhuan; Ma, Hui

2018-02-01

In a recent attempt, we developed a colinear backscattering Mueller matrix microscope by adding polarization state generator (PSG) and polarization state analyzer (PSA) into the illumination and detection optical paths of a commercial metallurgical microscope. It is found that specific efforts have to be made to reduce the artifacts due to the intrinsic residual polarizations of the optical system, particularly the dichroism due to the 45 degrees beam splitter. In this paper, we present a new calibration method based on numerical reconstruction of the instrument matrix to remove the artifacts introduced by beam splitter. Preliminary tests using a mirror as a standard sample show that the maximum Muller matrix element error of the colinear backscattering Muller matrix microscope can be reduced to a few percent.

Imaging the microscopic structure of shear thinning and thickening colloidal suspensions.

PubMed

Cheng, Xiang; McCoy, Jonathan H; Israelachvili, Jacob N; Cohen, Itai

2011-09-02

The viscosity of colloidal suspensions varies with shear rate, an important effect encountered in many natural and industrial processes. Although this non-Newtonian behavior is believed to arise from the arrangement of suspended particles and their mutual interactions, microscopic particle dynamics are difficult to measure. By combining fast confocal microscopy with simultaneous force measurements, we systematically investigate a suspension's structure as it transitions through regimes of different flow signatures. Our measurements of the microscopic single-particle dynamics show that shear thinning results from the decreased relative contribution of entropic forces and that shear thickening arises from particle clustering induced by hydrodynamic lubrication forces. This combination of techniques illustrates an approach that complements current methods for determining the microscopic origins of non-Newtonian flow behavior in complex fluids.

Single-channel stereoscopic ophthalmology microscope based on TRD

NASA Astrophysics Data System (ADS)

Radfar, Edalat; Park, Jihoon; Lee, Sangyeob; Ha, Myungjin; Yu, Sungkon; Jang, Seulki; Jung, Byungjo

2016-03-01

A stereoscopic imaging modality was developed for the application of ophthalmology surgical microscopes. A previous study has already introduced a single-channel stereoscopic video imaging modality based on a transparent rotating deflector (SSVIM-TRD), in which two different view angles, image disparity, are generated by imaging through a transparent rotating deflector (TRD) mounted on a stepping motor and is placed in a lens system. In this case, the image disparity is a function of the refractive index and the rotation angle of TRD. Real-time single-channel stereoscopic ophthalmology microscope (SSOM) based on the TRD is improved by real-time controlling and programming, imaging speed, and illumination method. Image quality assessments were performed to investigate images quality and stability during the TRD operation. Results presented little significant difference in image quality in terms of stability of structural similarity (SSIM). A subjective analysis was performed with 15 blinded observers to evaluate the depth perception improvement and presented significant improvement in the depth perception capability. Along with all evaluation results, preliminary results of rabbit eye imaging presented that the SSOM could be utilized as an ophthalmic operating microscopes to overcome some of the limitations of conventional ones.

3D image restoration for confocal microscopy: toward a wavelet deconvolution for the study of complex biological structures

NASA Astrophysics Data System (ADS)

Boutet de Monvel, Jacques; Le Calvez, Sophie; Ulfendahl, Mats

2000-05-01

Image restoration algorithms provide efficient tools for recovering part of the information lost in the imaging process of a microscope. We describe recent progress in the application of deconvolution to confocal microscopy. The point spread function of a Biorad-MRC1024 confocal microscope was measured under various imaging conditions, and used to process 3D-confocal images acquired in an intact preparation of the inner ear developed at Karolinska Institutet. Using these experiments we investigate the application of denoising methods based on wavelet analysis as a natural regularization of the deconvolution process. Within the Bayesian approach to image restoration, we compare wavelet denoising with the use of a maximum entropy constraint as another natural regularization method. Numerical experiments performed with test images show a clear advantage of the wavelet denoising approach, allowing to `cool down' the image with respect to the signal, while suppressing much of the fine-scale artifacts appearing during deconvolution due to the presence of noise, incomplete knowledge of the point spread function, or undersampling problems. We further describe a natural development of this approach, which consists of performing the Bayesian inference directly in the wavelet domain.

Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens.

PubMed

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

2013-11-01

This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10(-2) Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

Development of an adaptable coherent x-ray diffraction microscope with the emphasis on imaging hydrated specimens

NASA Astrophysics Data System (ADS)

Nam, Daewoong; Park, Jaehyun; Gallagher-Jones, Marcus; Shimada, Hiroki; Kim, Sangsoo; Kim, Sunam; Kohmura, Yoshiki; Ishikawa, Tetsuya; Song, Changyong

2013-11-01

This paper describes the development of a versatile coherent x-ray diffraction microscope capable of imaging biological specimens in solution. The microscope is a flexible platform accommodating various conditions, from low vacuum (10-2 Pa) to helium gas filled ambient pressure. This flexibility greatly expands the application area, from in situ materials science to biology systems in their native state, by significantly relaxing restrictions to the sample environment. The coherent diffraction microscope has been used successfully to image a yeast cell immersed in buffer solution. We believe that the design of this coherent diffraction microscope can be directly adapted to various platforms such as table top soft x-ray laser, synchrotron x-ray sources, and x-ray free electron laser with minor relevant adjustments.

Programmable Colored Illumination Microscopy (PCIM): A practical and flexible optical staining approach for microscopic contrast enhancement

NASA Astrophysics Data System (ADS)

Zuo, Chao; Sun, Jiasong; Feng, Shijie; Hu, Yan; Chen, Qian

2016-03-01

Programmable colored illumination microscopy (PCIM) has been proposed as a flexible optical staining technique for microscopic contrast enhancement. In this method, we replace the condenser diaphragm of a conventional microscope with a programmable thin film transistor-liquid crystal display (TFT-LCD). By displaying different patterns on the LCD, numerous established imaging modalities can be realized, such as bright field, dark field, phase contrast, oblique illumination, and Rheinberg illuminations, which conventionally rely on intricate alterations in the respective microscope setups. Furthermore, the ease of modulating both the color and the intensity distribution at the aperture of the condenser opens the possibility to combine multiple microscopic techniques, or even realize completely new methods for optical color contrast staining, such as iridescent dark-field and iridescent phase-contrast imaging. The versatility and effectiveness of PCIM is demonstrated by imaging of several transparent colorless specimens, such as unstained lung cancer cells, diatom, textile fibers, and a cryosection of mouse kidney. Finally, the potentialities of PCIM for RGB-splitting imaging with stained samples are also explored by imaging stained red blood cells and a histological section.

A portable confocal hyperspectral microscope without any scan or tube lens and its application in fluorescence and Raman spectral imaging

NASA Astrophysics Data System (ADS)

Li, Jingwei; Cai, Fuhong; Dong, Yongjiang; Zhu, Zhenfeng; Sun, Xianhe; Zhang, Hequn; He, Sailing

2017-06-01

In this study, a portable confocal hyperspectral microscope is developed. In traditional confocal laser scanning microscopes, scan lens and tube lens are utilized to achieve a conjugate relationship between the galvanometer and the back focal plane of the objective, in order to achieve a better resolution. However, these lenses make it difficult to scale down the volume of the system. In our portable confocal hyperspectral microscope (PCHM), the objective is placed directly next to the galvomirror. Thus, scan lens and tube lens are not included in our system and the size of this system is greatly reduced. Furthermore, the resolution is also acceptable in many biomedical and food-safety applications. Through reducing the optical length of the system, the signal detection efficiency is enhanced. This is conducive to realizing both the fluorescence and Raman hyperspectral imaging. With a multimode fiber as a pinhole, an improved image contrast is also achieved. Fluorescent spectral images for HeLa cells/fingers and Raman spectral images of kumquat pericarp are present. The spectral resolution and spatial resolutions are about 0.4 nm and 2.19 μm, respectively. These results demonstrate that this portable hyperspectral microscope can be used in in-vivo fluorescence imaging and in situ Raman spectral imaging.

Novel Bacterial Genus Found Only in Spacecraft Assembly Clean Rooms

NASA Image and Video Library

2013-11-06

This microscopic image shows dozens of individual bacterial cells of the recently discovered species, Tersicoccus phoenicis, found in only two places: clean rooms in Florida and South America where spacecraft are assembled for launch.

Fluid Physics

NASA Image and Video Library

2002-12-12

These are video microscope images of magnetorheological (MR) fluids, illuminated with a green light. Those on Earth, left, show the MR fluid forming columns or spikes structures. On the right, the fluids in microgravity aboard the International Space Station (ISS), formed broader columns.

Martian Rock Harrison in Color, Showing Crystals

NASA Image and Video Library

2014-01-29

This view of a Martian rock target called /Harrison merges images from two cameras onboard NASA Curiosity Mars rover to provide both color and microscopic detail. The elongated crystals are likely feldspars, and the matrix is pyroxene-dominated.

A high stability and repeatability electrochemical scanning tunneling microscope.

PubMed

Xia, Zhigang; Wang, Jihao; Hou, Yubin; Lu, Qingyou

2014-12-01

We present a home built electrochemical scanning tunneling microscope (ECSTM) with very high stability and repeatability. Its coarse approach is driven by a closely stacked piezo motor of GeckoDrive type with four rigid clamping points, which enhances the rigidity, compactness, and stability greatly. It can give high clarity atomic resolution images without sound and vibration isolations. Its drifting rates in XY and Z directions in solution are as low as 84 pm/min and 59 pm/min, respectively. In addition, repeatable coarse approaches in solution within 2 mm travel distance show a lateral deviation less than 50 nm. The gas environment can be well controlled to lower the evaporation rate of the cell, thus reducing the contamination and elongating the measurement time. Atomically resolved SO4(2-) image on Au (111) work electrode is demonstrated to show the performance of the ECSTM.

Evolution and control of the phase competition morphology in a manganite film

NASA Astrophysics Data System (ADS)

Zhou, Haibiao; Wang, Lingfei; Hou, Yubin; Huang, Zhen; Lu, Qingyou; Wu, Wenbin

2015-11-01

The competition among different phases in perovskite manganites is pronounced since their energies are very close under the interplay of charge, spin, orbital and lattice degrees of freedom. To reveal the roles of underlying interactions, many efforts have been devoted towards directly imaging phase transitions at microscopic scales. Here we show images of the charge-ordered insulator (COI) phase transition from a pure ferromagnetic metal with reducing field or increasing temperature in a strained phase-separated manganite film, using a home-built magnetic force microscope. Compared with the COI melting transition, this reverse transition is sharp, cooperative and martensitic-like with astonishingly unique yet diverse morphologies. The COI domains show variable-dimensional growth at different temperatures and their distribution can illustrate the delicate balance of the underlying interactions in manganites. Our findings also display how phase domain engineering is possible and how the phase competition can be tuned in a controllable manner.

Evolution and control of the phase competition morphology in a manganite film.

PubMed

Zhou, Haibiao; Wang, Lingfei; Hou, Yubin; Huang, Zhen; Lu, Qingyou; Wu, Wenbin

2015-11-25

The competition among different phases in perovskite manganites is pronounced since their energies are very close under the interplay of charge, spin, orbital and lattice degrees of freedom. To reveal the roles of underlying interactions, many efforts have been devoted towards directly imaging phase transitions at microscopic scales. Here we show images of the charge-ordered insulator (COI) phase transition from a pure ferromagnetic metal with reducing field or increasing temperature in a strained phase-separated manganite film, using a home-built magnetic force microscope. Compared with the COI melting transition, this reverse transition is sharp, cooperative and martensitic-like with astonishingly unique yet diverse morphologies. The COI domains show variable-dimensional growth at different temperatures and their distribution can illustrate the delicate balance of the underlying interactions in manganites. Our findings also display how phase domain engineering is possible and how the phase competition can be tuned in a controllable manner.

Design and analysis of multilayer x ray/XUV microscope

NASA Technical Reports Server (NTRS)

Shealy, David L.

1990-01-01

The design and analysis of a large number of normal incidence multilayer x ray microscopes based on the spherical mirror Schwarzschild configuration is examined. Design equations for the spherical mirror Schwarzschild microscopes are summarized and used to evaluate mirror parameters for microscopes with magnifications ranging from 2 to 50x. Ray tracing and diffraction analyses are carried out for many microscope configurations to determine image resolution as a function of system parameters. The results are summarized in three publication included herein. A preliminary study of advanced reflecting microscope configurations, where aspherics are used in place of the spherical microscope mirror elements, has indicated that the aspherical elements will improve off-axis image resolution and increase the effective field of view.

Comparisons between conventional optical imaging and parametric indirect microscopic imaging on human skin detection

NASA Astrophysics Data System (ADS)

Liu, Guoyan; Gao, Kun; Liu, Xuefeng; Ni, Guoqiang

2016-10-01

We report a new method, polarization parameters indirect microscopic imaging with a high transmission infrared light source, to detect the morphology and component of human skin. A conventional reflection microscopic system is used as the basic optical system, into which a polarization-modulation mechanics is inserted and a high transmission infrared light source is utilized. The near-field structural characteristics of human skin can be delivered by infrared waves and material coupling. According to coupling and conduction physics, changes of the optical wave parameters can be calculated and curves of the intensity of the image can be obtained. By analyzing the near-field polarization parameters in nanoscale, we can finally get the inversion images of human skin. Compared with the conventional direct optical microscope, this method can break diffraction limit and achieve a super resolution of sub-100nm. Besides, the method is more sensitive to the edges, wrinkles, boundaries and impurity particles.

An integrated single- and two-photon non-diffracting light-sheet microscope

NASA Astrophysics Data System (ADS)

Lau, Sze Cheung; Chiu, Hoi Chun; Zhao, Luwei; Zhao, Teng; Loy, M. M. T.; Du, Shengwang

2018-04-01

We describe a fluorescence optical microscope with both single-photon and two-photon non-diffracting light-sheet excitations for large volume imaging. With a special design to accommodate two different wavelength ranges (visible: 400-700 nm and near infrared: 800-1200 nm), we combine the line-Bessel sheet (LBS, for single-photon excitation) and the scanning Bessel beam (SBB, for two-photon excitation) light sheet together in a single microscope setup. For a transparent thin sample where the scattering can be ignored, the LBS single-photon excitation is the optimal imaging solution. When the light scattering becomes significant for a deep-cell or deep-tissue imaging, we use SBB light-sheet two-photon excitation with a longer wavelength. We achieved nearly identical lateral/axial resolution of about 350/270 nm for both imagings. This integrated light-sheet microscope may have a wide application for live-cell and live-tissue three-dimensional high-speed imaging.

Helium Ion Microscope: A New Tool for Sub-nanometer Imaging of Soft Materials

NASA Astrophysics Data System (ADS)

Shutthanandan, V.; Arey, B.; Smallwood, C. R.; Evans, J. E.

2017-12-01

High-resolution inspection of surface details is needed in many biological and environmental researches to understand the Soil organic material (SOM)-mineral interactions along with identifying microbial communities and their interactions. SOM shares many imaging characteristics with biological samples and getting true surface details from these materials are challenging since they consist of low atomic number materials. FE-SEM imaging is the main imagining technique used to image these materials in the past. These SEM images often show loss of resolution and increase noise due to beam damage and charging issues. Newly developed Helium Ion Microscope (HIM), on the other hand can overcome these difficulties and give very fine details. HIM is very similar to scanning electron microscopy (SEM) but instead of using electrons as a probe beam, HIM uses helium ions with energy ranges from 5 to 40 keV. HIM offers a series of advantages compared to SEM such as nanometer and sub-nanometer image resolutions (about 0.35 nm), detailed surface topography, high surface sensitivity, low Z material imaging (especially for polymers and biological samples), high image contrast, and large depth of field. In addition, HIM also has the ability to image insulating materials without any conductive coatings so that surface details are not modified. In this presentation, several scientific applications across biology and geochemistry will be presented to highlight the effectiveness of this powerful microscope. Acknowledgements: Research was performed using the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at PNNL. Work was supported by DOE-BER Mesoscale to Molecules Bioimaging Project FWP# 66382.

Nanosecond Time-Resolved Microscopic Gate-Modulation Imaging of Polycrystalline Organic Thin-Film Transistors

NASA Astrophysics Data System (ADS)

Matsuoka, Satoshi; Tsutsumi, Jun'ya; Matsui, Hiroyuki; Kamata, Toshihide; Hasegawa, Tatsuo

2018-02-01

We develop a time-resolved microscopic gate-modulation (μ GM ) imaging technique to investigate the temporal evolution of the channel current and accumulated charges in polycrystalline pentacene thin-film transistors (TFTs). A time resolution of as high as 50 ns is achieved by using a fast image-intensifier system that could amplify a series of instantaneous optical microscopic images acquired at various time intervals after the stepped gate bias is switched on. The differential images obtained by subtracting the gate-off image allows us to acquire a series of temporal μ GM images that clearly show the gradual propagation of both channel charges and leaked gate fields within the polycrystalline channel layers. The frontal positions for the propagations of both channel charges and leaked gate fields coincide at all the time intervals, demonstrating that the layered gate dielectric capacitors are successively transversely charged up along the direction of current propagation. The initial μ GM images also indicate that the electric field effect is originally concentrated around a limited area with a width of a few micrometers bordering the channel-electrode interface, and that the field intensity reaches a maximum after 200 ns and then decays. The time required for charge propagation over the whole channel region with a length of 100 μ m is estimated at about 900 ns, which is consistent with the measured field-effect mobility and the temporal-response model for organic TFTs. The effect of grain boundaries can be also visualized by comparison of the μ GM images for the transient and the steady states, which confirms that the potential barriers at the grain boundaries cause the transient shift in the accumulated charges or the transient accumulation of additional charges around the grain boundaries.

Moessbauer Footprint in the Soil

NASA Technical Reports Server (NTRS)

2004-01-01

This 3-D image taken by the microscopic imager onboard the Mars Exploration Rover Opportunity shows a circular imprint left in the Meridiani Planum soil by the rover's Moessbauer spectrometer, an instrument located on its arm that detects iron-bearing minerals. Scientists are studying the curiously rounded grains for clues about the soil's history. The observed area is 3 centimeters (1.2 inches) across.

'Blueberry' Exposed

NASA Technical Reports Server (NTRS)

2004-01-01

This three-dimensional model shows a postage-stamp-sized patch of the rock target in the outcrop near the Mars Exploration Rover Opportunity's landing site. A sliced sphere-like particle, or 'blueberry,' can be seen to the far right of the model. The model was created from images taken by the rover's microscopic imager, after the surface of the rock was scraped away with the rock abrasion tool.

Hyaline cartilage surface study with an environmental scanning electron microscope. An experimental study.

PubMed

Sastre, S; Suso, S; Segur, J M; Bori, G; Carbonell, J A; Agustí, E; Nuñez, M

2009-11-01

To obtain images of the articular surface of fresh osteochondral grafts using an environmental scanning electron microscope (ESEM). To evaluate and compare the main morphological aspects of the chondral surface of the fresh grafts. To develop a validated classification system on the basis of the images obtained via the ESEM. The study was based on osteochondral fragments from the internal condyle of the knee joint of New Zealand rabbits, corresponding to fresh chondral surface. One hundred images were obtained via the ESEM and these were classified by two observers according to a category system. The Kappa index and the corresponding confidence interval (CI) were calculated. Of the samples analysed, 62-72% had an even surface. Among the samples with an uneven surface 17-22% had a hillocky appearance and 12-16% a knobbly appearance. As regards splits, these were not observed in 92-95% of the surfaces; 4-7% showed superficial splits and only 1% deep splits. In 78-82% of cases no lacunae in the surface were observed, while 17-20% showed filled lacunae and only 1-2% presented empty lacunae. The study demonstrates that the ESEM is useful for obtaining and classifying images of osteochondral grafts.

Direct in situ observation of ZnO nucleation and growth via transmission X-ray microscopy

NASA Astrophysics Data System (ADS)

Tay, S. E. R.; Goode, A. E.; Nelson Weker, J.; Cruickshank, A. A.; Heutz, S.; Porter, A. E.; Ryan, M. P.; Toney, M. F.

