Статті в журналах: "Microscopy images"

1

Govil, Anurag, David M. Pallister, and Michael D. Morris. "Three-Dimensional Digital Confocal Raman Microscopy." Applied Spectroscopy 47, no. 1 (January 1993): 75–79. http://dx.doi.org/10.1366/0003702934048497.

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We describe an iterative image restoration technique which functions as digital confocal microscopy for Raman images. We deconvolute the lateral and axial components of the microscope point spread function from a series of optical sections, to generate a stack of well-resolved Raman images which describe the three-dimensional topology of a sample. The technique provides an alternative to confocal microscopy for three-dimensional microscopic Raman imaging.

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2

Mund, Markus, and Jonas Ries. "How good are my data? Reference standards in superresolution microscopy." Molecular Biology of the Cell 31, no. 19 (September 1, 2020): 2093–96. http://dx.doi.org/10.1091/mbc.e19-04-0189.

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Superresolution microscopy is becoming increasingly widespread in biological labs. While it holds enormous potential for biological discovery, it is a complex imaging technique that requires thorough optimization of various experimental parameters to yield data of the highest quality. Unfortunately, it remains challenging even for seasoned users to judge from the acquired images alone whether their superresolution microscopy pipeline is performing at its optimum, or if the image quality could be improved. Here, we describe how superresolution microscopists can objectively characterize their imaging pipeline using suitable reference standards, which are stereotypic so that the same structure can be imaged everywhere, every time, on every microscope. Quantitative analysis of reference standard images helps characterizing the performance of one’s own microscopes over time, allows objective benchmarking of newly developed microscopy and labeling techniques, and finally increases comparability of superresolution microscopy data between labs.

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3

Kinosita, K., H. Itoh, S. Ishiwata, K. Hirano, T. Nishizaka, and T. Hayakawa. "Dual-view microscopy with a single camera: real-time imaging of molecular orientations and calcium." Journal of Cell Biology 115, no. 1 (October 1, 1991): 67–73. http://dx.doi.org/10.1083/jcb.115.1.67.

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A new microscope technique, termed "W" (double view video) microscopy, enables simultaneous observation of two different images of an object through a single video camera or by eye. The image pair may, for example, be transmission and fluorescence, fluorescence at different wavelengths, or mutually perpendicular components of polarized fluorescence. Any video microscope can be converted into a dual imager by simple insertion of a small optical device. The continuous appearance of the dual image assures the best time resolution in existing and future video microscopes. As an application, orientations of actin protomers in individual, moving actin filaments have been imaged at the video rate. Asymmetric calcium influxes into a cell exposed to an intense electric pulse have also been visualized.

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4

Bell, David C. "Contrast Mechanisms and Image Formation in Helium Ion Microscopy." Microscopy and Microanalysis 15, no. 2 (March 16, 2009): 147–53. http://dx.doi.org/10.1017/s1431927609090138.

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AbstractThe helium ion microscope is a unique imaging instrument. Based on an atomic level imaging system using the principle of field ion microscopy, the helium ion source has been shown to be incredibly stable and reliable, itself a remarkable engineering feat. Here we show that the image contrast is fundamentally different to other microscopes such as the scanning electron microscope (SEM), although showing many operational similarities due to the physical ion interaction mechanisms with the sample. Secondary electron images show enhanced surface contrast due the small surface interaction volume as well as elemental contrast differences, such as for nanowires imaged on a substrate. We present images of nanowires and nanoparticles for comparison with SEM imaging. Applications of Rutherford backscattered ion imaging as a unique and novel imaging mechanism are described. The advantages of the contrast mechanisms offered by this instrument for imaging nanomaterials are clearly apparent due to the high resolution and surface sensitivity afforded in the images. Future developments of the helium ion microscope should yield yet further improvements in imaging and provide a platform for continued advances in microscope science and nanoscale research.

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5

Zhao, Xiaocui, Nils O. Petersen, and Zhifeng Ding. "Comparison study of live cells by atomic force microscopy, confocal microscopy, and scanning electrochemical microscopy." Canadian Journal of Chemistry 85, no. 3 (March 1, 2007): 175–83. http://dx.doi.org/10.1139/v07-007.