2016-01-01

The nucleation and growth of a nanostructure controls its size and morphology, and ultimately its functional properties. Hence it is crucial to investigate growth mechanisms under relevant growth conditions at the nanometer length scale. Here we image the nucleation and growth of electrodeposited ZnO nanostructures in situ, using a transmission X-ray microscope and specially designed electrochemical cell. We show that this imaging technique leads to new insights into the nucleation and growth mechanisms in electrodeposited ZnO including direct, in situ observations of instantaneous versus delayed nucleation.The nucleation and growth of a nanostructure controls its size and morphology, and ultimately its functional properties. Hence it is crucial to investigate growth mechanisms under relevant growth conditions at the nanometer length scale. Here we image the nucleation and growth of electrodeposited ZnO nanostructures in situ, using a transmission X-ray microscope and specially designed electrochemical cell. We show that this imaging technique leads to new insights into the nucleation and growth mechanisms in electrodeposited ZnO including direct, in situ observations of instantaneous versus delayed nucleation. Electronic supplementary information (ESI) available: Methods and videos of nanoparticle growth. See DOI: 10.1039/c5nr07019h

Tracking of Cells with a Compact Microscope Imaging System with Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2007-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to autofocus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously

Tracking of cells with a compact microscope imaging system with intelligent controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2007-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to auto-focus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously.

A multi-modal stereo microscope based on a spatial light modulator.

PubMed

Lee, M P; Gibson, G M; Bowman, R; Bernet, S; Ritsch-Marte, M; Phillips, D B; Padgett, M J

2013-07-15

Spatial Light Modulators (SLMs) can emulate the classic microscopy techniques, including differential interference (DIC) contrast and (spiral) phase contrast. Their programmability entails the benefit of flexibility or the option to multiplex images, for single-shot quantitative imaging or for simultaneous multi-plane imaging (depth-of-field multiplexing). We report the development of a microscope sharing many of the previously demonstrated capabilities, within a holographic implementation of a stereo microscope. Furthermore, we use the SLM to combine stereo microscopy with a refocusing filter and with a darkfield filter. The instrument is built around a custom inverted microscope and equipped with an SLM which gives various imaging modes laterally displaced on the same camera chip. In addition, there is a wide angle camera for visualisation of a larger region of the sample.

Multiresolution multiscale active mask segmentation of fluorescence microscope images

NASA Astrophysics Data System (ADS)

Srinivasa, Gowri; Fickus, Matthew; Kovačević, Jelena

2009-08-01

We propose an active mask segmentation framework that combines the advantages of statistical modeling, smoothing, speed and flexibility offered by the traditional methods of region-growing, multiscale, multiresolution and active contours respectively. At the crux of this framework is a paradigm shift from evolving contours in the continuous domain to evolving multiple masks in the discrete domain. Thus, the active mask framework is particularly suited to segment digital images. We demonstrate the use of the framework in practice through the segmentation of punctate patterns in fluorescence microscope images. Experiments reveal that statistical modeling helps the multiple masks converge from a random initial configuration to a meaningful one. This obviates the need for an involved initialization procedure germane to most of the traditional methods used to segment fluorescence microscope images. While we provide the mathematical details of the functions used to segment fluorescence microscope images, this is only an instantiation of the active mask framework. We suggest some other instantiations of the framework to segment different types of images.

Designed Er(3+)-singly doped NaYF4 with double excitation bands for simultaneous deep macroscopic and microscopic upconverting bioimaging.

PubMed

Wen, Xuanyuan; Wang, Baoju; Wu, Ruitao; Li, Nana; He, Sailing; Zhan, Qiuqiang

2016-06-01

Simultaneous deep macroscopic imaging and microscopic imaging is in urgent demand, but is challenging to achieve experimentally due to the lack of proper fluorescent probes. Herein, we have designed and successfully synthesized simplex Er(3+)-doped upconversion nanoparticles (UCNPs) with double excitation bands for simultaneous deep macroscopic and microscopic imaging. The material structure and the excitation wavelength of Er(3+)-singly doped UCNPs were further optimized to enhance the upconversion emission efficiency. After optimization, we found that NaYF4:30%Er(3+)@NaYF4:2%Er(3+) could simultaneously achieve efficient two-photon excitation (2PE) macroscopic tissue imaging and three-photon excitation (3PE) deep microscopic when excited by 808 nm continuous wave (CW) and 1480 nm CW lasers, respectively. In vitro cell imaging and in vivo imaging have also been implemented to demonstrate the feasibility and potential of the proposed simplex Er(3+)-doped UCNPs as bioprobe.

Automatic Recognition of Acute Myelogenous Leukemia in Blood Microscopic Images Using K-means Clustering and Support Vector Machine.

PubMed

Kazemi, Fatemeh; Najafabadi, Tooraj Abbasian; Araabi, Babak Nadjar

2016-01-01

Acute myelogenous leukemia (AML) is a subtype of acute leukemia, which is characterized by the accumulation of myeloid blasts in the bone marrow. Careful microscopic examination of stained blood smear or bone marrow aspirate is still the most significant diagnostic methodology for initial AML screening and considered as the first step toward diagnosis. It is time-consuming and due to the elusive nature of the signs and symptoms of AML; wrong diagnosis may occur by pathologists. Therefore, the need for automation of leukemia detection has arisen. In this paper, an automatic technique for identification and detection of AML and its prevalent subtypes, i.e., M2-M5 is presented. At first, microscopic images are acquired from blood smears of patients with AML and normal cases. After applying image preprocessing, color segmentation strategy is applied for segmenting white blood cells from other blood components and then discriminative features, i.e., irregularity, nucleus-cytoplasm ratio, Hausdorff dimension, shape, color, and texture features are extracted from the entire nucleus in the whole images containing multiple nuclei. Images are classified to cancerous and noncancerous images by binary support vector machine (SVM) classifier with 10-fold cross validation technique. Classifier performance is evaluated by three parameters, i.e., sensitivity, specificity, and accuracy. Cancerous images are also classified into their prevalent subtypes by multi-SVM classifier. The results show that the proposed algorithm has achieved an acceptable performance for diagnosis of AML and its common subtypes. Therefore, it can be used as an assistant diagnostic tool for pathologists.

Optical second harmonic images of 90 deg domain structure in BaTiO3 and periodically inverted antiparallel domains in LiTaO3

NASA Astrophysics Data System (ADS)

Uesu, Y.; Kurimura, S.; Yamamoto, Y.

1995-04-01

Applied is a microscope to observations of 90 deg ferroelectric domain structure in BaTiO3 and inverted periodically are ferroelectric domains in LiTaO3. It is founded that the second harmonic generation microscope gives information which cannot be obtained by ordinary optical microscopes. The developed nonlinear optical microscope builds two dimensional second harmonic image of a specimen with inhomogenous distribution of d(sub ijk) and applied the microscope to observations of inhomogeneity in some nonlinear-optical organic microcrystals.

ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy.

PubMed

Brama, Elisabeth; Peddie, Christopher J; Wilkes, Gary; Gu, Yan; Collinson, Lucy M; Jones, Martin L

2016-12-13

In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables 'smart collection' of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables 'smart tracking' of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.

ScanImage: flexible software for operating laser scanning microscopes.

PubMed

Pologruto, Thomas A; Sabatini, Bernardo L; Svoboda, Karel

2003-05-17

Laser scanning microscopy is a powerful tool for analyzing the structure and function of biological specimens. Although numerous commercial laser scanning microscopes exist, some of the more interesting and challenging applications demand custom design. A major impediment to custom design is the difficulty of building custom data acquisition hardware and writing the complex software required to run the laser scanning microscope. We describe a simple, software-based approach to operating a laser scanning microscope without the need for custom data acquisition hardware. Data acquisition and control of laser scanning are achieved through standard data acquisition boards. The entire burden of signal integration and image processing is placed on the CPU of the computer. We quantitate the effectiveness of our data acquisition and signal conditioning algorithm under a variety of conditions. We implement our approach in an open source software package (ScanImage) and describe its functionality. We present ScanImage, software to run a flexible laser scanning microscope that allows easy custom design.

Improving confocal microscopy with solid-state semiconductor excitation sources

NASA Astrophysics Data System (ADS)

Sivers, Nelson L.

To efficiently excite the fluorescent dyes used in imaging biological samples with a confocal microscope, the wavelengths of the exciting laser must be near the fluorochrome absorption peak. However, this causes imaging problems when the fluorochrome absorption and emission spectra overlap significantly, i.e. have small Stokes shifts, which is the case for most fluorochromes that emit in the red to infrared. As a result, the reflected laser excitation cannot be distinguished from the information-containing fluorescence signal. However, cryogenically cooling the exciting laser diode enabled the laser emission wavelengths to be tuned to shorter wavelengths, decreasing the interference between the laser and the fluorochrome's fluorescence. This reduced the amount of reflected laser light in the confocal image. However, the cooled laser diode's shorter wavelength signal resulted in slightly less efficient fluorochrome excitation. Spectrophotometric analysis showed that as the laser diodes were cooled, their output power increased, which more than compensated for the lower fluorochrome excitation and resulted in significantly more intense fluorescence. Thus, by tuning the laser diode emission wavelengths away from the fluorescence signal, less reflected laser light and more fluorescence information reached the detector, creating images with better signal to noise ratios. Additionally, new, high, luminous flux, light-emitting diodes (LEDs) are now powerful enough to create confocal fluorescence signals comparable to those produced by the traditional laser excitation sources in fluorescence confocal microscopes. The broader LED spectral response effectively excited the fluorochrome, yet was spectrally limited enough for standard filter sets to separate the LED excitation from the fluorochrome fluorescence signal. Spectrophotometric analysis of the excitation and fluorescence spectra of several fluorochromes showed that high-powered, LED-induced fluorescence contained the same spectral information and could be more intense than that produced by lasers. An alternative, LED-based, confocal microscope is proposed in this thesis that would be capable of exciting multiple fluorochromes in a single specimen, producing images of several distinct cellular components simultaneously. The inexpensive, LED-based, confocal microscope would require lower peak excitation intensities to produce fluorescence signals equal to those produced by laser excitation, reducing cellular damage and slowing fluorochrome photobleaching.

Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images.

PubMed

Yothers, Mitchell P; Browder, Aaron E; Bumm, Lloyd A

2017-01-01

We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform. Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as a model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.

Real-space post-processing correction of thermal drift and piezoelectric actuator nonlinearities in scanning tunneling microscope images

NASA Astrophysics Data System (ADS)

Yothers, Mitchell P.; Browder, Aaron E.; Bumm, Lloyd A.

2017-01-01

We have developed a real-space method to correct distortion due to thermal drift and piezoelectric actuator nonlinearities on scanning tunneling microscope images using Matlab. The method uses the known structures typically present in high-resolution atomic and molecularly resolved images as an internal standard. Each image feature (atom or molecule) is first identified in the image. The locations of each feature's nearest neighbors are used to measure the local distortion at that location. The local distortion map across the image is simultaneously fit to our distortion model, which includes thermal drift in addition to piezoelectric actuator hysteresis and creep. The image coordinates of the features and image pixels are corrected using an inverse transform from the distortion model. We call this technique the thermal-drift, hysteresis, and creep transform. Performing the correction in real space allows defects, domain boundaries, and step edges to be excluded with a spatial mask. Additional real-space image analyses are now possible with these corrected images. Using graphite(0001) as a model system, we show lattice fitting to the corrected image, averaged unit cell images, and symmetry-averaged unit cell images. Statistical analysis of the distribution of the image features around their best-fit lattice sites measures the aggregate noise in the image, which can be expressed as feature confidence ellipsoids.

LIPS database with LIPService: a microscopic image database of intracellular structures in Arabidopsis guard cells.

PubMed

Higaki, Takumi; Kutsuna, Natsumaro; Hasezawa, Seiichiro

2013-05-16

Intracellular configuration is an important feature of cell status. Recent advances in microscopic imaging techniques allow us to easily obtain a large number of microscopic images of intracellular structures. In this circumstance, automated microscopic image recognition techniques are of extreme importance to future phenomics/visible screening approaches. However, there was no benchmark microscopic image dataset for intracellular organelles in a specified plant cell type. We previously established the Live Images of Plant Stomata (LIPS) database, a publicly available collection of optical-section images of various intracellular structures of plant guard cells, as a model system of environmental signal perception and transduction. Here we report recent updates to the LIPS database and the establishment of a database table, LIPService. We updated the LIPS dataset and established a new interface named LIPService to promote efficient inspection of intracellular structure configurations. Cell nuclei, microtubules, actin microfilaments, mitochondria, chloroplasts, endoplasmic reticulum, peroxisomes, endosomes, Golgi bodies, and vacuoles can be filtered using probe names or morphometric parameters such as stomatal aperture. In addition to the serial optical sectional images of the original LIPS database, new volume-rendering data for easy web browsing of three-dimensional intracellular structures have been released to allow easy inspection of their configurations or relationships with cell status/morphology. We also demonstrated the utility of the new LIPS image database for automated organelle recognition of images from another plant cell image database with image clustering analyses. The updated LIPS database provides a benchmark image dataset for representative intracellular structures in Arabidopsis guard cells. The newly released LIPService allows users to inspect the relationship between organellar three-dimensional configurations and morphometrical parameters.

Biocytin-Derived MRI Contrast Agent for Longitudinal Brain Connectivity Studies

PubMed Central

2011-01-01

To investigate the connectivity of brain networks noninvasively and dynamically, we have developed a new strategy to functionalize neuronal tracers and designed a biocompatible probe that can be visualized in vivo using magnetic resonance imaging (MRI). Furthermore, the multimodal design used allows combined ex vivo studies with microscopic spatial resolution by conventional histochemical techniques. We present data on the functionalization of biocytin, a well-known neuronal tract tracer, and demonstrate the validity of the approach by showing brain networks of cortical connectivity in live rats under MRI, together with the corresponding microscopic details, such as fibers and neuronal morphology under light microscopy. We further demonstrate that the developed molecule is the first MRI-visible probe to preferentially trace retrograde connections. Our study offers a new platform for the development of multimodal molecular imaging tools of broad interest in neuroscience, that capture in vivo the dynamics of large scale neural networks together with their microscopic characteristics, thereby spanning several organizational levels. PMID:22860157

Precise Orientation of a Single C60 Molecule on the Tip of a Scanning Probe Microscope

NASA Astrophysics Data System (ADS)

Chiutu, C.; Sweetman, A. M.; Lakin, A. J.; Stannard, A.; Jarvis, S.; Kantorovich, L.; Dunn, J. L.; Moriarty, P.

2012-06-01

We show that the precise orientation of a C60 molecule which terminates the tip of a scanning probe microscope can be determined with atomic precision from submolecular contrast images of the fullerene cage. A comparison of experimental scanning tunneling microscopy data with images simulated using computationally inexpensive Hückel theory provides a robust method of identifying molecular rotation and tilt at the end of the probe microscope tip. Noncontact atomic force microscopy resolves the atoms of the C60 cage closest to the surface for a range of molecular orientations at tip-sample separations where the molecule-substrate interaction potential is weakly attractive. Measurements of the C60C60 pair potential acquired using a fullerene-terminated tip are in excellent agreement with theoretical predictions based on a pairwise summation of the van der Waals interactions between C atoms in each cage, i.e., the Girifalco potential [L. Girifalco, J. Phys. Chem. 95, 5370 (1991)JPCHAX0022-365410.1021/j100167a002].

A study of cavity preparation by Er:YAG laser--observation of hard tooth structures by laser scanning microscope and examination of the time necessary to remove caries.

PubMed

Shigetani, Yoshimi; Okamoto, Akira; Abu-Bakr, Neamat; Iwaku, Masaaki

2002-03-01

The purpose of this study was to observe and measure the morphological changes that occur in the hard tissue after the application of Er:YAG laser. Another objective was to evaluate and compare the duration of application of both the laser apparatus and a conventional cutting device. In this study, sound and newly extracted carious tissues were used. The morphological changes in hard tooth structures produced by Er:YAG laser irradiation were examined by using a laser scanning microscope. Results showed that appropriate laser irradiation was 100 mJ/pulse for dentin, and 200 mJ/pulse for enamel. Also, the laser scanning microscope images were less damaged than the SEM images due to pretreatment of the specimens. The time taken to remove carious enamel by laser irradiation was slightly longer than the compared rotary cutting device; however, no differences between the two methods were observed in case of carious dentin removal.

Evaluation of the microscopic distribution of florfenicol in feed pellets for salmon by Fourier Transform infrared imaging and multivariate analysis.

PubMed

Bastidas, Camila Y; von Plessing, Carlos; Troncoso, José; Del P Castillo, Rosario

2018-04-15

Fourier Transform infrared imaging and multivariate analysis were used to identify, at the microscopic level, the presence of florfenicol (FF), a heavily-used antibiotic in the salmon industry, supplied to fishes in feed pellets for the treatment of salmonid rickettsial septicemia (SRS). The FF distribution was evaluated using Principal Component Analysis (PCA) and Augmented Multivariate Curve Resolution with Alternating Least Squares (augmented MCR-ALS) on the spectra obtained from images with pixel sizes of 6.25 μm × 6.25 μm and 1.56 μm × 1.56 μm, in different zones of feed pellets. Since the concentration of the drug was 3.44 mg FF/g pellet, this is the first report showing the powerful ability of the used of spectroscopic techniques and multivariate analysis, especially the augmented MCR-ALS, to describe the FF distribution in both the surface and inner parts of feed pellets at low concentration, in a complex matrix and at the microscopic level. The results allow monitoring the incorporation of the drug into the feed pellets. Copyright © 2018 Elsevier B.V. All rights reserved.

Feature Tracking for High Speed AFM Imaging of Biopolymers.

PubMed

Hartman, Brett; Andersson, Sean B

2018-03-31

The scanning speed of atomic force microscopes continues to advance with some current commercial microscopes achieving on the order of one frame per second and at least one reaching 10 frames per second. Despite the success of these instruments, even higher frame rates are needed with scan ranges larger than are currently achievable. Moreover, there is a significant installed base of slower instruments that would benefit from algorithmic approaches to increasing their frame rate without requiring significant hardware modifications. In this paper, we present an experimental demonstration of high speed scanning on an existing, non-high speed instrument, through the use of a feedback-based, feature-tracking algorithm that reduces imaging time by focusing on features of interest to reduce the total imaging area. Experiments on both circular and square gratings, as well as silicon steps and DNA strands show a reduction in imaging time by a factor of 3-12 over raster scanning, depending on the parameters chosen.

A sparse representation of the pathologist's interaction with whole slide images to improve the assigned relevance of regions of interest

NASA Astrophysics Data System (ADS)

Santiago, Daniel; Corredor, Germán.; Romero, Eduardo

2017-11-01

During a diagnosis task, a Pathologist looks over a Whole Slide Image (WSI), aiming to find out relevant pathological patterns. Nonetheless, a virtual microscope captures these structures, but also other cellular patterns with different or none diagnostic meaning. Annotation of these images depends on manual delineation, which in practice becomes a hard task. This article contributes a new method for detecting relevant regions in WSI using the routine navigations in a virtual microscope. This method constructs a sparse representation or dictionary of each navigation path and determines the hidden relevance by maximizing the incoherence between several paths. The resulting dictionaries are then projected onto each other and relevant information is set to the dictionary atoms whose similarity is higher than a custom threshold. Evaluation was performed with 6 pathological images segmented from a skin biopsy already diagnosed with basal cell carcinoma (BCC). Results show that our proposal outperforms the baseline by more than 20%.

MEMS-based handheld confocal microscope for in-vivo skin imaging

PubMed Central

Arrasmith, Christopher L.; Dickensheets, David L.; Mahadevan-Jansen, Anita

2010-01-01

This paper describes a handheld laser scanning confocal microscope for skin microscopy. Beam scanning is accomplished with an electromagnetic MEMS bi-axial micromirror developed for pico projector applications, providing 800x600 (SVGA) resolution at 56 frames per second. The design uses commercial objective lenses with an optional hemisphere front lens, operating with a range of numerical aperture from NA=0.35 to NA=1.1 and corresponding diagonal field of view ranging from 653 μm to 216 μm. Using NA=1.1 and a laser wavelength of 830 nm we measured the axial response to be 1.14 μm full width at half maximum, with a corresponding 10%-90% lateral edge response of 0.39 μm. Image examples showing both epidermal and dermal features including capillary blood flow are provided. These images represent the highest resolution and frame rate yet achieved for tissue imaging with a MEMS bi-axial scan mirror. PMID:20389391

Adaptation of in-situ microscopy for crystallization processes

NASA Astrophysics Data System (ADS)

Bluma, A.; Höpfner, T.; Rudolph, G.; Lindner, P.; Beutel, S.; Hitzmann, B.; Scheper, T.

2009-08-01

In biotechnological and pharmaceutical engineering, the study of crystallization processes gains importance. An efficient analytical inline sensor could help to improve the knowledge about these processes in order to increase efficiency and yields. The in-situ microscope (ISM) is an optical sensor developed for the monitoring of bioprocesses. A new application for this sensor is the monitoring in downstream processes, e.g. the crystallization of proteins and other organic compounds. This contribution shows new aspects of using in-situ microscopy to monitor crystallization processes. Crystals of different chemical compounds were precipitated from supersaturated solutions and the crystal growth was monitored. Exemplified morphological properties and different forms of crystals could be distinguished on the basis of offline experiments. For inline monitoring of crystallization processes, a special 0.5 L stirred tank reactor was developed and equipped with the in-situ microscope. This reactor was utilized to carry out batch experiments for crystallizations of O-acetylsalicyclic acid (ASS) and hen egg white lysozyme (HEWL). During the whole crystallization process, the in-situ microscope system acquired images directly from the crystallization broth. For the data evaluation, an image analysis algorithm was developed and implemented in the microscope analysis software.

Investigating the impact of blood pressure increase to the brain using high resolution serial histology and image processing

NASA Astrophysics Data System (ADS)

Lesage, F.; Castonguay, A.; Tardif, P. L.; Lefebvre, J.; Li, B.

2015-09-01

A combined serial OCT/confocal scanner was designed to image large sections of biological tissues at microscopic resolution. Serial imaging of organs embedded in agarose blocks is performed by cutting through tissue using a vibratome which sequentially cuts slices in order to reveal new tissue to image, overcoming limited light penetration encountered in microscopy. Two linear stages allow moving the tissue with respect to the microscope objective, acquiring a 2D grid of volumes (1x1x0.3 mm) with OCT and a 2D grid of images (1x1mm) with the confocal arm. This process is repeated automatically, until the entire sample is imaged. Raw data is then post-processed to re-stitch each individual acquisition and obtain a reconstructed volume of the imaged tissue. This design is being used to investigate correlations between white matter and microvasculature changes with aging and with increase in pulse pressure following transaortic constriction in mice. The dual imaging capability of the system allowed to reveal different contrast information: OCT imaging reveals changes in refractive indices giving contrast between white and grey matter in the mouse brain, while transcardial perfusion of FITC or pre-sacrifice injection of Evans Blue shows microsvasculature properties in the brain with confocal imaging.

The influence of structure depth on image blurring of micrometres-thick specimens in MeV transmission electron imaging.

PubMed

Wang, Fang; Sun, Ying; Cao, Meng; Nishi, Ryuji

2016-04-01

This study investigates the influence of structure depth on image blurring of micrometres-thick films by experiment and simulation with a conventional transmission electron microscope (TEM). First, ultra-high-voltage electron microscope (ultra-HVEM) images of nanometer gold particles embedded in thick epoxy-resin films were acquired in the experiment and compared with simulated images. Then, variations of image blurring of gold particles at different depths were evaluated by calculating the particle diameter. The results showed that with a decrease in depth, image blurring increased. This depth-related property was more apparent for thicker specimens. Fortunately, larger particle depth involves less image blurring, even for a 10-μm-thick epoxy-resin film. The quality dependence on depth of a 3D reconstruction of particle structures in thick specimens was revealed by electron tomography. The evolution of image blurring with structure depth is determined mainly by multiple elastic scattering effects. Thick specimens of heavier materials produced more blurring due to a larger lateral spread of electrons after scattering from the structure. Nevertheless, increasing electron energy to 2MeV can reduce blurring and produce an acceptable image quality for thick specimens in the TEM. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multidirectional Image Sensing for Microscopy Based on a Rotatable Robot.

PubMed

Shen, Yajing; Wan, Wenfeng; Zhang, Lijun; Yong, Li; Lu, Haojian; Ding, Weili

2015-12-15

Image sensing at a small scale is essentially important in many fields, including microsample observation, defect inspection, material characterization and so on. However, nowadays, multi-directional micro object imaging is still very challenging due to the limited field of view (FOV) of microscopes. This paper reports a novel approach for multi-directional image sensing in microscopes by developing a rotatable robot. First, a robot with endless rotation ability is designed and integrated with the microscope. Then, the micro object is aligned to the rotation axis of the robot automatically based on the proposed forward-backward alignment strategy. After that, multi-directional images of the sample can be obtained by rotating the robot within one revolution under the microscope. To demonstrate the versatility of this approach, we view various types of micro samples from multiple directions in both optical microscopy and scanning electron microscopy, and panoramic images of the samples are processed as well. The proposed method paves a new way for the microscopy image sensing, and we believe it could have significant impact in many fields, especially for sample detection, manipulation and characterization at a small scale.

Multiparallel Three-Dimensional Optical Microscopy

NASA Technical Reports Server (NTRS)

Nguyen, Lam K.; Price, Jeffrey H.; Kellner, Albert L.; Bravo-Zanoquera, Miguel

2010-01-01

Multiparallel three-dimensional optical microscopy is a method of forming an approximate three-dimensional image of a microscope sample as a collection of images from different depths through the sample. The imaging apparatus includes a single microscope plus an assembly of beam splitters and mirrors that divide the output of the microscope into multiple channels. An imaging array of photodetectors in each channel is located at a different distance along the optical path from the microscope, corresponding to a focal plane at a different depth within the sample. The optical path leading to each photodetector array also includes lenses to compensate for the variation of magnification with distance so that the images ultimately formed on all the photodetector arrays are of the same magnification. The use of optical components common to multiple channels in a simple geometry makes it possible to obtain high light-transmission efficiency with an optically and mechanically simple assembly. In addition, because images can be read out simultaneously from all the photodetector arrays, the apparatus can support three-dimensional imaging at a high scanning rate.

Fundamental quantum noise mapping with tunnelling microscopes tested at surface structures of subatomic lateral size.

PubMed

Herz, Markus; Bouvron, Samuel; Ćavar, Elizabeta; Fonin, Mikhail; Belzig, Wolfgang; Scheer, Elke

2013-10-21

We present a measurement scheme that enables quantitative detection of the shot noise in a scanning tunnelling microscope while scanning the sample. As test objects we study defect structures produced on an iridium single crystal at low temperatures. The defect structures appear in the constant current images as protrusions with curvature radii well below the atomic diameter. The measured power spectral density of the noise is very near to the quantum limit with Fano factor F = 1. While the constant current images show detailed structures expected for tunnelling involving d-atomic orbitals of Ir, we find the current noise to be without pronounced spatial variation as expected for shot noise arising from statistically independent events.

Temporal focusing-based multiphoton excitation microscopy via digital micromirror device.

PubMed

Yih, Jenq-Nan; Hu, Yvonne Yuling; Sie, Yong Da; Cheng, Li-Chung; Lien, Chi-Hsiang; Chen, Shean-Jen

2014-06-01

This Letter presents an enhanced temporal focusing-based multiphoton excitation (MPE) microscope in which the conventional diffraction grating is replaced by a digital micromirror device (DMD). Experimental results from imaging a thin fluorescence film show that the 4.0 μm axial resolution of the microscope is comparable with that of a setup incorporating a 600  lines/mm grating; hence, the optical sectioning ability of the proposed setup is demonstrated. Similar to a grating, the DMD diffracts illuminating light frequencies for temporal focusing; additionally, it generates arbitrary patterns. Since the DMD is placed on the image-conjugate plane of the objective lens' focal plane, the MPE pattern can be projected on the focal plane precisely.

'Berries' on the Ground 2 (3-D)

NASA Technical Reports Server (NTRS)

2004-01-01

This is the 3-D anaglyph showing a microscopic image taken of soil featuring round, blueberry-shaped rock formations on the crater floor at Meridiani Planum, Mars. This image was taken on the 13th day of the Mars Exploration Rover Opportunity's journey, before the Moessbauer spectrometer, an instrument located on the rover's instrument deployment device, or 'arm,' was pressed down to take measurements. The area in this image is approximately 3 centimeters (1.2 inches) across.

X-Tip: a New Tool for Nanoscience or How to Combine X-Ray Spectroscopies to Local Probe Analysis

NASA Astrophysics Data System (ADS)

Olivier, Dhez; Mario, Rodrigues; Fabio, Comin; Roberto, Felici; Joel, Chevrier

2007-01-01

With the advent of nanoscale science, the need of tools able to image samples and bring the region of interest to the X-ray beam is essential. We show the possibility of using the high resolution imaging capability of a scanning probe microscope to image and align a sample relative to the X-ray beam, as well as the possibility to record the photoelectrons emitted by the sample.

Ripples in The Soil

NASA Technical Reports Server (NTRS)

2004-01-01

This is a three-dimensional stereo anaglyph of an image taken by the front navigation camera onboard the Mars Exploration Rover Spirit, showing an interesting patch of rippled soil. Spirit took this image on sol 37 (Feb. 9, 2004) after completing the longest drive ever made by a rover on another planet - 21.2 meters (69.6 feet). On sol 38 scientists plan to investigate this interesting location with the microscopic imager and Moessbauer spectrometer on Spirit's instrument deployment device.

Characterizing Fibrosis in Mouse Kidney using Label Free Fluorescence Lifetime and Second Harmonic Generation Imaging Microscopy in Unilateral Ureteral Obstruction Model

PubMed Central

Ranjit, Suman; Dobrinskikh, Evgenia; Montford, John; Dvornikov, Alexander; Lehman, Allison; Orlicky, David J.; Nemenoff, Raphael; Gratton, Enrico; Levi, Moshe; Furgeson, Seth

2017-01-01

All forms of progressive renal diseases develop a final pathway of tubulointerstitial fibrosis and glomerulosclerosis. Renal fibrosis is usually quantified using histological staining, a process that is time-consuming and pathologist dependent. The work described here shows the development of a fast and operator-independent method to measure fibrosis. To study renal fibrosis, the unilateral ureteral obstruction (UUO) model was chosen. Mice develop a time-dependent increase in obstructed kidneys; contralateral kidneys are used as controls. After UUO, kidneys were analyzed at three time points: 7 days, 14 days, and 21 days. Fibrosis was investigated using FLIM (Fluorescence Lifetime Imaging) and SHG (Second Harmonic Generation) in the deep tissue imaging microscope called DIVER (Deep Imaging via Enhanced photon Recovery). This microscope was developed for deep tissue and SHG and THG (Third Harmonic Generation) imaging and has extraordinary sensitivity towards harmonic generation. SHG data suggests the presence of more fibrillar collagen in the diseased kidneys. The combinations of short wavelength FLIM and SHG analysis results in a robust analysis procedure independent of observer interpretation and let us create a criterion to quantify the extent of fibrosis directly from the image. The progression of fibrosis in UUO model has been studied using this new FLIM-SHG technique and it shows remarkable improvement in quantification of fibrosis compared to standard histological techniques. PMID:27555119

A high-stability scanning tunneling microscope achieved by an isolated tiny scanner with low voltage imaging capability.

PubMed

Wang, Qi; Hou, Yubin; Wang, Junting; Lu, Qingyou

2013-11-01

We present a novel homebuilt scanning tunneling microscope (STM) with high quality atomic resolution. It is equipped with a small but powerful GeckoDrive piezoelectric motor which drives a miniature and detachable scanning part to implement coarse approach. The scanning part is a tiny piezoelectric tube scanner (industry type: PZT-8, whose d31 coefficient is one of the lowest) housed in a slightly bigger polished sapphire tube, which is riding on and spring clamped against the knife edges of a tungsten slot. The STM so constructed shows low back-lashing and drifting and high repeatability and immunity to external vibrations. These are confirmed by its low imaging voltages, low distortions in the spiral scanned images, and high atomic resolution quality even when the STM is placed on the ground of the fifth floor without any external or internal vibration isolation devices.

Microscopy imaging device with advanced imaging properties

DOEpatents

Ghosh, Kunal; Burns, Laurie; El Gamal, Abbas; Schnitzer, Mark J.; Cocker, Eric; Ho, Tatt Wei

2015-11-24

Systems, methods and devices are implemented for microscope imaging solutions. One embodiment of the present disclosure is directed toward an epifluorescence microscope. The microscope includes an image capture circuit including an array of optical sensor. An optical arrangement is configured to direct excitation light of less than about 1 mW to a target object in a field of view of that is at least 0.5 mm.sup.2 and to direct epi-fluorescence emission caused by the excitation light to the array of optical sensors. The optical arrangement and array of optical sensors are each sufficiently close to the target object to provide at least 2.5 .mu.m resolution for an image of the field of view.

Microscopy imaging device with advanced imaging properties

DOEpatents

Ghosh, Kunal; Burns, Laurie; El Gamal, Abbas; Schnitzer, Mark J.; Cocker, Eric; Ho, Tatt Wei

2016-10-25

Systems, methods and devices are implemented for microscope imaging solutions. One embodiment of the present disclosure is directed toward an epifluorescence microscope. The microscope includes an image capture circuit including an array of optical sensor. An optical arrangement is configured to direct excitation light of less than about 1 mW to a target object in a field of view of that is at least 0.5 mm.sup.2 and to direct epi-fluorescence emission caused by the excitation light to the array of optical sensors. The optical arrangement and array of optical sensors are each sufficiently close to the target object to provide at least 2.5 .mu.m resolution for an image of the field of view.

Microscopy imaging device with advanced imaging properties

DOEpatents

Ghosh, Kunal; Burns, Laurie; El Gamal, Abbas; Schnitzer, Mark J.; Cocker, Eric; Ho, Tatt Wei

2016-11-22

Systems, methods and devices are implemented for microscope imaging solutions. One embodiment of the present disclosure is directed toward an epifluorescence microscope. The microscope includes an image capture circuit including an array of optical sensor. An optical arrangement is configured to direct excitation light of less than about 1 mW to a target object in a field of view of that is at least 0.5 mm.sup.2 and to direct epi-fluorescence emission caused by the excitation light to the array of optical sensors. The optical arrangement and array of optical sensors are each sufficiently close to the target object to provide at least 2.5 .mu.m resolution for an image of the field of view.

Microscopy imaging device with advanced imaging properties

DOEpatents

Ghosh, Kunal; Burns, Laurie; El Gamal, Abbas; Schnitzer, Mark J.; Cocker, Eric; Ho, Tatt Wei

2017-04-25

Systems, methods and devices are implemented for microscope imaging solutions. One embodiment of the present disclosure is directed toward an epifluorescence microscope. The microscope includes an image capture circuit including an array of optical sensor. An optical arrangement is configured to direct excitation light of less than about 1 mW to a target object in a field of view of that is at least 0.5 mm.sup.2 and to direct epi-fluorescence emission caused by the excitation light to the array of optical sensors. The optical arrangement and array of optical sensors are each sufficiently close to the target object to provide at least 2.5 .mu.m resolution for an image of the field of view.

Control and acquisition systems for new scanning transmission x-ray microscopes at Advanced Light Source (abstract)

NASA Astrophysics Data System (ADS)

Tyliszczak, T.; Hitchcock, P.; Kilcoyne, A. L. D.; Ade, H.; Hitchcock, A. P.; Fakra, S.; Steele, W. F.; Warwick, T.

2002-03-01

Two new scanning x-ray transmission microscopes are being built at beamline 5.3.2 and beamline 7.0 of the Advanced Light Source that have novel aspects in their control and acquisition systems. Both microscopes use multiaxis laser interferometry to improve the precision of pixel location during imaging and energy scans as well as to remove image distortions. Beam line 5.3.2 is a new beam line where the new microscope will be dedicated to studies of polymers in the 250-600 eV energy range. Since this is a bending magnet beam line with lower x-ray brightness than undulator beam lines, special attention is given to the design not only to minimize distortions and vibrations but also to optimize the controls and acquisition to improve data collection efficiency. 5.3.2 microscope control and acquisition is based on a PC computer running WINDOWS 2000. All mechanical stages are moved by stepper motors with rack mounted controllers. A dedicated counter board is used for counting and timing and a multi-input/output board is used for analog acquisition and control of the focusing mirror. A three axis differential laser interferometer is being used to improve stability and precision by careful tracking of the relative positions of the sample and zone plate. Each axis measures the relative distance between a mirror placed on the sample stage and a mirror attached to the zone plate holder. Agilent Technologies HP 10889A servo-axis interferometer boards are used. While they were designed to control servo motors, our tests show that they can be used to directly control the piezo stage. The use of the interferometer servo-axis boards provides excellent point stability for spectral measurements. The interferometric feedback also provides active vibration isolation which reduces deleterious impact of mechanical vibrations up to 20-30 Hz. It also can improve the speed and precision of image scans. Custom C++ software has been written to provide user friendly control of the microscope and integration with visual light microscopy indexing of the samples. The beam line 7.0 microscope upgrade is a new design which will replace the existing microscope. The design is similar to that of beam line 5.3.2, including interferometric position encoding. However the acquisition and control is based on VXI systems, a Sun computer, and LABVIEW™ software. The main objective of the BL 7.0 microscope upgrade is to achieve precise image scans at very high speed (pixel dwells as short as 10 μs) to take full advantage of the high brightness of the 7.0 undulator beamline. Results of tests and a discussion of the benefits of our scanning microscope designs will be presented.

The different ways to obtain digital images of urine microscopy findings: Their advantages and limitations.

PubMed

Fogazzi, G B; Garigali, G

2017-03-01

We describe three ways to take digital images of urine sediment findings. Way 1 encompasses a digital camera permanently mounted on the microscope and connected with a computer equipped with a proprietary software to acquire, process and store the images. Way 2 is based on the use of inexpensive compact digital cameras, held by hands - or mounted on a tripod - close to one eyepiece of the microscope. Way 3 is based on the use of smartphones, held by hands close to one eyepiece of the microscope or connected to the microscope by an adapter. The procedures, advantages and limitations of each way are reported. Copyright © 2017. Published by Elsevier B.V.

Handy Microscopic Close-Range Videogrammetry

NASA Astrophysics Data System (ADS)

Esmaeili, F.; Ebadi, H.

2017-09-01

The modeling of small-scale objects is used in different applications such as medicine, industry, and cultural heritage. The capability of modeling small-scale objects using imaging with the help of hand USB digital microscopes and use of videogrammetry techniques has been implemented and evaluated in this paper. Use of this equipment and convergent imaging of the environment for modeling, provides an appropriate set of images for generation of three-dimensional models. The results of the measurements made with the help of a microscope micrometer calibration ruler have demonstrated that self-calibration of a hand camera-microscope set can help obtain a three-dimensional detail extraction precision of about 0.1 millimeters on small-scale environments.

Image Analysis, Microscopic, and Spectrochemical Study of the PVC Dry Blending Process,

DTIC Science & Technology

The dry blending process used in the production of electrical grade pvc formulations has been studies using a combination of image analysis , microscopic...by image analysis techniques. Optical and scanning electron microscopy were used to assess morphological differences. Spectrochemical techniques were used to indicate chemical changes.

Computer Aided Solution for Automatic Segmenting and Measurements of Blood Leucocytes Using Static Microscope Images.