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In this report, three kinds of scanning probe microscopy techniques, atomic force microscopy (AFM), confocal microscopy (CM), and scanning electrochemical microscopy (SECM), were used to study live cells in the physiological environment. Two model cell lines, CV-1 and COS-7, were studied. Time-lapse images were obtained with both contact and tapping mode AFM techniques. Cells were more easily scratched or moved by contact mode AFM than by tapping mode AFM. Detailed surface structures such as filamentous structures on the cell membrane can be obtained and easily discerned with tapping mode AFM. The toxicity of ferrocenemethanol (Fc) on live cells was studied by CM in reflection mode by recording the time-lapse images of controlled live cells and live cells with different Fc concentrations. No significant change in the morphology of cells was caused by Fc. Cells were imaged by SECM with Fc as the mediator at a biased potential of 0.35 V (vs. Ag/AgCl with a saturated KCl solution). Cells did not change visibly within 1 h, which indicated that SECM was a noninvasive technique and thus has a unique advantage for the study of soft cells, since the electrode scanned above the cells instead of in contact with them. Reactive oxygen species (ROS) generated by the cells were detected and images based on these chemical species were obtained. It is demonstrated that SECM can provide not only the topographical images but also the images related to the chemical or biochemical species released by the live cells.Key words: live cells, atomic force microscopy, confocal microscopy, scanning electrochemical microscopy.

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6

Mansfield, John F. "Digital imaging: When should one take the plunge?" Proceedings, annual meeting, Electron Microscopy Society of America 54 (August 11, 1996): 602–3. http://dx.doi.org/10.1017/s0424820100165471.

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The current imaging trend in optical microscopy, scanning electron microscopy (SEM) or transmission electron microscopy (TEM) is to record all data digitally. Most manufacturers currently market digital acquisition systems with their microscope packages. The advantages of digital acquisition include: almost instant viewing of the data as a high-quaity positive image (a major benefit when compared to TEM images recorded onto film, where one must wait until after the microscope session to develop the images); the ability to readily quantify features in the images and measure intensities; and extremely compact storage (removable 5.25” storage devices which now can hold up to several gigabytes of data).The problem for many researchers, however, is that they have perfectly serviceable microscopes that they routinely use that have no digital imaging capabilities with little hope of purchasing a new instrument.

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7

Grudin, B. N., E. L. Kuleshov, V. S. Plotnikov, N. A. Smolyaninov, and S. V. Polischuk. "Modeling monofractal microscopy images." Bulletin of the Russian Academy of Sciences: Physics 77, no. 8 (August 2013): 999–1003. http://dx.doi.org/10.3103/s1062873813080121.

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8

Levi-Setti, R., J. M. Chabala, and Y. L. Wang. "Scanning ion microscopy images." Proceedings, annual meeting, Electron Microscopy Society of America 45 (August 1987): 180–81. http://dx.doi.org/10.1017/s042482010012583x.

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Finely focused beams extracted from liquid metal ion sources (LMIS) provide a wealth of secondary signals which can be exploited to create high resolution images by the scanning method. The images of scanning ion microscopy (SIM) encompass a variety of contrast mechanisms which we classify into two broad categories: a) Emission contrast and b) Analytical contrast.Emission contrast refers to those mechanisms inherent to the emission of secondaries by solids under ion bombardment. The contrast-carrying signals consist of ion-induced secondary electrons (ISE) and secondary ions (ISI). Both signals exhibit i) topographic emission contrast due to the existence of differential geometric emission and collection effects, ii) crystallographic emission contrast, due to primary ion channeling phenomena and differential oxidation of crystalline surfaces, iii) chemical emission or Z-contrast, related to the dependence of the secondary emission yields on the Z and surface chemical state of the target.

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9

Chen, Weiyang, Bo Liao, Weiwei Li, Xiangjun Dong, Matthew Flavel, Markandeya Jois, Guojun Li, and Bo Xian. "Segmenting Microscopy Images of Multi-Well Plates Based on Image Contrast." Microscopy and Microanalysis 23, no. 5 (July 17, 2017): 932–37. http://dx.doi.org/10.1017/s1431927617012375.