PubMed

Abdulhay, Enas; Mohammed, Mazin Abed; Ibrahim, Dheyaa Ahmed; Arunkumar, N; Venkatraman, V

2018-02-17

Blood leucocytes segmentation in medical images is viewed as difficult process due to the variability of blood cells concerning their shape and size and the difficulty towards determining location of Blood Leucocytes. Physical analysis of blood tests to recognize leukocytes is tedious, time-consuming and liable to error because of the various morphological components of the cells. Segmentation of medical imagery has been considered as a difficult task because of complexity of images, and also due to the non-availability of leucocytes models which entirely captures the probable shapes in each structures and also incorporate cell overlapping, the expansive variety of the blood cells concerning their shape and size, various elements influencing the outer appearance of the blood leucocytes, and low Static Microscope Image disparity from extra issues outcoming about because of noise. We suggest a strategy towards segmentation of blood leucocytes using static microscope images which is a resultant of three prevailing systems of computer vision fiction: enhancing the image, Support vector machine for segmenting the image, and filtering out non ROI (region of interest) on the basis of Local binary patterns and texture features. Every one of these strategies are modified for blood leucocytes division issue, in this manner the subsequent techniques are very vigorous when compared with its individual segments. Eventually, we assess framework based by compare the outcome and manual division. The findings outcome from this study have shown a new approach that automatically segments the blood leucocytes and identify it from a static microscope images. Initially, the method uses a trainable segmentation procedure and trained support vector machine classifier to accurately identify the position of the ROI. After that, filtering out non ROI have proposed based on histogram analysis to avoid the non ROI and chose the right object. Finally, identify the blood leucocytes type using the texture feature. The performance of the foreseen approach has been tried in appearing differently in relation to the system against manual examination by a gynaecologist utilizing diverse scales. A total of 100 microscope images were used for the comparison, and the results showed that the proposed solution is a viable alternative to the manual segmentation method for accurately determining the ROI. We have evaluated the blood leucocytes identification using the ROI texture (LBP Feature). The identification accuracy in the technique used is about 95.3%., with 100 sensitivity and 91.66% specificity.

Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme

PubMed Central

Woringer, Maxime; Darzacq, Xavier; Zimmer, Christophe

2017-01-01

Three-dimensional fluorescence microscopy based on Nyquist sampling of focal planes faces harsh trade-offs between acquisition time, light exposure, and signal-to-noise. We propose a 3D compressed sensing approach that uses temporal modulation of the excitation intensity during axial stage sweeping and can be adapted to fluorescence microscopes without hardware modification. We describe implementations on a lattice light sheet microscope and an epifluorescence microscope, and show that images of beads and biological samples can be reconstructed with a 5-10 fold reduction of light exposure and acquisition time. Our scheme opens a new door towards faster and less damaging 3D fluorescence microscopy. PMID:28788909

Excitation of propagating surface plasmons with a scanning tunnelling microscope.

PubMed

Wang, T; Boer-Duchemin, E; Zhang, Y; Comtet, G; Dujardin, G

2011-04-29

Inelastic electron tunnelling excitation of propagating surface plasmon polaritons (SPPs) on a thin gold film is demonstrated. This is done by combining a scanning tunnelling microscope (STM) with an inverted optical microscope. Analysis of the leakage radiation in both the image and Fourier planes unambiguously shows that the majority (up to 99.5%) of the detected photons originate from propagating SPPs with propagation lengths of the order of 10  µm. The remaining photon emission is localized under the STM tip and is attributed to a tip-gold film coupled plasmon resonance as evidenced by the bimodal spectral distribution and enhanced emission intensity observed using a silver STM tip for excitation.

Multiscale Imaging of the Mouse Cortex Using Two-Photon Microscopy and Wide-Field Illumination

NASA Astrophysics Data System (ADS)

Bumstead, Jonathan R.

The mouse brain can be studied over vast spatial scales ranging from microscopic imaging of single neurons to macroscopic measurements of hemodynamics acquired over the majority of the mouse cortex. However, most neuroimaging modalities are limited by a fundamental trade-off between the spatial resolution and the field-of-view (FOV) over which the brain can be imaged, making it difficult to fully understand the functional and structural architecture of the healthy mouse brain and its disruption in disease. My dissertation has focused on developing multiscale optical systems capable of imaging the mouse brain at both microscopic and mesoscopic spatial scales, specifically addressing the difference in spatial scales imaged with two-photon microscopy (TPM) and optical intrinsic signal imaging (OISI). Central to this work has been the formulation of a principled design strategy for extending the FOV of the two-photon microscope. Using this design approach, we constructed a TPM system with subcellular resolution and a FOV area 100 times greater than a conventional two-photon microscope. To image the ellipsoidal shape of the mouse cortex, we also developed the microscope to image arbitrary surfaces within a single frame using an electrically tunable lens. Finally, to address the speed limitations of the TPM systems developed during my dissertation, I also conducted research in large-scale neural phenomena occurring in the mouse brain imaged with high-speed OISI. The work conducted during my dissertation addresses some of the fundamental principles in designing and applying optical systems for multiscale imaging of the mouse brain.

Scanning tunneling microscopy and atomic force microscopy: application to biology and technology.

PubMed

Hansma, P K; Elings, V B; Marti, O; Bracker, C E

1988-10-14

The scanning tunneling microscope (STM) and the atomic force microscope (AFM) are scanning probe microscopes capable of resolving surface detail down to the atomic level. The potential of these microscopes for revealing subtle details of structure is illustrated by atomic resolution images including graphite, an organic conductor, an insulating layered compound, and individual adsorbed oxygen atoms on a semiconductor. Application of the STM for imaging biological materials directly has been hampered by the poor electron conductivity of most biological samples. The use of thin conductive metal coatings and replicas has made it possible to image some biological samples, as indicated by recently obtained images of a recA-DNA complex, a phospholipid bilayer, and an enzyme crystal. The potential of the AFM, which does not require a conductive sample, is shown with molecular resolution images of a nonconducting organic monolayer and an amino acid crystal that reveals individual methyl groups on the ends of the amino acids. Applications of these new microscopes to technology are demonstrated with images of an optical disk stamper, a diffraction grating, a thin-film magnetic recording head, and a diamond cutting tool. The STM has even been used to improve the quality of diffraction gratings and magnetic recording heads.

Defocus and magnification dependent variation of TEM image astigmatism.

PubMed

Yan, Rui; Li, Kunpeng; Jiang, Wen

2018-01-10

Daily alignment of the microscope is a prerequisite to reaching optimal lens conditions for high resolution imaging in cryo-EM. In this study, we have investigated how image astigmatism varies with the imaging conditions (e.g. defocus, magnification). We have found that the large change of defocus/magnification between visual correction of astigmatism and subsequent data collection tasks, or during data collection, will inevitably result in undesirable astigmatism in the final images. The dependence of astigmatism on the imaging conditions varies significantly from time to time, so that it cannot be reliably compensated by pre-calibration of the microscope. Based on these findings, we recommend that the same magnification and the median defocus of the intended defocus range for final data collection are used in the objective lens astigmatism correction task during microscope alignment and in the focus mode of the iterative low-dose imaging. It is also desirable to develop a fast, accurate method that can perform dynamic correction of the astigmatism for different intended defocuses during automated imaging. Our findings also suggest that the slope of astigmatism changes caused by varying defocuses can be used as a convenient measurement of objective lens rotation symmetry and potentially an acceptance test of new electron microscopes.

Long-working-distance fluorescence microscope with high-numerical-aperture objectives for variable-magnification imaging in live mice from macro- to subcellular

NASA Astrophysics Data System (ADS)

Kimura, Hiroaki; Momiyama, Masashi; Tomita, Katsuro; Tsuchiya, Hiroyuki; Hoffman, Robert M.

2010-11-01

We demonstrate the development of a long-working-distance fluorescence microscope with high-numerical-aperture objectives for variable-magnification imaging in live mice from macro- to subcellular. To observe cytoplasmic and nuclear dynamics of cancer cells in the living mouse, 143B human osteosarcoma cells are labeled with green fluorescent protein in the nucleus and red fluorescent protein in the cytoplasm. These dual-color cells are injected by a vascular route in an abdominal skin flap in nude mice. The mice are then imaged with the Olympus MVX10 macroview fluorescence microscope. With the MVX10, the nuclear and cytoplasmic behavior of cancer cells trafficking in blood vessels of live mice is observed. We also image lung metastases in live mice from the macro- to the subcellular level by opening the chest wall and imaging the exposed lung in live mice. Injected splenocytes, expressing cyan fluorescent protein, could also be imaged on the lung of live mice. We demonstrate that the MVX10 microscope offers the possibility of full-range in vivo fluorescence imaging from macro- to subcellular and should enable widespread use of powerful imaging technologies enabled by genetic reporters and other fluorophores.

Handheld nonlinear microscope system comprising a 2 MHz repetition rate, mode-locked Yb-fiber laser for in vivo biomedical imaging

PubMed Central

Krolopp, Ádám; Csákányi, Attila; Haluszka, Dóra; Csáti, Dániel; Vass, Lajos; Kolonics, Attila; Wikonkál, Norbert; Szipőcs, Róbert

2016-01-01

A novel, Yb-fiber laser based, handheld 2PEF/SHG microscope imaging system is introduced. It is suitable for in vivo imaging of murine skin at an average power level as low as 5 mW at 200 kHz sampling rate. Amplified and compressed laser pulses having a spectral bandwidth of 8 to 12 nm at around 1030 nm excite the biological samples at a ~1.89 MHz repetition rate, which explains how the high quality two-photon excitation fluorescence (2PEF) and second harmonic generation (SHG) images are obtained at the average power level of a laser pointer. The scanning, imaging and detection head, which comprises a conventional microscope objective for beam focusing, has a physical length of ~180 mm owing to the custom designed imaging telescope system between the laser scanner mirrors and the entrance aperture of the microscope objective. Operation of the all-fiber, all-normal dispersion Yb-fiber ring laser oscillator is electronically controlled by a two-channel polarization controller for Q-switching free mode-locked operation. The whole nonlinear microscope imaging system has the main advantages of the low price of the fs laser applied, fiber optics flexibility, a relatively small, light-weight scanning and detection head, and a very low risk of thermal or photochemical damage of the skin samples. PMID:27699118

Handheld nonlinear microscope system comprising a 2 MHz repetition rate, mode-locked Yb-fiber laser for in vivo biomedical imaging.

PubMed

Krolopp, Ádám; Csákányi, Attila; Haluszka, Dóra; Csáti, Dániel; Vass, Lajos; Kolonics, Attila; Wikonkál, Norbert; Szipőcs, Róbert

2016-09-01

A novel, Yb-fiber laser based, handheld 2PEF/SHG microscope imaging system is introduced. It is suitable for in vivo imaging of murine skin at an average power level as low as 5 mW at 200 kHz sampling rate. Amplified and compressed laser pulses having a spectral bandwidth of 8 to 12 nm at around 1030 nm excite the biological samples at a ~1.89 MHz repetition rate, which explains how the high quality two-photon excitation fluorescence (2PEF) and second harmonic generation (SHG) images are obtained at the average power level of a laser pointer. The scanning, imaging and detection head, which comprises a conventional microscope objective for beam focusing, has a physical length of ~180 mm owing to the custom designed imaging telescope system between the laser scanner mirrors and the entrance aperture of the microscope objective. Operation of the all-fiber, all-normal dispersion Yb-fiber ring laser oscillator is electronically controlled by a two-channel polarization controller for Q-switching free mode-locked operation. The whole nonlinear microscope imaging system has the main advantages of the low price of the fs laser applied, fiber optics flexibility, a relatively small, light-weight scanning and detection head, and a very low risk of thermal or photochemical damage of the skin samples.

Phytoplankton bloom along the coast of Namibia

NASA Technical Reports Server (NTRS)

2002-01-01

This MODIS true-color image, acquired March 4, 2002, shows a phytoplankton bloom along the coast of Namibia. Phytoplankton is a microscopic organism that utilizes chlorophyll, which sunlight reflects off of to create this intense blue-green color in the water. Also prominent in this image is the Skeleton Coast Game Park, which runs along Namibia's northern coast and here glows a beautiful coral-orange color.

Image alignment for tomography reconstruction from synchrotron X-ray microscopic images.

PubMed

Cheng, Chang-Chieh; Chien, Chia-Chi; Chen, Hsiang-Hsin; Hwu, Yeukuang; Ching, Yu-Tai

2014-01-01

A synchrotron X-ray microscope is a powerful imaging apparatus for taking high-resolution and high-contrast X-ray images of nanoscale objects. A sufficient number of X-ray projection images from different angles is required for constructing 3D volume images of an object. Because a synchrotron light source is immobile, a rotational object holder is required for tomography. At a resolution of 10 nm per pixel, the vibration of the holder caused by rotating the object cannot be disregarded if tomographic images are to be reconstructed accurately. This paper presents a computer method to compensate for the vibration of the rotational holder by aligning neighboring X-ray images. This alignment process involves two steps. The first step is to match the "projected feature points" in the sequence of images. The matched projected feature points in the x-θ plane should form a set of sine-shaped loci. The second step is to fit the loci to a set of sine waves to compute the parameters required for alignment. The experimental results show that the proposed method outperforms two previously proposed methods, Xradia and SPIDER. The developed software system can be downloaded from the URL, http://www.cs.nctu.edu.tw/~chengchc/SCTA or http://goo.gl/s4AMx.

Characteristics of different frequency ranges in scanning electron microscope images

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

Sim, K. S., E-mail: kssim@mmu.edu.my; Nia, M. E.; Tan, T. L.

2015-07-22

We demonstrate a new approach to characterize the frequency range in general scanning electron microscope (SEM) images. First, pure frequency images are generated from low frequency to high frequency, and then, the magnification of each type of frequency image is implemented. By comparing the edge percentage of the SEM image to the self-generated frequency images, we can define the frequency ranges of the SEM images. Characterization of frequency ranges of SEM images benefits further processing and analysis of those SEM images, such as in noise filtering and contrast enhancement.

A hybrid scanning force and light microscope for surface imaging and three-dimensional optical sectioning in differential interference contrast.

PubMed

Stemmer, A

1995-04-01

The design of a scanned-cantilever-type force microscope is presented which is fully integrated into an inverted high-resolution video-enhanced light microscope. This set-up allows us to acquire thin optical sections in differential interference contrast (DIC) or polarization while the force microscope is in place. Such a hybrid microscope provides a unique platform to study how cell surface properties determine, or are affected by, the three-dimensional dynamic organization inside the living cell. The hybrid microscope presented in this paper has proven reliable and versatile for biological applications. It is the only instrument that can image a specimen by force microscopy and high-power DIC without having either to translate the specimen or to remove the force microscope. Adaptation of the design features could greatly enhance the suitability of other force microscopes for biological work.

Digital image processing of bone - Problems and potentials

NASA Technical Reports Server (NTRS)

Morey, E. R.; Wronski, T. J.

1980-01-01

The development of a digital image processing system for bone histomorphometry and fluorescent marker monitoring is discussed. The system in question is capable of making measurements of UV or light microscope features on a video screen with either video or computer-generated images, and comprises a microscope, low-light-level video camera, video digitizer and display terminal, color monitor, and PDP 11/34 computer. Capabilities demonstrated in the analysis of an undecalcified rat tibia include the measurement of perimeter and total bone area, and the generation of microscope images, false color images, digitized images and contoured images for further analysis. Software development will be based on an existing software library, specifically the mini-VICAR system developed at JPL. It is noted that the potentials of the system in terms of speed and reliability far exceed any problems associated with hardware and software development.

'Berries' on the Ground 2 (3-D)

NASA Technical Reports Server (NTRS)

2004-01-01

This is the 3-D anaglyph showing a microscopic image taken of soil featuring round, blueberry-shaped rock formations on the crater floor at Meridiani Planum, Mars. This image was taken on the 13th day of the Mars Exploration Rover Opportunity's journey, after the Moessbauer spectrometer, an instrument located on the rover's instrument deployment device, or 'arm,' was pressed down to measure the soil's iron mineralogy. Note the donut-shaped imprint of the instrument in the lower part of the image. The area in this image is approximately 3 centimeters (1.2 inches) across.

Hybrid reflecting objectives for functional multiphoton microscopy in turbid media

PubMed Central

Vučinić, Dejan; Bartol, Thomas M.; Sejnowski, Terrence J.

2010-01-01

Most multiphoton imaging of biological specimens is performed using microscope objectives optimized for high image quality under wide-field illumination. We present a class of objectives designed de novo without regard for these traditional constraints, driven exclusively by the needs of fast multiphoton imaging in turbid media: the delivery of femtosecond pulses without dispersion and the efficient collection of fluorescence. We model the performance of one such design optimized for a typical brain-imaging setup and show that it can greatly outperform objectives commonly used for this task. PMID:16880851

Lensless digital holographic microscopy and its applications in biomedicine and environmental monitoring.

PubMed

Wu, Yichen; Ozcan, Aydogan

2018-03-01

Optical compound microscope has been a major tool in biomedical imaging for centuries. Its performance relies on relatively complicated, bulky and expensive lenses and alignment mechanics. In contrast, the lensless microscope digitally reconstructs microscopic images of specimens without using any lenses, as a result of which it can be made much smaller, lighter and lower-cost. Furthermore, the limited space-bandwidth product of objective lenses in a conventional microscope can be significantly surpassed by a lensless microscope. Such lensless imaging designs have enabled high-resolution and high-throughput imaging of specimens using compact, portable and cost-effective devices to potentially address various point-of-care, global-health and telemedicine related challenges. In this review, we discuss the operation principles and the methods behind lensless digital holographic on-chip microscopy. We also go over various applications that are enabled by cost-effective and compact implementations of lensless microscopy, including some recent work on air quality monitoring, which utilized machine learning for high-throughput and accurate quantification of particulate matter in air. Finally, we conclude with a brief future outlook of this computational imaging technology. Copyright © 2017 Elsevier Inc. All rights reserved.

In vivo fiber-optic confocal reflectance microscope with an injection-molded plastic miniature objective lens.

PubMed

Carlson, Kristen; Chidley, Matthew; Sung, Kung-Bin; Descour, Michael; Gillenwater, Ann; Follen, Michele; Richards-Kortum, Rebecca

2005-04-01

For in vivo optical diagnostic technologies to be distributed to the developed and developing worlds, optical imaging systems must be constructed of inexpensive components. We present a fiber-optic confocal reflectance microscope with a cost-effective injection-molded plastic miniature objective lens for in vivo imaging of human tissues in near real time. The measured lateral resolution is less than 2.2 microm, and the measured axial resolution is 10 microm. Confocal images of ex vivo cervical tissue biopsies and in vivo human lip taken at 15 frames/s demonstrate the microscope's capability of imaging cell morphology and tissue architecture.

Fiber-optic confocal reflectance microscope with miniature objective for in vivo imaging of human tissues.

PubMed

Sung, Kung-Bin; Liang, Chen; Descour, Michael; Collier, Tom; Follen, Michele; Richards-Kortum, Rebecca

2002-10-01

We have built a fiber-optic confocal reflectance microscope capable of imaging human tissues in near real time. Miniaturization of the objective lens and the mechanical components for positioning and axially scanning the objective enables the device to be used in inner organs of the human body. The lateral resolution is 2 micrometers and axial resolution is 10 micrometers. Confocal images of fixed tissue biopsies and the human lip in vivo have been obtained at 15 frames/s without any fluorescent stains. Both cell morphology and tissue architecture can be appreciated from images obtained with this microscope.

Fluorescence-guided tumor visualization using a custom designed NIR attachment to a surgical microscope for high sensitivity imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kittle, David S.; Patil, Chirag G.; Mamelak, Adam; Hansen, Stacey; Perry, Jeff; Ishak, Laura; Black, Keith L.; Butte, Pramod V.

2016-03-01

Current surgical microscopes are limited in sensitivity for NIR fluorescence. Recent developments in tumor markers attached with NIR dyes require newer, more sensitive imaging systems with high resolution to guide surgical resection. We report on a small, single camera solution enabling advanced image processing opportunities previously unavailable for ultra-high sensitivity imaging of these agents. The system captures both visible reflectance and NIR fluorescence at 300 fps while displaying full HD resolution video at 60 fps. The camera head has been designed to easily mount onto the Zeiss Pentero microscope head for seamless integration into surgical procedures.

Fractal evaluation of drug amorphicity from optical and scanning electron microscope images

NASA Astrophysics Data System (ADS)

Gavriloaia, Bogdan-Mihai G.; Vizireanu, Radu C.; Neamtu, Catalin I.; Gavriloaia, Gheorghe V.

2013-09-01

Amorphous materials are metastable, more reactive than the crystalline ones, and have to be evaluated before pharmaceutical compound formulation. Amorphicity is interpreted as a spatial chaos, and patterns of molecular aggregates of dexamethasone, D, were investigated in this paper by using fractal dimension, FD. Images having three magnifications of D were taken from an optical microscope, OM, and with eight magnifications, from a scanning electron microscope, SEM, were analyzed. The average FD for pattern irregularities of OM images was 1.538, and about 1.692 for SEM images. The FDs of the two kinds of images are less sensitive of threshold level. 3D images were shown to illustrate dependence of FD of threshold and magnification level. As a result, optical image of single scale is enough to characterize the drug amorphicity. As a result, the OM image at a single scale is enough to characterize the amorphicity of D.

HETEROGENEOUS SOOT NANOSTRUCTURE IN ATMOSPHERIC AND COMBUSTION SOURCE AEROSOLS

EPA Science Inventory

Microscopic images of soot emissions from wildfire and a wide range of anthropogenic combustion sources show that the nanostructures of individual particles in these emissions are predominantly heterogeneous, decidedly influenced by the fuel composition and by the particular comb...

Expansion Mini-Microscopy: An Enabling Alternative in Point-of-Care Diagnostics

PubMed Central

Zhang, Yu Shrike; Santiago, Grissel Trujillo-de; Alvarez, Mario Moisés; Schiff, Steven J.; Boyden, Edward S.; Khademhosseini, Ali

2017-01-01

Diagnostics play a significant role in health care. In the developing world and low-resource regions the utility for point-of-care (POC) diagnostics becomes even greater. This need has long been recognized, and diagnostic technology has seen tremendous progress with the development of portable instrumentation such as miniature imagers featuring low complexity and cost. However, such inexpensive devices have not been able to achieve a resolution sufficient for POC detection of pathogens at very small scales, such as single-cell parasites, bacteria, fungi, and viruses. To this end, expansion microscopy (ExM) is a recently developed technique that, by physically expanding preserved biological specimens through a chemical process, enables super-resolution imaging on conventional microscopes and improves imaging resolution of a given microscope without the need to modify the existing microscope hardware. Here we review recent advances in ExM and portable imagers, respectively, and discuss the rational combination of the two technologies, that we term expansion mini-microscopy (ExMM). In ExMM, the physical expansion of a biological sample followed by imaging on a mini-microscope achieves a resolution as high as that attainable by conventional high-end microscopes imaging non-expanded samples, at significant reduction in cost. We believe that this newly developed ExMM technique is likely to find widespread applications in POC diagnostics in resource-limited and remote regions by expanded-scale imaging of biological specimens that are otherwise not resolvable using low-cost imagers. PMID:29062977

[Detection of marginal leakage of Class V restorations in vitro by micro-CT].

PubMed

Gu, Lin-juan; Zhao, Xin-yi; Li, Shi-bao

2012-09-01

To evaluate the reliability and superiority of micro-CT in marginal leakage assessment of Class V restorations. Class V preparations with gingival margins in dentin and occlusal in enamel were made in sixteen extracted non-carious human molars and restored with dental bonding agents and composite resin. All teeth were then immersed in 50% ammonia-silver nitrate solution for 12 hours, followed by developing solution for 8 hours. Each restoration was scanned by a micro-CT and silver leakage was measured and three-dimensional image of the silver leakage alone cavity wall were reconstructed. Afterward, all restorations were sectioned and examined for leakage depth using a microscope. The silver leakage depth of each restoration obtained by micro-CT and microscope were compared for equivalency. The silver leakage depths in gingival wall obtained with micro-CT (0.78 mm) and microscope (0.74 mm) showed no significant difference (P > 0.05), while the judgment of leakage depths in occlusal wall in micro-CT image (0.40 mm) was affected by adjacent enamel structure, giving less leakage depths compared to microscope (0.72 mm)(P < 0.01). The three-dimensional shapes of the microleakages displayed clearly by micro-CT alone wall of Class V restorations were multiform and some leakages showed channels on their way to spreading. Micro-CT can detect precisely the silver leakage in the dentin wall of a restoration and display its three-dimensional shape fully. Enamel structure affects the detection of the silver leakage next to it.

A numerical analysis of the Born approximation for image formation modeling of differential interference contrast microscopy for human embryos

NASA Astrophysics Data System (ADS)

Trattner, Sigal; Feigin, Micha; Greenspan, Hayit; Sochen, Nir

2008-03-01

The differential interference contrast (DIC) microscope is commonly used for the visualization of live biological specimens. It enables the view of the transparent specimens while preserving their viability, being a non-invasive modality. Fertility clinics often use the DIC microscope for evaluation of human embryos quality. Towards quantification and reconstruction of the visualized specimens, an image formation model for DIC imaging is sought and the interaction of light waves with biological matter is examined. In many image formation models the light-matter interaction is expressed via the first Born approximation. The validity region of this approximation is defined in a theoretical bound which limits its use to very small specimens with low dielectric contrast. In this work the Born approximation is investigated via the Helmholtz equation, which describes the interaction between the specimen and light. A solution on the lens field is derived using the Gaussian Legendre quadrature formulation. This numerical scheme is considered both accurate and efficient and has shortened significantly the computation time as compared to integration methods that required a great amount of sampling for satisfying the Whittaker - Shannon sampling theorem. By comparing the numerical results with the theoretical values it is shown that the theoretical bound is not directly relevant to microscopic imaging and is far too limiting. The numerical exhaustive experiments show that the Born approximation is inappropriate for modeling the visualization of thick human embryos.

Compact Microscope Imaging System With Intelligent Controls Improved

NASA Technical Reports Server (NTRS)

McDowell, Mark

2004-01-01

The Compact Microscope Imaging System (CMIS) with intelligent controls is a diagnostic microscope analysis tool with intelligent controls for use in space, industrial, medical, and security applications. This compact miniature microscope, which can perform tasks usually reserved for conventional microscopes, has unique advantages in the fields of microscopy, biomedical research, inline process inspection, and space science. Its unique approach integrates a machine vision technique with an instrumentation and control technique that provides intelligence via the use of adaptive neural networks. The CMIS system was developed at the NASA Glenn Research Center specifically for interface detection used for colloid hard spheres experiments; biological cell detection for patch clamping, cell movement, and tracking; and detection of anode and cathode defects for laboratory samples using microscope technology.

The plant virus microscope image registration method based on mismatches removing.

PubMed

Wei, Lifang; Zhou, Shucheng; Dong, Heng; Mao, Qianzhuo; Lin, Jiaxiang; Chen, Riqing

2016-01-01

The electron microscopy is one of the major means to observe the virus. The view of virus microscope images is limited by making specimen and the size of the camera's view field. To solve this problem, the virus sample is produced into multi-slice for information fusion and image registration techniques are applied to obtain large field and whole sections. Image registration techniques have been developed in the past decades for increasing the camera's field of view. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Alternatively, the methods are conceived just to provide visually pleasant registration for high overlap ratio image sequence. This work presents a method for virus microscope image registration acquired with detailed visual information and subpixel accuracy, even when overlap ratio of image sequence is 10% or less. The method proposed focus on the correspondence set and interimage transformation. A mismatch removal strategy is proposed by the spatial consistency and the components of keypoint to enrich the correspondence set. And the translation model parameter as well as tonal inhomogeneities is corrected by the hierarchical estimation and model select. In the experiments performed, we tested different registration approaches and virus images, confirming that the translation model is not always stationary, despite the fact that the images of the sample come from the same sequence. The mismatch removal strategy makes building registration of virus microscope images at subpixel accuracy easier and optional parameters for building registration according to the hierarchical estimation and model select strategies make the proposed method high precision and reliable for low overlap ratio image sequence. Copyright © 2015 Elsevier Ltd. All rights reserved.

Free and open-source automated 3-D microscope.

PubMed

Wijnen, Bas; Petersen, Emily E; Hunt, Emily J; Pearce, Joshua M

2016-11-01

Open-source technology not only has facilitated the expansion of the greater research community, but by lowering costs it has encouraged innovation and customizable design. The field of automated microscopy has continued to be a challenge in accessibility due the expense and inflexible, noninterchangeable stages. This paper presents a low-cost, open-source microscope 3-D stage. A RepRap 3-D printer was converted to an optical microscope equipped with a customized, 3-D printed holder for a USB microscope. Precision measurements were determined to have an average error of 10 μm at the maximum speed and 27 μm at the minimum recorded speed. Accuracy tests yielded an error of 0.15%. The machine is a true 3-D stage and thus able to operate with USB microscopes or conventional desktop microscopes. It is larger than all commercial alternatives, and is thus capable of high-depth images over unprecedented areas and complex geometries. The repeatability is below 2-D microscope stages, but testing shows that it is adequate for the majority of scientific applications. The open-source microscope stage costs less than 3-9% of the closest proprietary commercial stages. This extreme affordability vastly improves accessibility for 3-D microscopy throughout the world. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

The Athena Pancam and Color Microscopic Imager (CMI)

NASA Technical Reports Server (NTRS)

Bell, J. F., III; Herkenhoff, K. E.; Schwochert, M.; Morris, R. V.; Sullivan, R.

2000-01-01

The Athena Mars rover payload includes two primary science-grade imagers: Pancam, a multispectral, stereo, panoramic camera system, and the Color Microscopic Imager (CMI), a multispectral and variable depth-of-field microscope. Both of these instruments will help to achieve the primary Athena science goals by providing information on the geology, mineralogy, and climate history of the landing site. In addition, Pancam provides important support for rover navigation and target selection for Athena in situ investigations. Here we describe the science goals, instrument designs, and instrument performance of the Pancam and CMI investigations.

Mobile microscopy as a screening tool for oral cancer in India: A pilot study.

PubMed

Skandarajah, Arunan; Sunny, Sumsum P; Gurpur, Praveen; Reber, Clay D; D'Ambrosio, Michael V; Raghavan, Nisheena; James, Bonney Lee; Ramanjinappa, Ravindra D; Suresh, Amritha; Kandasarma, Uma; Birur, Praveen; Kumar, Vinay V; Galmeanu, Honorius-Cezar; Itu, Alexandru Mihail; Modiga-Arsu, Mihai; Rausch, Saskia; Sramek, Maria; Kollegal, Manohar; Paladini, Gianluca; Kuriakose, Moni; Ladic, Lance; Koch, Felix; Fletcher, Daniel

2017-01-01

Oral cancer is the most common type of cancer among men in India and other countries in South Asia. Late diagnosis contributes significantly to this mortality, highlighting the need for effective and specific point-of-care diagnostic tools. The same regions with high prevalence of oral cancer have seen extensive growth in mobile phone infrastructure, which enables widespread access to telemedicine services. In this work, we describe the evaluation of an automated tablet-based mobile microscope as an adjunct for telemedicine-based oral cancer screening in India. Brush biopsy, a minimally invasive sampling technique was combined with a simplified staining protocol and a tablet-based mobile microscope to facilitate local collection of digital images and remote evaluation of the images by clinicians. The tablet-based mobile microscope (CellScope device) combines an iPad Mini with collection optics, LED illumination and Bluetooth-controlled motors to scan a slide specimen and capture high-resolution images of stained brush biopsy samples. Researchers at the Mazumdar Shaw Medical Foundation (MSMF) in Bangalore, India used the instrument to collect and send randomly selected images of each slide for telepathology review. Evaluation of the concordance between gold standard histology, conventional microscopy cytology, and remote pathologist review of the images was performed as part of a pilot study of mobile microscopy as a screening tool for oral cancer. Results indicated that the instrument successfully collected images of sufficient quality to enable remote diagnoses that show concordance with existing techniques. Further studies will evaluate the effectiveness of oral cancer screening with mobile microscopy by minimally trained technicians in low-resource settings.

Long-term imaging of mouse embryos using adaptive harmonic generation microscopy

NASA Astrophysics Data System (ADS)

Thayil, Anisha; Watanabe, Tomoko; Jesacher, Alexander; Wilson, Tony; Srinivas, Shankar; Booth, Martin

2011-04-01

We present a detailed description of an adaptive harmonic generation (HG) microscope and culture techniques that permit long-term, three-dimensional imaging of mouse embryos. HG signal from both pre- and postimplantation stage (0.5-5.5 day-old) mouse embryos are fully characterized. The second HG images reveal central spindles during cytokinesis whereas third HG images show several features, such as lipid droplets, nucleoli, and plasma membranes. The embryos are found to develop normally during one-day-long discontinuous HG imaging, permitting the observation of several dynamic events, such as morula compaction and blastocyst formation.

Fluorescence correlation spectroscopy, Raster image correlation spectroscopy and Number & Brightness on a commercial confocal laser scanning microscope with analog detectors (Nikon C1)

PubMed Central

Moens, Pierre D.J.; Gratton, Enrico; Salvemini, Iyrri L.

2010-01-01

Fluorescence correlation spectroscopy (FCS) was developed in 1972 by Magde, Elson and Webb (Magde et al., 1972). Photon counting detectors and avalanche photodiodes have become standards in FCS to the point that there is a widespread belief that these detectors are essential to perform FCS experiments, despite the fact that FCS was developed using analog detectors. Spatial and temporal intensity fluctuation correlations using analog detection on a commercial Olympus Fluoview 300 microscope has been reported by Brown et al. (2008). However, each analog instrument has its own idiosyncrasies that need to be understood before using the instrument for FCS. In this work we explore the capabilities of the Nikon C1, a low cost confocal microscope, to obtain single point FCS, Raster-scan Image Correlation Spectroscopy (RICS) and Number & Brightness data both in solution and incorporated into the membrane of Giant Unilamellar Vesicles (GUVs). We show that it is possible to obtain dynamic information about fluorescent molecules from single point FCS, RICS and Number & Brightness using the Nikon C1. We highlighted the fact that care should be taken in selecting the acquisition parameters in order to avoid possible artifacts due to the detector noise. However, due to relatively large errors in determining the distribution of digital levels for a given microscope setting, the system is probably only adequate for determining relative brightness within the same image. PMID:20734406

Microscopy with multimode fibers

NASA Astrophysics Data System (ADS)

Moser, Christophe; Papadopoulos, Ioannis; Farahi, Salma; Psaltis, Demetri

2013-04-01

Microscopes are usually thought of comprising imaging elements such as objectives and eye-piece lenses. A different type of microscope, used for endoscopy, consists of waveguiding elements such as fiber bundles, where each fiber in the bundle transports the light corresponding to one pixel in the image. Recently a new type of microscope has emerged that exploits the large number of propagating modes in a single multimode fiber. We have successfully produced fluorescence images of neural cells with sub-micrometer resolution via a 200 micrometer core multimode fiber. The method for achieving imaging consists of using digital phase conjugation to reproduce a focal spot at the tip of the multimode fiber. The image is formed by scanning the focal spot digitally and collecting the fluorescence point by point.

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

Rosch, R.; Boutin, J. Y.; Le Breton, J. P.

This article describes x-ray imaging with grazing-incidence microscopes, developed for the experimental program carried out on the Ligne d'Integration Laser (LIL) facility [J. P. Le Breton et al., Inertial Fusion Sciences and Applications 2001 (Elsevier, Paris, 2002), pp. 856-862] (24 kJ, UV--0.35 nm). The design includes a large target-to-microscope (400-700 mm) distance required by the x-ray ablation issues anticipated on the Laser MegaJoule facility [P. A. Holstein et al., Laser Part. Beams 17, 403 (1999)] (1.8 MJ) which is under construction. Two eight-image Kirkpatrick-Baez microscopes [P. Kirkpatrick and A. V. Baez J. Opt. Soc. Am. 38, 766 (1948)] with differentmore » spectral wavelength ranges and with a 400 mm source-to-mirror distance image the target on a custom-built framing camera (time resolution of {approx}80 ps). The soft x-ray version microscope is sensitive below 1 keV and its spatial resolution is better than 30 {mu}m over a 2-mm-diam region. The hard x-ray version microscope has a 10 {mu}m resolution over an 800-{mu}m-diam region and is sensitive in the 1-5 keV energy range. Two other x-ray microscopes based on an association of toroidal/spherical surfaces (T/S microscopes) produce an image on a streak camera with a spatial resolution better than 30 {mu}m over a 3 mm field of view in the direction of the camera slit. Both microscopes have been designed to have, respectively, a maximum sensitivity in the 0.1-1 and 1-5 keV energy range. We present the original design of these four microscopes and their test on a dc x-ray tube in the laboratory. The diagnostics were successfully used on LIL first experiments early in 2005. Results of soft x-ray imaging of a radiative jet during conical shaped laser interaction are shown.« less

On-axis programmable microscope using liquid crystal spatial light modulator

NASA Astrophysics Data System (ADS)

García-Martínez, Pascuala; Martínez, José Luís.; Moreno, Ignacio

2017-06-01

Spatial light modulators (SLM) are currently used in many applications in optical microscopy and imaging. One of the most promising methods is the use of liquid crystal displays (LCD) as programmable phase diffractive optical elements (DOE) placed in the Fourier plane giving access to the spatial frequencies which can be phased shifted individually, allowing to emulate a wealth of contrast enhancing methods for both amplitude and phase samples. We use phase and polarization modulation of LCD to implement an on-axis microscope optical system. The LCD used are Hamamatsu liquid crystal on silicon (LCOS) SLM free of flicker, thus showing a full profit of the SLM space bandwidth, as opposed to optical systems in the literature forced to work off-axis due to the strong zero-order component. Taking benefits of the phase modulation of the LCOS we have implemented different microscopic imaging operations, such as high-pass and low-pass filtering in parallel using programmable blazed gratings. Moreover, we are able to control polarization modulation to display two orthogonal linear state of polarization images than can be subtracted or added by changing the period of the blazed grating. In that sense, Differential Interference Contrast (DIC) microscopy can be easily done by generating two images exploiting the polarization splitting properties when a blazed grating is displayed in the SLM. Biological microscopy samples are also used.

Resolution and throughput optimized intraoperative spectrally encoded coherence tomography and reflectometry (iSECTR) for multimodal imaging during ophthalmic microsurgery

NASA Astrophysics Data System (ADS)

Malone, Joseph D.; El-Haddad, Mohamed T.; Leeburg, Kelsey C.; Terrones, Benjamin D.; Tao, Yuankai K.

2018-02-01

Limited visualization of semi-transparent structures in the eye remains a critical barrier to improving clinical outcomes and developing novel surgical techniques. While increases in imaging speed has enabled intraoperative optical coherence tomography (iOCT) imaging of surgical dynamics, several critical barriers to clinical adoption remain. Specifically, these include (1) static field-of-views (FOVs) requiring manual instrument-tracking; (2) high frame-rates require sparse sampling, which limits FOV; and (3) small iOCT FOV also limits the ability to co-register data with surgical microscopy. We previously addressed these limitations in image-guided ophthalmic microsurgery by developing microscope-integrated multimodal intraoperative swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography. Complementary en face images enabled orientation and coregistration with the widefield surgical microscope view while OCT imaging enabled depth-resolved visualization of surgical instrument positions relative to anatomic structures-of-interest. In addition, we demonstrated novel integrated segmentation overlays for augmented-reality surgical guidance. Unfortunately, our previous system lacked the resolution and optical throughput for in vivo retinal imaging and necessitated removal of cornea and lens. These limitations were predominately a result of optical aberrations from imaging through a shared surgical microscope objective lens, which was modeled as a paraxial surface. Here, we present an optimized intraoperative spectrally encoded coherence tomography and reflectometry (iSECTR) system. We use a novel lens characterization method to develop an accurate model of surgical microscope objective performance and balance out inherent aberrations using iSECTR relay optics. Using this system, we demonstrate in vivo multimodal ophthalmic imaging through a surgical microscope

Destructive Single-Event Effects in Diodes

NASA Technical Reports Server (NTRS)

Casey, Megan C.; Lauenstein, Jean-Marie; Campola, Michael J.; Wilcox, Edward P.; Phan, Anthony M.; Label, Kenneth A.

2017-01-01

In this work, we discuss the observed single-event effects in a variety of types of diodes. In addition, we conduct failure analysis on several Schottky diodes that were heavy-ion irradiated. High- and low-magnitude optical microscope images, infrared camera images, and scanning electron microscope images are used to identify and describe the failure locations.

Fostering Student Engagement with Digital Microscopic Images Using ThingLink, an Image Annotation Program

ERIC Educational Resources Information Center

Appasamy, Pierette

2018-01-01

The teaching of histology has changed dramatically with virtual microscopy. Fewer students of histology spend significant time viewing slides on a microscope and instead study images available in digital slide sets, generally accessible via the internet. However, students must still be able to correctly identify the defining characteristics of…

Capturing and displaying microscopic images used in medical diagnostics and forensic science using 4K video resolution - an application in higher education.