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AbstractImage segmentation is a key process in analyzing biological images. However, it is difficult to detect the differences between foreground and background when the image is unevenly illuminated. The unambiguous segmenting of multi-well plate microscopy images with various uneven illuminations is a challenging problem. Currently, no publicly available method adequately solves these various problems in bright-field multi-well plate images. Here, we propose a new method based on contrast values which removes the need for illumination correction. The presented method is effective enough to distinguish foreground and therefore a model organism (Caenorhabditis elegans) from an unevenly illuminated microscope image. In addition, the method also can solve a variety of problems caused by different uneven illumination scenarios. By applying this methodology across a wide range of multi-well plate microscopy images, we show that our approach can consistently analyze images with uneven illuminations with unparalleled accuracy and successfully solve various problems associated with uneven illumination. It can be used to process the microscopy images captured from multi-well plates and detect experimental subjects from an unevenly illuminated background.

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10

Jost, Anna Payne-Tobin, and Jennifer C. Waters. "Designing a rigorous microscopy experiment: Validating methods and avoiding bias." Journal of Cell Biology 218, no. 5 (March 20, 2019): 1452–66. http://dx.doi.org/10.1083/jcb.201812109.

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Images generated by a microscope are never a perfect representation of the biological specimen. Microscopes and specimen preparation methods are prone to error and can impart images with unintended attributes that might be misconstrued as belonging to the biological specimen. In addition, our brains are wired to quickly interpret what we see, and with an unconscious bias toward that which makes the most sense to us based on our current understanding. Unaddressed errors in microscopy images combined with the bias we bring to visual interpretation of images can lead to false conclusions and irreproducible imaging data. Here we review important aspects of designing a rigorous light microscopy experiment: validation of methods used to prepare samples and of imaging system performance, identification and correction of errors, and strategies for avoiding bias in the acquisition and analysis of images.

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11

Jiang, Weixin, Eric Schwenker, Trevor Spreadbury, Oliver Cossairt, and Maria KY Chan. "A hybrid image retrieval system for microscopy images." Microscopy and Microanalysis 27, S1 (July 30, 2021): 474–76. http://dx.doi.org/10.1017/s1431927621002191.

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12

Avinash, Gopal B. "Image compression and data integrity in confocal microscopy." Proceedings, annual meeting, Electron Microscopy Society of America 51 (August 1, 1993): 206–7. http://dx.doi.org/10.1017/s0424820100146874.

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In confocal microscopy, one method of managing large data is to store the data in a compressed form using image compression algorithms. These algorithms can be either lossless or lossy. Lossless algorithms compress images without losing any information with modest compression ratios (memory for the original / memory for the compressed) which are usually between 1 and 2 for typical confocal 2-D images. However, lossy algorithms can provide higher compression ratios (3 to 8) at the expense of information content in the images. The main purpose of this study is to empirically demonstrate the use of lossy compression techniques to images obtained from a confocal microscope while retaining the qualitative and quantitative image integrity under certain criteria.A fluorescent pollen specimen was imaged using ODYSSEY, a real-time laser scanning confocal microscope from NORAN Instruments, Inc. The images (128 by 128) consisted of a single frame (scanned in 33ms), a 4-frame average, a 64-frame average and an edge-preserving smoothed image of the single frame.

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13

Reder, Nicholas P., Adam K. Glaser, Erin F. McCarty, Ye Chen, Lawrence D. True, and Jonathan T. C. Liu. "Open-Top Light-Sheet Microscopy Image Atlas of Prostate Core Needle Biopsies." Archives of Pathology & Laboratory Medicine 143, no. 9 (March 20, 2019): 1069–75. http://dx.doi.org/10.5858/arpa.2018-0466-oa.