PubMed

Maier, Hans; de Heer, Gert; Ortac, Ajda; Kuijten, Jan

2015-11-01

To analyze, interpret and evaluate microscopic images, used in medical diagnostics and forensic science, video images for educational purposes were made with a very high resolution of 4096 × 2160 pixels (4K), which is four times as many pixels as High-Definition Video (1920 × 1080 pixels). The unprecedented high resolution makes it possible to see details that remain invisible to any other video format. The images of the specimens (blood cells, tissue sections, hair, fibre, etc.) are recorded using a 4K video camera which is attached to a light microscope. After processing, this resulted in very sharp and highly detailed images. This material was then used in education for classroom discussion. Spoken explanation by experts in the field of medical diagnostics and forensic science was also added to the high-resolution video images to make it suitable for self-study. © 2015 The Authors. Journal of Microscopy published by John Wiley & Sons Ltd on behalf of Royal Microscopical Society.

FluoroSim: A Visual Problem-Solving Environment for Fluorescence Microscopy

PubMed Central

Quammen, Cory W.; Richardson, Alvin C.; Haase, Julian; Harrison, Benjamin D.; Taylor, Russell M.; Bloom, Kerry S.

2010-01-01

Fluorescence microscopy provides a powerful method for localization of structures in biological specimens. However, aspects of the image formation process such as noise and blur from the microscope's point-spread function combine to produce an unintuitive image transformation on the true structure of the fluorescing molecules in the specimen, hindering qualitative and quantitative analysis of even simple structures in unprocessed images. We introduce FluoroSim, an interactive fluorescence microscope simulator that can be used to train scientists who use fluorescence microscopy to understand the artifacts that arise from the image formation process, to determine the appropriateness of fluorescence microscopy as an imaging modality in an experiment, and to test and refine hypotheses of model specimens by comparing the output of the simulator to experimental data. FluoroSim renders synthetic fluorescence images from arbitrary geometric models represented as triangle meshes. We describe three rendering algorithms on graphics processing units for computing the convolution of the specimen model with a microscope's point-spread function and report on their performance. We also discuss several cases where the microscope simulator has been used to solve real problems in biology. PMID:20431698

Direct microscopic image and measurement of the atomization process of a port fuel injector

NASA Astrophysics Data System (ADS)

Esmail, Mohamed; Kawahara, Nobuyuki; Tomita, Eiji; Sumida, Mamoru

2010-07-01

The main objective of this study is to observe and investigate the phenomena of atomization, i.e. the fuel break-up process very close to the nozzle exit of a practical port fuel injector (PFI). In order to achieve this objective, direct microscopic images of the atomization process were obtained using an ultra-high-speed video camera that could record 102 frames at rates of up to 1 Mfps, coupled with a long-distance microscope and Barlow lens. The experiments were carried out using a PFI in a closed chamber at atmospheric pressure. Time-series images of the spray behaviour were obtained with a high temporal resolution using backlighting. The direct microscopic images of a liquid column break-up were compared with experimental results from laser-induced exciplex fluorescence (LIEF), and the wavelength obtained from the experimental results compared with that predicated from the Kelvin-Helmholtz break-up model. The droplet size diameters from a ligament break-up were compared with results predicated from Weber's analysis. Furthermore, experimental results of the mean droplet diameter from a direct microscopic image were compared with the results obtained from phase Doppler anemometry (PDA) experimental results. Three conclusions were obtained from this study. The atomization processes and detailed characterizations of the break-up of a liquid column were identified; the direct microscopic image results were in good agreement with the results obtained from LIEF, experimental results of the wavelength were in good agreement with those from the Kelvin-Helmholtz break-up model. The break-up process of liquid ligaments into droplets was investigated, and Weber's analysis of the predicated droplet diameter from ligament break-up was found to be applicable only at larger wavelengths. Finally, the direct microscopic image method and PDA method give qualitatively similar trends for droplet size distribution and quantitatively similar values of Sauter mean diameter.

Large scale infrared imaging of tissue micro arrays (TMAs) using a tunable Quantum Cascade Laser (QCL) based microscope.

PubMed

Bassan, Paul; Weida, Miles J; Rowlette, Jeremy; Gardner, Peter

2014-08-21

Chemical imaging in the field of vibrational spectroscopy is developing into a promising tool to complement digital histopathology. Applications include screening of biopsy tissue via automated recognition of tissue/cell type and disease state based on the chemical information from the spectrum. For integration into clinical practice, data acquisition needs to be speeded up to implement a rack based system where specimens are rapidly imaged to compete with current visible scanners where 100's of slides can be scanned overnight. Current Fourier transform infrared (FTIR) imaging with focal plane array (FPA) detectors are currently the state-of-the-art instrumentation for infrared absorption chemical imaging, however recent development in broadly tunable lasers in the mid-IR range is considered the most promising potential candidate for next generation microscopes. In this paper we test a prototype quantum cascade laser (QCL) based spectral imaging microscope with a focus on discrete frequency chemical imaging. We demonstrate how a protein chemical image of the amide I band (1655 cm(-1)) of a 2 × 2.4 cm(2) breast tissue microarray (TMA) containing over 200 cores can be measured in 9 min. This result indicates that applications requiring chemical images from a few key wavelengths would be ideally served by laser-based microscopes.

Improvements in low-cost label-free QPI microscope for live cell imaging

NASA Astrophysics Data System (ADS)

Seniya, C.; Towers, C. E.; Towers, D. P.

2017-07-01

This paper reports an improvement in the development of a low-cost QPI microscope offering new capabilities in term of phase measurement accuracy for label-free live samples in the longer term (i.e., hours to days). The spatially separated scattered and non-scattered image light fields are reshaped in the Fourier plane and modulated to form an interference image at a CCD camera. The apertures that enable these two beams to be generated have been optimised by means of laser-cut apertures placed on the mirrors of a Michelson interferometer and has improved the phase measuring and reconstruction capability of the QPI microscope. The microscope was tested with transparent onion cells as an object of interest.

Construction and characterization of the fringe field monochromator for a field emission gun

PubMed

Mook; Kruit

2000-04-01

Although some microscopes have shown stabilities sufficient to attain below 0.1 eV spectral resolution in high-resolution electron energy loss spectroscopy, the intrinsic energy width of the high brightness source (0.3-0.6 eV) has been limiting the resolution. To lower the energy width of the source to 50 meV without unnecessary loss of brightness, a monochromator has been designed consisting of a short (4 mm) fringe field Wien filter and a 150 nm energy selection slit (nanoslit) both to be incorporated in the gun area of the microscope. A prototype has been built and tested in an ultra-high-vacuum setup (10(-9) mbar). The monochromator, operating on a Schottky field emission gun, showed stable and reproducible operation. The nanoslits did not contaminate and the structure remained stable. By measuring the current through the slit structure a direct image of the beam in the monochromator could be attained and the monochromator could be aligned without the use of a microscope. Good dispersed imaging conditions were found indicating an ultimate resolution of 55 meV. A Mark II fringe field monochromator (FFM) was designed and constructed compatible with the cold tungsten field emitter of the VG scanning transmission microscope. The monochromator was incorporated in the gun area of the microscope at IBM T.J. Watson research center, New York. The monochromator was aligned on 100 kV and the energy distribution measured using the monochromator displayed a below 50 meV filtering capability. The retarding Wien filter spectrometer was used to show a 61 meV EELS system resolution. The FFM is shown to be a monochromator which can be aligned without the use of the electron microscope. This makes it directly applicable for scanning transmission microscopy and low-voltage scanning electron microscopy, where it can lower the resolution loss which is caused by chromatic blur of the spot.

Design and calibration of a vacuum compatible scanning tunneling microscope

NASA Technical Reports Server (NTRS)

Abel, Phillip B.

1990-01-01

A vacuum compatible scanning tunneling microscope was designed and built, capable of imaging solid surfaces with atomic resolution. The single piezoelectric tube design is compact, and makes use of sample mounting stubs standard to a commercially available surface analysis system. Image collection and display is computer controlled, allowing storage of images for further analysis. Calibration results from atomic scale images are presented.

Unsupervised segmentation of low-contrast multichannel images: discrimination of tissue components in microscopic images of unstained specimens

NASA Astrophysics Data System (ADS)

Kopriva, Ivica; Popović Hadžija, Marijana; Hadžija, Mirko; Aralica, Gorana

2015-06-01

Low-contrast images, such as color microscopic images of unstained histological specimens, are composed of objects with highly correlated spectral profiles. Such images are very hard to segment. Here, we present a method that nonlinearly maps low-contrast color image into an image with an increased number of non-physical channels and a decreased correlation between spectral profiles. The method is a proof-of-concept validated on the unsupervised segmentation of color images of unstained specimens, in which case the tissue components appear colorless when viewed under the light microscope. Specimens of human hepatocellular carcinoma, human liver with metastasis from colon and gastric cancer and mouse fatty liver were used for validation. The average correlation between the spectral profiles of the tissue components was greater than 0.9985, and the worst case correlation was greater than 0.9997. The proposed method can potentially be applied to the segmentation of low-contrast multichannel images with high spatial resolution that arise in other imaging modalities.

Design of an imaging microscope for soft X-ray applications

NASA Astrophysics Data System (ADS)

Hoover, Richard B.; Shealy, David L.; Gabardi, David R.; Walker, Arthur B. C., Jr.; Lindblom, Joakim F.

1988-01-01

An imaging soft X-ray microscope with a spatial resolution of 0.1 micron and normal incidence multilayer optics is discussed. The microscope has a Schwarzschild configuration, which consists of two concentric spherical mirrors with radii of curvature which minimize third-order spherical aberration, coma, and astigmatism. The performance of the Stanford/MSFC Cassegrain X-ray telescope and its relevance to the present microscope are addressed. A ray tracing analysis of the optical system indicates that diffraction-limited performance can be expected for an object height of 0.2 mm.

A versatile atomic force microscope integrated with a scanning electron microscope.

PubMed

Kreith, J; Strunz, T; Fantner, E J; Fantner, G E; Cordill, M J

2017-05-01

A versatile atomic force microscope (AFM), which can be installed in a scanning electron microscope (SEM), is introduced. The flexible design of the instrument enables correlated analysis for different experimental configurations, such as AFM imaging directly after nanoindentation in vacuum. In order to demonstrate the capabilities of the specially designed AFM installed inside a SEM, slip steps emanating around nanoindents in single crystalline brass were examined. This example showcases how the combination of AFM and SEM imaging can be utilized for quantitative dislocation analysis through the measurement of the slip step heights without the hindrance of oxide formation. Finally, an in situ nanoindentation technique is introduced, illustrating the use of AFM imaging during indentation experiments to examine plastic deformation occurring under the indenter tip. The mechanical indentation data are correlated to the SEM and AFM images to estimate the number of dislocations emitted to the surface.

Note: Tandem Kirkpatrick-Baez microscope with sixteen channels for high-resolution laser-plasma diagnostics

NASA Astrophysics Data System (ADS)

Yi, Shengzhen; Zhang, Zhe; Huang, Qiushi; Zhang, Zhong; Wang, Zhanshan; Wei, Lai; Liu, Dongxiao; Cao, Leifeng; Gu, Yuqiu

2018-03-01

Multi-channel Kirkpatrick-Baez (KB) microscopes, which have better resolution and collection efficiency than pinhole cameras, have been widely used in laser inertial confinement fusion to diagnose time evolution of the target implosion. In this study, a tandem multi-channel KB microscope was developed to have sixteen imaging channels with the precise control of spatial resolution and image intervals. This precise control was created using a coarse assembly of mirror pairs with high-accuracy optical prisms, followed by precise adjustment in real-time x-ray imaging experiments. The multilayers coated on the KB mirrors were designed to have substantially the same reflectivity to obtain a uniform brightness of different images for laser-plasma temperature analysis. The study provides a practicable method to achieve the optimum performance of the microscope for future high-resolution applications in inertial confinement fusion experiments.

A multiphoton laser scanning microscope setup for transcranial in vivo brain imaging on mice

NASA Astrophysics Data System (ADS)

Nase, Gabriele; Helm, P. Johannes; Reppen, Trond; Ottersen, Ole Petter

2005-12-01

We describe a multiphoton laser scanning microscope setup for transcranial in vivo brain imaging in mice. The modular system is based on a modified industrial standard Confocal Scanning Laser Microscope (CSLM) and is assembled mainly from commercially available components. A special multifunctional stage, which is optimized for both laser scanning microscopic observation and preparative animal surgery, has been developed and built. The detection unit includes a highly efficient photomultiplier tube installed in a Peltier-cooled thermal box shielding the detector from changes in room temperature and from distortions caused by external electromagnetic fields. The images are recorded using a 12-bit analog-to-digital converter. Depending on the characteristics of the staining, individual nerve cells can be imaged down to at least 100μm below the intact cranium and down to at least 200μm below the opened cranium.

Setting Up a Simple Light Sheet Microscope for In Toto Imaging of C. elegans Development

PubMed Central

Bertrand, Vincent; Lenne, Pierre-François

2014-01-01

Fast and low phototoxic imaging techniques are pre-requisite to study the development of organisms in toto. Light sheet based microscopy reduces photo-bleaching and phototoxic effects compared to confocal microscopy, while providing 3D images with subcellular resolution. Here we present the setup of a light sheet based microscope, which is composed of an upright microscope and a small set of opto-mechanical elements for the generation of the light sheet. The protocol describes how to build, align the microscope and characterize the light sheet. In addition, it details how to implement the method for in toto imaging of C. elegans embryos using a simple observation chamber. The method allows the capture of 3D two-colors time-lapse movies over few hours of development. This should ease the tracking of cell shape, cell divisions and tagged proteins over long periods of time. PMID:24836407

21 CFR 864.3600 - Microscopes and accessories.

Code of Federal Regulations, 2010 CFR

2010-04-01

... enlarge images of specimens, preparations, and cultures for medical purposes. Variations of microscopes... light. (3) Inverted stage microscopes, which permit examination of tissue cultures or other biological...

Magnetic microscopic imaging with an optically pumped magnetometer and flux guides

DOE PAGES

Kim, Young Jin; Savukov, Igor Mykhaylovich; Huang, Jen -Huang; ...

2017-01-23

Here, by combining an optically pumped magnetometer (OPM) with flux guides (FGs) and by installing a sample platform on automated translation stages, we have implemented an ultra-sensitive FG-OPM scanning magnetic imaging system that is capable of detecting magnetic fields of ~20 pT with spatial resolution better than 300 μm (expected to reach ~10 pT sensitivity and ~100 μm spatial resolution with optimized FGs). As a demonstration of one possible application of the FG-OPM device, we conducted magnetic imaging of micron-size magnetic particles. Magnetic imaging of such particles, including nano-particles and clusters, is very important for many fields, especially for medicalmore » cancer diagnostics and biophysics applications. For rapid, precise magnetic imaging, we constructed an automatic scanning system, which holds and moves a target sample containing magnetic particles at a given stand-off distance from the FG tips. We show that the device was able to produce clear microscopic magnetic images of 10 μm-size magnetic particles. In addition, we also numerically investigated how the magnetic flux from a target sample at a given stand-off distance is transmitted to the OPM vapor cell.« less

Multimodal ophthalmic imaging using spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography

NASA Astrophysics Data System (ADS)

El-Haddad, Mohamed T.; Malone, Joseph D.; Li, Jianwei D.; Bozic, Ivan; Arquitola, Amber M.; Joos, Karen M.; Patel, Shriji N.; Tao, Yuankai K.

2017-08-01

Ophthalmic surgery involves manipulation of delicate, layered tissue structures on milli- to micrometer scales. Traditional surgical microscopes provide an inherently two-dimensional view of the surgical field with limited depth perception which precludes accurate depth-resolved visualization of these tissue layers, and limits the development of novel surgical techniques. We demonstrate multimodal swept-source spectrally encoded scanning laser ophthalmoscopy and optical coherence tomography (SS-SESLO-OCT) to address current limitations of image-guided ophthalmic microsurgery. SS-SESLO-OCT provides inherently co-registered en face and cross-sectional field-of-views (FOVs) at a line rate of 400 kHz and >2 GPix/s throughput. We show in vivo imaging of the anterior segment and retinal fundus of a healthy volunteer, and preliminary results of multi-volumetric mosaicking for ultrawide-field retinal imaging with 90° FOV. Additionally, a scan-head was rapid-prototyped with a modular architecture which enabled integration of SS-SESLO-OCT with traditional surgical microscope and slit-lamp imaging optics. Ex vivo surgical maneuvers were simulated in cadaveric porcine eyes. The system throughput enabled volumetric acquisition at 10 volumes-per-second (vps) and allowed visualization of surgical dynamics in corneal sweeps, compressions, and dissections, and retinal sweeps, compressions, and elevations. SESLO en face images enabled simple real-time co-registration with the surgical microscope FOV, and OCT cross-sections provided depth-resolved visualization of instrument-tissue interactions. Finally, we demonstrate novel augmented-reality integration with the surgical view using segmentation overlays to aid surgical guidance. SS-SESLO-OCT may benefit clinical diagnostics by enabling aiming, registration, and mosaicking; and intraoperative imaging by allowing for real-time surgical feedback, instrument tracking, and overlays of computationally extracted biomarkers of disease.

Advantages of intermediate X-ray energies in Zernike phase contrast X-ray microscopy.

PubMed

Wang, Zhili; Gao, Kun; Chen, Jian; Hong, Youli; Ge, Xin; Wang, Dajiang; Pan, Zhiyun; Zhu, Peiping; Yun, Wenbing; Jacobsen, Chris; Wu, Ziyu

2013-01-01

Understanding the hierarchical organizations of molecules and organelles within the interior of large eukaryotic cells is a challenge of fundamental interest in cell biology. Light microscopy is a powerful tool for observations of the dynamics of live cells, its resolution attainable is limited and insufficient. While electron microscopy can produce images with astonishing resolution and clarity of ultra-thin (<1 μm thick) sections of biological specimens, many questions involve the three-dimensional organization of a cell or the interconnectivity of cells. X-ray microscopy offers superior imaging resolution compared to light microscopy, and unique capability of nondestructive three-dimensional imaging of hydrated unstained biological cells, complementary to existing light and electron microscopy. Until now, X-ray microscopes operating in the "water window" energy range between carbon and oxygen k-shell absorption edges have produced outstanding 3D images of cryo-preserved cells. The relatively low X-ray energy (<540 eV) of the water window imposes two important limitations: limited penetration (<10 μm) not suitable for imaging larger cells or tissues, and small depth of focus (DoF) for high resolution 3D imaging (e.g., ~1 μm DoF for 20 nm resolution). An X-ray microscope operating at intermediate energy around 2.5 keV using Zernike phase contrast can overcome the above limitations and reduces radiation dose to the specimen. Using a hydrated model cell with an average chemical composition reported in literature, we calculated the image contrast and the radiation dose for absorption and Zernike phase contrast, respectively. The results show that an X-ray microscope operating at ~2.5 keV using Zernike phase contrast offers substantial advantages in terms of specimen size, radiation dose and depth-of-focus. Copyright © 2012 Elsevier Inc. All rights reserved.

Ghost microscope imaging system from the perspective of coherent-mode representation

NASA Astrophysics Data System (ADS)

Shen, Qian; Bai, Yanfeng; Shi, Xiaohui; Nan, Suqin; Qu, Lijie; Li, Hengxing; Fu, Xiquan

2018-03-01

The coherent-mode representation theory of partially coherent fields is firstly used to analyze a two-arm ghost microscope imaging system. It is shown that imaging quality of the generated images depend crucially on the distribution of the decomposition coefficients of the object imaged when the light source is fixed. This theory is also suitable for demonstrating the effects from the distance the object is moved away from the original plane on imaging quality. Our results are verified theoretically and experimentally.