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Context.— Ex vivo microscopy encompasses a range of techniques to examine fresh or fixed tissue with microscopic resolution, eliminating the need to embed the tissue in paraffin or produce a glass slide. One such technique is light-sheet microscopy, which enables rapid 3D imaging. Our pathology-engineering collaboration has resulted in an open-top light-sheet (OTLS) microscope that is specifically tailored to the needs of pathology practice. Objective.— To present an image atlas of OTLS images of prostate core needle biopsies. Design.— Core needle biopsies (N = 9) were obtained from fresh radical prostatectomy specimens. Each biopsy was fixed in formalin, dehydrated in ethanol, stained with TO-PRO3 and eosin, optically cleared, and imaged using OTLS microscopy. The biopsies were then processed, paraffin embedded, and sectioned. Hematoxylin-eosin and immunohistochemical staining for cytokeratin 5 and cytokeratin 8 was performed. Results.— Benign and neoplastic histologic structures showed high fidelity between OTLS and traditional light microscopy. OTLS microscopy had no discernible effect on hematoxylin-eosin or immunohistochemical staining in this pilot study. The 3D histology information obtained using OTLS microscopy enabled new structural insights, including the observation of cribriform and well-formed gland morphologies within the same contiguous glandular structures, as well as the continuity of poorly formed glands with well-formed glands. Conclusions.— Three-dimensional OTLS microscopy images have a similar appearance to traditional hematoxylin-eosin histology images, with the added benefit of useful 3D structural information. Further studies are needed to continue to document the OTLS appearance of a wide range of tissues and to better understand 3D histologic structures.

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14

Schatten, G., S. Paddock, P. Cooke, and J. Pawley. "Confocal microscopy at the integrated microscopy resource for biomedical research (IMR) of the university of wisconsin." Proceedings, annual meeting, Electron Microscopy Society of America 46 (1988): 92–93. http://dx.doi.org/10.1017/s0424820100102547.

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Confocal microscopy holds great promise for improved imaging of fluorescent or reflective biomedical specimens. The IMR is actively investigating the advantages and optimal usage of the Medical Research Council's Lasersharp laser - scanning confocal microscope and Tracor/Northern's Tandem Scanning Microscope, which benefits from the principles outlined by Petran et al. and Boyde.Quantitative evaluation of microscopic images has always been complicated by the effect of out-of-focus structures on the final image. These effects can be greatly reduced if the conventional light microscope is replaced by a scanning-confocal light microscope. In such an instrument two conditions are met: 1) only a single point of the sample is illuminated at any time and 2) this point on the sample is then imaged onto the pinhole at the entrance to the photodetector. Because little light from out-of-focus planes will pass through the pinhole, only in-focus data is recorded.

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15

Carmichael, Stephen W. "Using Antibodies to Make Images." Microscopy Today 8, no. 3 (April 2000): 3–7. http://dx.doi.org/10.1017/s1551929500061010.

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The atomic force microscope (AFM), the workhorse of scanning probe microscopes, has become even more versatile. Anneliese Raab, Wenhai Han, Dirk Badt, Sandra Smith-Gill, Stuart Lindsay, Hansgeorg Schindler, and Peter Hinterdorfer have demonstrated that the AFM, in the dynamic force mode, can use antibodies as a probe. Dynamic force microscopy uses a magnetized tip that is oscillated in an alternating magnetic field as the tip scans the surface. This provides a very gentile interaction that can be recorded as a high resolution topographic image. Raab et al., showed that more information can be obtained from the specimen.

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16

Shotton, D. M. "Video-enhanced light microscopy and its applications in cell biology." Journal of Cell Science 89, no. 2 (February 1, 1988): 129–50. http://dx.doi.org/10.1242/jcs.89.2.129.

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The combination of novel optical microscopic techniques with advanced video and digital image-processing technology now permits dramatic improvements in the quality of light-microscope images. Such video-enhanced light microscopy has lead to a renaissance in the applications of the light microscope for the study of living cells in two important areas: the intensification of faint fluorescence images, permitting observation of fluorescently labelled cells under conditions of very low illuminating intensity; and the enhancement of extremely low contrast images generated by minute cellular structures, so that these may be clearly seen and their normal intracellular movements recorded. Application of both these aspects of video-enhanced light microscopy have recently led to major discoveries concerning the functioning of the living cell. In this review I discuss the equipment, procedures and image-processing principles employed in these applications, and describe and illustrate some of the spectacular results that have recently been obtained.