Monitoring synaptic and neuronal activity in 3D with synthetic and genetic indicators using a compact acousto-optic lens two-photon microscope☆

PubMed Central

Fernández-Alfonso, Tomás; Nadella, K.M. Naga Srinivas; Iacaruso, M. Florencia; Pichler, Bruno; Roš, Hana; Kirkby, Paul A.; Silver, R. Angus

2014-01-01

Background Two-photon microscopy is widely used to study brain function, but conventional microscopes are too slow to capture the timing of neuronal signalling and imaging is restricted to one plane. Recent development of acousto-optic-deflector-based random access functional imaging has improved the temporal resolution, but the utility of these technologies for mapping 3D synaptic activity patterns and their performance at the excitation wavelengths required to image genetically encoded indicators have not been investigated. New method Here, we have used a compact acousto-optic lens (AOL) two-photon microscope to make high speed [Ca2+] measurements from spines and dendrites distributed in 3D with different excitation wavelengths (800–920 nm). Results We show simultaneous monitoring of activity from many synaptic inputs distributed over the 3D arborisation of a neuronal dendrite using both synthetic as well as genetically encoded indicators. We confirm the utility of AOL-based imaging for fast in vivo recordings by measuring, simultaneously, visually evoked responses in 100 neurons distributed over a 150 μm focal depth range. Moreover, we explore ways to improve the measurement of timing of neuronal activation by choosing specific regions within the cell soma. Comparison with existing methods These results establish that AOL-based 3D random access two-photon microscopy has a wider range of neuroscience applications than previously shown. Conclusions Our findings show that the compact AOL microscope design has the speed, spatial resolution, sensitivity and wavelength flexibility to measure 3D patterns of synaptic and neuronal activity on individual trials. PMID:24200507

Adaptive optical imaging through complex living plant cells

NASA Astrophysics Data System (ADS)

Tamada, Yosuke; Hayano, Yutaka; Murata, Takashi; Oya, Shin; Honma, Yusuke; Kanazawa, Minoru; Miura, Noriaki; Hasebe, Mitsuyasu; Kamei, Yasuhiro; Hattori, Masayuki

2017-04-01

Live-cell imaging using fluorescent molecules is now essential for biological researches. However, images of living cells are accompanied with blur, which becomes stronger according to the depth inside the cells and tissues. This image blur is caused by the disturbance on light that goes through optically inhomogeneous living cells and tissues. Here, we show adaptive optics (AO) imaging of living plant cells. AO has been developed in astronomy to correct the disturbance on light caused by atmospheric turbulence. We developed AO microscope effective for the observation of living plant cells with strong disturbance by chloroplasts, and successfully obtained clear images inside plant cells.

Variations in contrast of scanning electron microscope images for microstructure analysis of Si-based semiconductor materials.

PubMed

Itakura, Masaru; Kuwano, Noriyuki; Sato, Kaoru; Tachibana, Shigeaki

2010-08-01

Image contrasts of Si-based semiconducting materials have been investigated by using the latest scanning electron microscope with various detectors under a range of experimental conditions. Under a very low accelerating voltage (500 V), we obtained a good image contrast between crystalline SiGe whiskers and the amorphous matrix using an in-lens secondary electron (SE) detector, while the conventional topographic SE image and the compositional backscattered electron (BSE) image gave no distinct contrast. By using an angular-selective BSE (AsB) detector for wide-angle scattered BSE, on the other hand, the crystal grains in amorphous matrix can be clearly visualized as 'channelling contrast'. The image contrast is very similar to that of their transmission electron microscope image. The in-lens SE (true SE falling dots SE1) and the AsB (channelling) contrasts are quite useful to distinguish crystalline parts from amorphous ones.

A universal fluid cell for the imaging of biological specimens in the atomic force microscope.

PubMed

Kasas, Sandor; Radotic, Ksenja; Longo, Giovanni; Saha, Bashkar; Alonso-Sarduy, Livan; Dietler, Giovanni; Roduit, Charles

2013-04-01

Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set-up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Copyright © 2013 Wiley Periodicals, Inc.

In situ dissolution analysis of pharmaceutical dosage forms using coherent anti-Stokes Raman scattering (CARS) microscopy

NASA Astrophysics Data System (ADS)

Fussell, A. L.; Garbacik, E. T.; Löbmann, K.; Offerhaus, H. L.; Kleinebudde, P.; Strachan, C. J.

2014-02-01

A custom-built intrinsic flow-through dissolution setup was developed and incorporated into a home-built CARS microscope consisting of a synchronously pumped optical parametric oscillator (OPO) and an inverted microscope with a 20X/0.5NA objective. CARS dissolution images (512×512 pixels) were collected every 1.12s for the duration of the dissolution experiment. Hyperspectral CARS images were obtained pre- and postdissolution by rapidly imaging while sweeping the wavelength of the OPO in discrete steps so that each frame in the data stack corresponds to a vibrational frequency. An image-processing routine projects this hyperspectral data into a single image wherein each compound appears with a unique color. Dissolution was conducted using theophylline and cimetidine-naproxen co-amorphous mixture. After 15 minutes of theophylline dissolution, hyperspectral imaging showed a conversion of theophylline anhydrate to the monohydrate, confirmed by a peak shift in the CARS spectra. CARS dissolution images showed that monohydrate crystal growth began immediately and reached a maximum with complete surface coverage at about 300s. This result correlated with the UV dissolution data where surface crystal growth on theophylline compacts resulted in a rapidly reducing dissolution rate during the first 300s. Co-amorphous cimetidinenaproxen didn't appear to crystallize during dissolution. We observed solid-state conversions on the compact's surface in situ during dissolution. Hyperspectral CARS imaging allowed visual discrimination between the solid-state forms on the compact's surface. In the case of theophylline we were able to correlate the solid-state change with a change in dissolution rate.

Differential dynamic microscopy to characterize Brownian motion and bacteria motility

NASA Astrophysics Data System (ADS)

Germain, David; Leocmach, Mathieu; Gibaud, Thomas

2016-03-01

We have developed a lab module for undergraduate students, which involves the process of quantifying the dynamics of a suspension of microscopic particles using Differential Dynamic Microscopy (DDM). DDM is a relatively new technique that constitutes an alternative method to more classical techniques such as dynamic light scattering (DLS) or video particle tracking (VPT). The technique consists of imaging a particle dispersion with a standard light microscope and a camera and analyzing the images using a digital Fourier transform to obtain the intermediate scattering function, an autocorrelation function that characterizes the dynamics of the dispersion. We first illustrate DDM in the textbook case of colloids under Brownian motion, where we measure the diffusion coefficient. Then we show that DDM is a pertinent tool to characterize biological systems such as motile bacteria.

High-resolution electron microscope

NASA Technical Reports Server (NTRS)

Nathan, R.

1977-01-01

Employing scanning transmission electron microscope as interferometer, relative phases of diffraction maximums can be determined by analysis of dark field images. Synthetic aperture technique and Fourier-transform computer processing of amplitude and phase information provide high resolution images at approximately one angstrom.

A laboratory 8 keV transmission full-field x-ray microscope with a polycapillary as condenser for bright and dark field imaging

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

Baumbach, S., E-mail: baumbach@rheinahrcampus.de; Wilhein, T.; Kanngießer, B.

2015-08-15

This article introduces a laboratory setup of a transmission full-field x-ray microscope at 8 keV photon energy. The microscope operates in bright and dark field imaging mode with a maximum field of view of 50 μm. Since the illumination geometry determines whether the sample is illuminated homogeneously and moreover, if different imaging methods can be applied, the condenser optic is one of the most significant parts. With a new type of x-ray condenser, a polycapillary optic, we realized bright field imaging and for the first time dark field imaging at 8 keV photon energy in a laboratory setup. A detectormore » limited spatial resolution of 210 nm is measured on x-ray images of Siemens star test patterns.« less

Fabrication and characterization of novel microsphere-embedded optical devices for enhancing microscopy resolution

NASA Astrophysics Data System (ADS)

Darafsheh, Arash

2018-02-01

Microsphere-assisted imaging can be incorporated onto conventional light microscopes allowing wide-field and flourescence imaging with enhanced resolution. We demonstrated that imaging of specimens containing subdiffraction-limited features is achievable through high-index microspheres embedded in a transparent thin film placed over the specimen. We fabricated novel microsphere-embedded microscope slides composed of barium titanate glass microspheres (with diameter 10-100 μm and refractive index 1.9-2.2) embedded in a transparent polydimethylsiloxane (PDMS) elastomer layer with controllable thickness. We characterized the imaging performance of such microsphere-embedded devices in white-light microscopies, by measuring the imaging resolution, field-of-view, and magnification as a function of microsphere size. Our results inform on the design of novel optical devices, such as microsphere-embedded microscope slides for imaging applications.

A laboratory 8 keV transmission full-field x-ray microscope with a polycapillary as condenser for bright and dark field imaging.

PubMed

Baumbach, S; Kanngießer, B; Malzer, W; Stiel, H; Wilhein, T

2015-08-01

This article introduces a laboratory setup of a transmission full-field x-ray microscope at 8 keV photon energy. The microscope operates in bright and dark field imaging mode with a maximum field of view of 50 μm. Since the illumination geometry determines whether the sample is illuminated homogeneously and moreover, if different imaging methods can be applied, the condenser optic is one of the most significant parts. With a new type of x-ray condenser, a polycapillary optic, we realized bright field imaging and for the first time dark field imaging at 8 keV photon energy in a laboratory setup. A detector limited spatial resolution of 210 nm is measured on x-ray images of Siemens star test patterns.

Dynamic Assessment of the Endothelialization of Tissue-Engineered Blood Vessels Using an Optical Coherence Tomography Catheter-Based Fluorescence Imaging System.

PubMed

Gurjarpadhye, Abhijit Achyut; DeWitt, Matthew R; Xu, Yong; Wang, Ge; Rylander, Marissa Nichole; Rylander, Christopher G

2015-07-01

Lumen endothelialization of bioengineered vascular scaffolds is essential to maintain small-diameter graft patency and prevent thrombosis postimplantation. Unfortunately, nondestructive imaging methods to visualize this dynamic process are lacking, thus slowing development and clinical translation of these potential tissue-engineering approaches. To meet this need, a fluorescence imaging system utilizing a commercial optical coherence tomography (OCT) catheter was designed to visualize graft endothelialization. C7 DragonFly™ intravascular OCT catheter was used as a channel for delivery and collection of excitation and emission spectra. Poly-dl-lactide (PDLLA) electrospun scaffolds were seeded with endothelial cells (ECs). Seeded cells were exposed to Calcein AM before imaging, causing the living cells to emit green fluorescence in response to blue laser. By positioning the catheter tip precisely over a specimen using high-fidelity electromechanical components, small regions of the specimen were excited selectively. The resulting fluorescence intensities were mapped on a two-dimensional digital grid to generate spatial distribution of fluorophores at single-cell-level resolution. Fluorescence imaging of endothelialization on glass and PDLLA scaffolds was performed using the OCT catheter-based imaging system as well as with a commercial fluorescence microscope. Cell coverage area was calculated for both image sets for quantitative comparison of imaging techniques. Tubular PDLLA scaffolds were maintained in a bioreactor on seeding with ECs, and endothelialization was monitored over 5 days using the OCT catheter-based imaging system. No significant difference was observed in images obtained using our imaging system to those acquired with the fluorescence microscope. Cell area coverage calculated using the images yielded similar values. Nondestructive imaging of endothelialization on tubular scaffolds showed cell proliferation with cell coverage area increasing from 15 ± 4% to 89 ± 6% over 5 days. In this study, we showed the capability of an OCT catheter-based imaging system to obtain single-cell resolution and to quantify endothelialization in tubular electrospun scaffolds. We also compared the resulting images with traditional microscopy, showing high fidelity in image capability. This imaging system, used in conjunction with OCT, could potentially be a powerful tool for in vitro optimization of scaffold cellularization, ensuring long-term graft patency postimplantation.

Closeup View of Compacted Soil

NASA Technical Reports Server (NTRS)

2004-01-01

Soil on Mars can be a bit clumpy, as shown in this image of soil after it was compacted by one of the wheels of NASA's Mars Exploration Rover Spirit. Scientists think the light-colored material may be a global layer of airfall dust. Spirit's microscopic imager took this picture, showing an area approximately 3 centimeters (1.2 inches) square, during the rover's 314th martian day, or sol (Nov. 19, 2004).

A Novel Hyperspectral Microscopic Imaging System for Evaluating Fresh Degree of Pork.

PubMed

Xu, Yi; Chen, Quansheng; Liu, Yan; Sun, Xin; Huang, Qiping; Ouyang, Qin; Zhao, Jiewen

2018-04-01

This study proposed a rapid microscopic examination method for pork freshness evaluation by using the self-assembled hyperspectral microscopic imaging (HMI) system with the help of feature extraction algorithm and pattern recognition methods. Pork samples were stored for different days ranging from 0 to 5 days and the freshness of samples was divided into three levels which were determined by total volatile basic nitrogen (TVB-N) content. Meanwhile, hyperspectral microscopic images of samples were acquired by HMI system and processed by the following steps for the further analysis. Firstly, characteristic hyperspectral microscopic images were extracted by using principal component analysis (PCA) and then texture features were selected based on the gray level co-occurrence matrix (GLCM). Next, features data were reduced dimensionality by fisher discriminant analysis (FDA) for further building classification model. Finally, compared with linear discriminant analysis (LDA) model and support vector machine (SVM) model, good back propagation artificial neural network (BP-ANN) model obtained the best freshness classification with a 100 % accuracy rating based on the extracted data. The results confirm that the fabricated HMI system combined with multivariate algorithms has ability to evaluate the fresh degree of pork accurately in the microscopic level, which plays an important role in animal food quality control.

A Novel Hyperspectral Microscopic Imaging System for Evaluating Fresh Degree of Pork

PubMed Central

Xu, Yi; Chen, Quansheng; Liu, Yan; Sun, Xin; Huang, Qiping; Ouyang, Qin; Zhao, Jiewen

2018-01-01

Abstract This study proposed a rapid microscopic examination method for pork freshness evaluation by using the self-assembled hyperspectral microscopic imaging (HMI) system with the help of feature extraction algorithm and pattern recognition methods. Pork samples were stored for different days ranging from 0 to 5 days and the freshness of samples was divided into three levels which were determined by total volatile basic nitrogen (TVB-N) content. Meanwhile, hyperspectral microscopic images of samples were acquired by HMI system and processed by the following steps for the further analysis. Firstly, characteristic hyperspectral microscopic images were extracted by using principal component analysis (PCA) and then texture features were selected based on the gray level co-occurrence matrix (GLCM). Next, features data were reduced dimensionality by fisher discriminant analysis (FDA) for further building classification model. Finally, compared with linear discriminant analysis (LDA) model and support vector machine (SVM) model, good back propagation artificial neural network (BP-ANN) model obtained the best freshness classification with a 100 % accuracy rating based on the extracted data. The results confirm that the fabricated HMI system combined with multivariate algorithms has ability to evaluate the fresh degree of pork accurately in the microscopic level, which plays an important role in animal food quality control. PMID:29805285

Model wavefront sensor for adaptive confocal microscopy

NASA Astrophysics Data System (ADS)

Booth, Martin J.; Neil, Mark A. A.; Wilson, Tony

2000-05-01

A confocal microscope permits 3D imaging of volume objects by the inclusion of a pinhole in the detector path which eliminates out of focus light. This configuration is however very sensitive to aberrations induced by the specimen or the optical system and would therefore benefit from an adaptive optics approach. We present a wavefront sensor capable of measuring directly the Zernike components of an aberrated wavefront and show that it is particularly applicable to the confocal microscope since only those wavefronts originating in the focal region contribute to the measured aberration.

VISUALIZATION FROM INTRAOPERATIVE SWEPT-SOURCE MICROSCOPE-INTEGRATED OPTICAL COHERENCE TOMOGRAPHY IN VITRECTOMY FOR COMPLICATIONS OF PROLIFERATIVE DIABETIC RETINOPATHY.

PubMed

Gabr, Hesham; Chen, Xi; Zevallos-Carrasco, Oscar M; Viehland, Christian; Dandrige, Alexandria; Sarin, Neeru; Mahmoud, Tamer H; Vajzovic, Lejla; Izatt, Joseph A; Toth, Cynthia A

2018-01-10

To evaluate the use of live volumetric (4D) intraoperative swept-source microscope-integrated optical coherence tomography in vitrectomy for proliferative diabetic retinopathy complications. In this prospective study, we analyzed a subgroup of patients with proliferative diabetic retinopathy complications who required vitrectomy and who were imaged by the research swept-source microscope-integrated optical coherence tomography system. In near real time, images were displayed in stereo heads-up display facilitating intraoperative surgeon feedback. Postoperative review included scoring image quality, identifying different diabetic retinopathy-associated pathologies and reviewing the intraoperatively documented surgeon feedback. Twenty eyes were included. Indications for vitrectomy were tractional retinal detachment (16 eyes), combined tractional-rhegmatogenous retinal detachment (2 eyes), and vitreous hemorrhage (2 eyes). Useful, good-quality 2D (B-scans) and 4D images were obtained in 16/20 eyes (80%). In these eyes, multiple diabetic retinopathy complications could be imaged. Swept-source microscope-integrated optical coherence tomography provided surgical guidance, e.g., in identifying dissection planes under fibrovascular membranes, and in determining residual membranes and traction that would benefit from additional peeling. In 4/20 eyes (20%), acceptable images were captured, but they were not useful due to high tractional retinal detachment elevation which was challenging for imaging. Swept-source microscope-integrated optical coherence tomography can provide important guidance during surgery for proliferative diabetic retinopathy complications through intraoperative identification of different complications and facilitation of intraoperative decision making.

Wide field video-rate two-photon imaging by using spinning disk beam scanner

NASA Astrophysics Data System (ADS)

Maeda, Yasuhiro; Kurokawa, Kazuo; Ito, Yoko; Wada, Satoshi; Nakano, Akihiko

2018-02-01

The microscope technology with wider view field, deeper penetration depth, higher spatial resolution and higher imaging speed are required to investigate the intercellular dynamics or interactions of molecules and organs in cells or a tissue in more detail. The two-photon microscope with a near infrared (NIR) femtosecond laser is one of the technique to improve the penetration depth and spatial resolution. However, the video-rate or high-speed imaging with wide view field is difficult to perform with the conventional two-photon microscope. Because point-to-point scanning method is used in conventional one, so it's difficult to achieve video-rate imaging. In this study, we developed a two-photon microscope with spinning disk beam scanner and femtosecond NIR fiber laser with around 10 W average power for the microscope system to achieve above requirements. The laser is consisted of an oscillator based on mode-locked Yb fiber laser, a two-stage pre-amplifier, a main amplifier based on a Yb-doped photonic crystal fiber (PCF), and a pulse compressor with a pair of gratings. The laser generates a beam with maximally 10 W average power, 300 fs pulse width and 72 MHz repetition rate. And the beam incident to a spinning beam scanner (Yokogawa Electric) optimized for two-photon imaging. By using this system, we achieved to obtain the 3D images with over 1mm-penetration depth and video-rate image with 350 x 350 um view field from the root of Arabidopsis thaliana.

In vivo imaging of middle-ear and inner-ear microstructures of a mouse guided by SD-OCT combined with a surgical microscope

PubMed Central

Cho, Nam Hyun; Jang, Jeong Hun; Jung, Woonggyu; Kim, Jeehyun

2014-01-01

We developed an augmented-reality system that combines optical coherence tomography (OCT) with a surgical microscope. By sharing the common optical path in the microscope and OCT, we could simultaneously acquire OCT and microscope views. The system was tested to identify the middle-ear and inner-ear microstructures of a mouse. Considering the probability of clinical application including otorhinolaryngology, diseases such as middle-ear effusion were visualized using in vivo mouse and OCT images simultaneously acquired through the eyepiece of the surgical microscope during surgical manipulation using the proposed system. This system is expected to realize a new practical area of OCT application. PMID:24787787

Statistical organelle dissection of Arabidopsis guard cells using image database LIPS.

PubMed

Higaki, Takumi; Kutsuna, Natsumaro; Hosokawa, Yoichiroh; Akita, Kae; Ebine, Kazuo; Ueda, Takashi; Kondo, Noriaki; Hasezawa, Seiichiro

2012-01-01

To comprehensively grasp cell biological events in plant stomatal movement, we have captured microscopic images of guard cells with various organelles markers. The 28,530 serial optical sections of 930 pairs of Arabidopsis guard cells have been released as a new image database, named Live Images of Plant Stomata (LIPS). We visualized the average organellar distributions in guard cells using probabilistic mapping and image clustering techniques. The results indicated that actin microfilaments and endoplasmic reticulum (ER) are mainly localized to the dorsal side and connection regions of guard cells. Subtractive images of open and closed stomata showed distribution changes in intracellular structures, including the ER, during stomatal movement. Time-lapse imaging showed that similar ER distribution changes occurred during stomatal opening induced by light irradiation or femtosecond laser shots on neighboring epidermal cells, indicating that our image analysis approach has identified a novel ER relocation in stomatal opening.

Dual-modal three-dimensional imaging of single cells with isometric high resolution using an optical projection tomography microscope

NASA Astrophysics Data System (ADS)

Miao, Qin; Rahn, J. Richard; Tourovskaia, Anna; Meyer, Michael G.; Neumann, Thomas; Nelson, Alan C.; Seibel, Eric J.

2009-11-01

The practice of clinical cytology relies on bright-field microscopy using absorption dyes like hematoxylin and eosin in the transmission mode, while the practice of research microscopy relies on fluorescence microscopy in the epi-illumination mode. The optical projection tomography microscope is an optical microscope that can generate 3-D images of single cells with isometric high resolution both in absorption and fluorescence mode. Although the depth of field of the microscope objective is in the submicron range, it can be extended by scanning the objective's focal plane. The extended depth of field image is similar to a projection in a conventional x-ray computed tomography. Cells suspended in optical gel flow through a custom-designed microcapillary. Multiple pseudoprojection images are taken by rotating the microcapillary. After these pseudoprojection images are further aligned, computed tomography methods are applied to create 3-D reconstruction. 3-D reconstructed images of single cells are shown in both absorption and fluorescence mode. Fluorescence spatial resolution is measured at 0.35 μm in both axial and lateral dimensions. Since fluorescence and absorption images are taken in two different rotations, mechanical error may cause misalignment of 3-D images. This mechanical error is estimated to be within the resolution of the system.

Photon event distribution sampling: an image formation technique for scanning microscopes that permits tracking of sub-diffraction particles with high spatial and temporal resolutions.

PubMed

Larkin, J D; Publicover, N G; Sutko, J L

2011-01-01

In photon event distribution sampling, an image formation technique for scanning microscopes, the maximum likelihood position of origin of each detected photon is acquired as a data set rather than binning photons in pixels. Subsequently, an intensity-related probability density function describing the uncertainty associated with the photon position measurement is applied to each position and individual photon intensity distributions are summed to form an image. Compared to pixel-based images, photon event distribution sampling images exhibit increased signal-to-noise and comparable spatial resolution. Photon event distribution sampling is superior to pixel-based image formation in recognizing the presence of structured (non-random) photon distributions at low photon counts and permits use of non-raster scanning patterns. A photon event distribution sampling based method for localizing single particles derived from a multi-variate normal distribution is more precise than statistical (Gaussian) fitting to pixel-based images. Using the multi-variate normal distribution method, non-raster scanning and a typical confocal microscope, localizations with 8 nm precision were achieved at 10 ms sampling rates with acquisition of ~200 photons per frame. Single nanometre precision was obtained with a greater number of photons per frame. In summary, photon event distribution sampling provides an efficient way to form images when low numbers of photons are involved and permits particle tracking with confocal point-scanning microscopes with nanometre precision deep within specimens. © 2010 The Authors Journal of Microscopy © 2010 The Royal Microscopical Society.

Snow crystal imaging using scanning electron microscopy: III. Glacier ice, snow and biota

USGS Publications Warehouse

Rango, A.; Wergin, W.P.; Erbe, E.F.; Josberger, E.G.

2000-01-01

Low-temperature scanning electron microscopy (SEM) was used to observe metamorphosed snow, glacial firn, and glacial ice obtained from South Cascade Glacier in Washington State, USA. Biotic samples consisting of algae (Chlamydomonas nivalis) and ice worms (a species of oligochaetes) were also collected and imaged. In the field, the snow and biological samples were mounted on copper plates, cooled in liquid nitrogen, and stored in dry shipping containers which maintain a temperature of -196??C. The firn and glacier ice samples were obtained by extracting horizontal ice cores, 8 mm in diameter, at different levels from larger standard glaciological (vertical) ice cores 7.5 cm in diameter. These samples were cooled in liquid nitrogen and placed in cryotubes, were stored in the same dry shipping container, and sent to the SEM facility. In the laboratory, the samples were sputter coated with platinum and imaged by a low-temperature SEM. To image the firn and glacier ice samples, the cores were fractured in liquid nitrogen, attached to a specimen holder, and then imaged. While light microscope images of snow and ice are difficult to interpret because of internal reflection and refraction, the SEM images provide a clear and unique view of the surface of the samples because they are generated from electrons emitted or reflected only from the surface of the sample. In addition, the SEM has a great depth of field with a wide range of magnifying capabilities. The resulting images clearly show the individual grains of the seasonal snowpack and the bonding between the snow grains. Images of firn show individual ice crystals, the bonding between the crystals, and connected air spaces. Images of glacier ice show a crystal structure on a scale of 1-2 mm which is considerably smaller than the expected crystal size. Microscopic air bubbles, less than 15 ??m in diameter, clearly marked the boundaries between these crystal-like features. The life forms associated with the glacier were easily imaged and studied. The low-temperature SEM sample collecting and handling methods proved to be operable in the field; the SEM analysis is applicable to glaciological studies and reveals details unattainable by conventional light microscopic methods.Low temperature scanning electron microscopy (SEM) was used to observe metamorphosed snow, glacial firn, and glacial ice obtained from South Cascade Glacier in Washington State, USA. Biotic samples consisting of algae and ice worms were also collected and imaged. The SEM images provide a clear and unique view of the surface of the samples because they are generated from electrons emitted or reflected only from the surface of the sample. The SEM has a great depth of field with a wide range of magnifying capabilities.

A two-dimensional Dirac fermion microscope

NASA Astrophysics Data System (ADS)

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-06-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots.

A two-dimensional Dirac fermion microscope

PubMed Central

Bøggild, Peter; Caridad, José M.; Stampfer, Christoph; Calogero, Gaetano; Papior, Nick Rübner; Brandbyge, Mads

2017-01-01

The electron microscope has been a powerful, highly versatile workhorse in the fields of material and surface science, micro and nanotechnology, biology and geology, for nearly 80 years. The advent of two-dimensional materials opens new possibilities for realizing an analogy to electron microscopy in the solid state. Here we provide a perspective view on how a two-dimensional (2D) Dirac fermion-based microscope can be realistically implemented and operated, using graphene as a vacuum chamber for ballistic electrons. We use semiclassical simulations to propose concrete architectures and design rules of 2D electron guns, deflectors, tunable lenses and various detectors. The simulations show how simple objects can be imaged with well-controlled and collimated in-plane beams consisting of relativistic charge carriers. Finally, we discuss the potential of such microscopes for investigating edges, terminations and defects, as well as interfaces, including external nanoscale structures such as adsorbed molecules, nanoparticles or quantum dots. PMID:28598421

Performance of bent-crystal x-ray microscopes for high energy density physics research

DOE PAGES

Schollmeier, Marius S.; Geissel, Matthias; Shores, Jonathon E.; ...

2015-05-29

We present calculations for the field of view (FOV), image fluence, image monochromaticity, spectral acceptance, and image aberrations for spherical crystal microscopes, which are used as self-emission imaging or backlighter systems at large-scale high energy density physics facilities. Our analytic results are benchmarked with ray-tracing calculations as well as with experimental measurements from the 6.151 keV backlighter system at Sandia National Laboratories. Furthermore, the analytic expressions can be used for x-ray source positions anywhere between the Rowland circle and object plane. We discovered that this enables quick optimization of the performance of proposed but untested, bent-crystal microscope systems to findmore » the best compromise between FOV, image fluence, and spatial resolution for a particular application.« less

Development of an automated MODS plate reader to detect early growth of Mycobacterium tuberculosis.

PubMed

Comina, G; Mendoza, D; Velazco, A; Coronel, J; Sheen, P; Gilman, R H; Moore, D A J; Zimic, M

2011-06-01

In this work, an automated microscopic observation drug susceptibility (MODS) plate reader has been developed. The reader automatically handles MODS plates and after autofocussing digital images are acquired of the characteristic microscopic cording structures of Mycobacterium tuberculosis, which are the identification method utilized in the MODS technique to detect tuberculosis and multidrug resistant tuberculosis. In conventional MODS, trained technicians manually move the MODS plate on the stage of an inverted microscope while trying to locate and focus upon the characteristic microscopic cording colonies. In centres with high tuberculosis diagnostic demand, sufficient time may not be available to adequately examine all cultures. An automated reader would reduce labour time and the handling of M. tuberculosis cultures by laboratory personnel. Two hundred MODS culture images (100 from tuberculosis positive and 100 from tuberculosis negative sputum samples confirmed by a standard MODS reading using a commercial microscope) were acquired randomly using the automated MODS plate reader. A specialist analysed these digital images with the help of a personal computer and designated them as M. tuberculosis present or absent. The specialist considered four images insufficiently clear to permit a definitive reading. The readings from the 196 valid images resulted in a 100% agreement with the conventional nonautomated standard reading. The automated MODS plate reader combined with open-source MODS pattern recognition software provides a novel platform for high throughput automated tuberculosis diagnosis. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

Imaging of cauda equina edema in lumbar canal stenosis by using gadolinium-enhanced MR imaging: experimental constriction injury.

PubMed

Kobayashi, S; Uchida, K; Takeno, K; Baba, H; Suzuki, Y; Hayakawa, K; Yoshizawa, H

2006-02-01

It has been reported that disturbance of blood flow arising from circumferential compression of the cauda equina by surrounding tissue plays a major role in the appearance of neurogenic intermittent claudication (NIC) associated with lumbar spinal canal stenosis (LSCS). We created a model of LSCS to clarify the mechanism of enhancement within the cauda equina on gadolinium-enhanced MR images from patients with LSCS. In 20 dogs, a lumbar laminectomy was performed by applying circumferential constriction to the cauda equina by using a silicon tube, to produce 30% stenosis of the circumferential diameter of the dural tube. After 1 and 3 weeks, gadolinium and Evans blue albumin were injected intravenously at the same time. The sections were used to investigate the status of the blood-nerve barrier function under a fluorescence microscope and we compared gadolinium-enhanced MR images with Evans blue albumin distribution in the nerve. The other sections were used for light and transmission electron microscopic study. In this model, histologic examination showed congestion and dilation in many of the intraradicular veins, as well as inflammatory cell infiltration. The intraradicular edema caused by venous congestion and Wallerian degeneration can also occur at sites that are not subject to mechanical compression. Enhanced MR imaging showed enhancement of the cauda equina at the stenosed region, demonstrating the presence of edema. Gadolinium-enhanced MR imaging may be a useful tool for the diagnosis of microcirculatory disorders of the cauda equina associated with LSCS.

Astigmatism compensation in digital holographic microscopy using complex-amplitude correlation

NASA Astrophysics Data System (ADS)

Tamrin, Khairul Fikri; Rahmatullah, Bahbibi; Samuri, Suzani Mohamad

2015-07-01

Digital holographic microscopy (DHM) is a promising tool for a three-dimensional imaging of microscopic particles. It offers the possibility of wavefront processing by manipulating amplitude and phase of the recorded digital holograms. With a view to compensate for aberration in the reconstructed particle images, this paper discusses a new approach of aberration compensation based on complex amplitude correlation and the use of a priori information. The approach is applied to holograms of microscopic particles flowing inside a cylindrical micro-channel recorded using an off-axis digital holographic microscope. The approach results in improvements in the image and signal qualities.

Implementation of stimulated Raman scattering microscopy for single cell analysis

NASA Astrophysics Data System (ADS)

D'Arco, Annalisa; Ferrara, Maria Antonietta; Indolfi, Maurizio; Tufano, Vitaliano; Sirleto, Luigi

2017-05-01

In this work, we present successfully realization of a nonlinear microscope, not purchasable in commerce, based on stimulated Raman scattering. It is obtained by the integration of a femtosecond SRS spectroscopic setup with an inverted research microscope equipped with a scanning unit. Taking account of strength of vibrational contrast of SRS, it provides label-free imaging of single cell analysis. Validation tests on images of polystyrene beads are reported to demonstrate the feasibility of the approach. In order to test the microscope on biological structures, we report and discuss the label-free images of lipid droplets inside fixed adipocyte cells.

Trace Element Mapping of a Biological Specimen by a Full-Field X-ray Fluorescence Imaging Microscope with a Wolter Mirror

NASA Astrophysics Data System (ADS)

Hoshino, Masato; Yamada, Norimitsu; Ishino, Toyoaki; Namiki, Takashi; Watanabe, Norio; Aoki, Sadao

2007-01-01

A full-field X-ray fluorescence imaging microscope with a Wolter mirror was applied to the element mapping of alfalfa seeds. The X-ray fluorescence microscope was built at the Photon Factory BL3C2 (KEK). X-ray fluorescence images of several growing stages of the alfalfa seeds were obtained. X-ray fluorescence energy spectra were measured with either a solid state detector or a CCD photon counting method. The element distributions of iron and zinc which were included in the seeds were obtained using a photon counting method.

Wide field of view common-path lateral-shearing digital holographic interference microscope

NASA Astrophysics Data System (ADS)

Vora, Priyanka; Trivedi, Vismay; Mahajan, Swapnil; Patel, Nimit; Joglekar, Mugdha; Chhaniwal, Vani; Moradi, Ali-Reza; Javidi, Bahram; Anand, Arun

2017-12-01

Quantitative three-dimensional (3-D) imaging of living cells provides important information about the cell morphology and its time variation. Off-axis, digital holographic interference microscopy is an ideal tool for 3-D imaging, parameter extraction, and classification of living cells. Two-beam digital holographic microscopes, which are usually employed, provide high-quality 3-D images of micro-objects, albeit with lower temporal stability. Common-path digital holographic geometries, in which the reference beam is derived from the object beam, provide higher temporal stability along with high-quality 3-D images. Self-referencing geometry is the simplest of the common-path techniques, in which a portion of the object beam itself acts as the reference, leading to compact setups using fewer optical elements. However, it has reduced field of view, and the reference may contain object information. Here, we describe the development of a common-path digital holographic microscope, employing a shearing plate and converting one of the beams into a separate reference by employing a pin-hole. The setup is as compact as self-referencing geometry, while providing field of view as wide as that of a two-beam microscope. The microscope is tested by imaging and quantifying the morphology and dynamics of human erythrocytes.

Wide field of view common-path lateral-shearing digital holographic interference microscope.

PubMed

Vora, Priyanka; Trivedi, Vismay; Mahajan, Swapnil; Patel, Nimit; Joglekar, Mugdha; Chhaniwal, Vani; Moradi, Ali-Reza; Javidi, Bahram; Anand, Arun

2017-12-01

Quantitative three-dimensional (3-D) imaging of living cells provides important information about the cell morphology and its time variation. Off-axis, digital holographic interference microscopy is an ideal tool for 3-D imaging, parameter extraction, and classification of living cells. Two-beam digital holographic microscopes, which are usually employed, provide high-quality 3-D images of micro-objects, albeit with lower temporal stability. Common-path digital holographic geometries, in which the reference beam is derived from the object beam, provide higher temporal stability along with high-quality 3-D images. Self-referencing geometry is the simplest of the common-path techniques, in which a portion of the object beam itself acts as the reference, leading to compact setups using fewer optical elements. However, it has reduced field of view, and the reference may contain object information. Here, we describe the development of a common-path digital holographic microscope, employing a shearing plate and converting one of the beams into a separate reference by employing a pin-hole. The setup is as compact as self-referencing geometry, while providing field of view as wide as that of a two-beam microscope. The microscope is tested by imaging and quantifying the morphology and dynamics of human erythrocytes. (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).

Catalog of microscopic organisms of the Everglades, Part 1—The cyanobacteria

USGS Publications Warehouse

Rosen, Barry H.; Mareš, Jan

2016-07-27

The microscopic organisms of the Everglades include numerous prokaryotic organisms, including the eubacteria, such as the cyanobacteria and non-photosynthetic bacteria, as well as several eukaryotic algae and protozoa that form the base of the food web. This report is part 1 in a series of reports that describe microscopic organisms encountered during the examination of several hundred samples collected in the southern Everglades. Part 1 describes the cyanobacteria and includes a suite of images and the most current taxonomic treatment of each taxon. The majority of the images are of live organisms, allowing their true color to be represented. A number of potential new species are illustrated; however, corroborating evidence from a genetic analysis of the morphological characteristics is needed to confirm these designations as new species. Part 1 also includes images of eubacteria that resemble cyanobacteria. Additional parts of the report on microscopic organisms of the Everglades are currently underway, such as the green algae and diatoms. The report also serves as the basis for a taxonomic image database that will provide a digital record of the Everglades microscopic flora and fauna. It is anticipated that these images will facilitate current and future ecological studies on the Everglades, such as understanding food-web dynamics, sediment formation and accumulation, the effects of nutrients and flow, and climate change.

Operation of a Cartesian Robotic System in a Compact Microscope with Intelligent Controls

NASA Technical Reports Server (NTRS)

McDowell, Mark (Inventor)

2006-01-01

A Microscope Imaging System (CMIS) with intelligent controls is disclosed that provides techniques for scanning, identifying, detecting and tracking microscopic changes in selected characteristics or features of various surfaces including, but not limited to, cells, spheres, and manufactured products subject to difficult-to-see imperfections. The practice of the present invention provides applications that include colloidal hard spheres experiments, biological cell detection for patch clamping, cell movement and tracking, as well as defect identification in products, such as semiconductor devices, where surface damage can be significant, but difficult to detect. The CMIS system is a machine vision system, which combines intelligent image processing with remote control capabilities and provides the ability to autofocus on a microscope sample, automatically scan an image, and perform machine vision analysis on multiple samples simultaneously.

A stand-alone compact EUV microscope based on gas-puff target source.

PubMed

Torrisi, Alfio; Wachulak, Przemyslaw; Węgrzyński, Łukasz; Fok, Tomasz; Bartnik, Andrzej; Parkman, Tomáš; Vondrová, Šárka; Turňová, Jana; Jankiewicz, Bartłomiej J; Bartosewicz, Bartosz; Fiedorowicz, Henryk

2017-02-01

We report on a very compact desk-top transmission extreme ultraviolet (EUV) microscope based on a laser-plasma source with a double stream gas-puff target, capable of acquiring magnified images of objects with a spatial (half-pitch) resolution of sub-50 nm. A multilayer ellipsoidal condenser is used to focus and spectrally narrow the radiation from the plasma, producing a quasi-monochromatic EUV radiation (λ = 13.8 nm) illuminating the object, whereas a Fresnel zone plate objective forms the image. Design details, development, characterization and optimization of the EUV source and the microscope are described and discussed. Test object and other samples were imaged to demonstrate superior resolution compared to visible light microscopy. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Influence of operating microscope in the sealing of cervical perforations.

PubMed

Schmidt, Bruna Schwingel; Zaccara, Ivana Maria; Reis Só, Marcus Vinícius; Kuga, Milton Carlos; Palma-Dibb, Regina Guenka; Kopper, Patrícia Maria Poli

2016-01-01

Accidental root canal perforations are among the main complications of endodontic treatment. This study evaluated the influence of operating microscope (OM) in the marginal adaptation of mineral trioxide aggregate (MTA) (Angelus(®)) and glass ionomer (Vitremer) inserted into cervical perforations. Perforations were made in the cervical third of the buccal wall of the root canal in mandibular incisors. Next, the teeth were divided into four groups (N = 10): MG - MTA without OM; VG - Vitremer without OM; MOMG - MTA with OM; VOMG - Vitremer with OM. The perforations were sealed according to the group and the teeth were prepared for analysis by confocal laser scanning microscope. Images of perforation region (1,024×) were made and the gap presented by the materials was measured using the Image J program. LEXT OLS4100 three dimensional (3D) measuring laser microscope measured the volumetric misfit. Data of gap were analyzed by Kruskal-Wallis and Dunn's tests. Analysis of variance (ANOVA) and Tukey's tests compared the volumetric misfits. The results showed lower volume and gap in the interface dentin/material in VOMG compared to the other groups (P < 0.05). The use of OM improved the quality of cervical perforations sealed with Vitremer, being indicated in clinical situations of iatrogenic cervical perforations.