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17

Filipiak, Krystyna, Agnieszka Malińska, Dariusz Krupa, and Maciej Zabel. "Innovative Methods of Archiving, Presentation and Providing Access to Histological Sections." Advances in Cell Biology 3, no. 3 (October 1, 2011): 41–53. http://dx.doi.org/10.2478/v10052-011-0003-4.

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Summary The dynamic development of technical sciences and informatics makes now possible acquisition of microscopic images of histological sections, not only using digital cameras, but also through specialized devices called scanners. The digitalized images stored in a computer storage device are called virtual slides and, together with special software, are known as virtual microscopy. The virtual slides can be analyzed on a computer screen by panoramic viewing or using a detailed image examination at higher magnification. In many research and education institutions in both the U.S. and Europe, the virtual microscopy is used for teaching and training purposes. In the academic year of 2009/10, Department of Histology and Embryology, University of Medical Sciences in Poznan, as one of the first in Poland, has created a virtual database for educational purposes. This database created by archiving the traditional images of histological slides in the form of digital images. So far, more than 130 virtual slides have been acquired and catalogued in 24 thematic folders, available for medical students participating in histology, embryology and cell biology courses. Telepathology is the second branch which uses virtual microscopy. Virtual microscope allows to discuss and resolve medical/diagnostic problems with the use of telecommunication systems and information technology. The existing internet platforms offer access to virtual microscopes and virtual slides. In June, 2011 the Center of Morphologic Images Archivization and Digital Database of Microscopic Pictures in the Department of Histology and Embryology, Poznan University of Medical Sciences has launched an online platform (www.caom.pl), aimed to provide the central database of scanned histological sections of physiological tissues, and pathological, rare and sporadic lesions, including tumor

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18

Itoh, J., R. Y. Osamura, and K. Watanabe. "Subcellular visualization of light microscopic specimens by laser scanning microscopy and computer analysis: a new application of image analysis." Journal of Histochemistry & Cytochemistry 40, no. 7 (July 1992): 955–67. http://dx.doi.org/10.1177/40.7.1607644.

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To identify subcellular organelles or to observe their pathological changes in sections prepared for light microscopy, immuno- and/or enzyme histochemical staining for the marker substances or enzymes of those subcellular organelles are frequently employed. With conventional light microscopes (CLM), however, it is hardly possible to determine whether or not the target organelles are properly stained and to confirm their fine structure. In the present study, the laser scanning microscope (LSM) was employed to obtain highly contrasted images of histochemically stained subcellular organelles at the limit of resolution in light microscopy. To refine or characterize those images, images built up as electronic signals in LSM were further processed in the Image Analysis System (IAS) with pipeline. Thus, the approximate figures of subcellular organelles such as microtubules, endoplasmic reticula, secretory granules, and mitochondria were visualized in brightfield on sections prepared for light microscopy (paraffin, frozen sections and cultured living cells). The validity of the images obtained by LSM or LSM-IAS was confirmed by immunoelectron microscopy when possible. The LSM images of histochemically stained suborganelles of various cells were definitely improved (refined and/or strengthened) by processing them with IAS.

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19

Zhang, Peiwei, Jufeng Zhao, Binbin Lin, Xiaohui Wu, and Guangmang Cui. "Hyperspectral microscopy imaging based on Fourier ptychographic microscopy." Journal of Optics 24, no. 5 (March 29, 2022): 055301. http://dx.doi.org/10.1088/2040-8986/ac57b3.

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Abstract Hyperspectral resolution, high spatial resolution, and a wide field of view (FOV) are the targets of optical spectral microscopy imaging. However, hyperspectral microscopy imaging technology cannot provide a wide FOV and a high spatial resolution at the same time. Fourier ptychographic microscopy (FPM) is a novel microscopy imaging technique that uses LEDs at varying angles to capture a series of low-spatial-resolution images that are used to recover images that have both high spatial resolution and a wide FOV. Since FPM cannot obtain the spectral resolution of the sample, in this paper, an efficient strategy based on the FPM system is proposed for the reconstruction of hyperspectral images. First, the traditional FPM setup is optimized, with a new experimental setup based on halogen lamp illumination and a narrow band-pass filter to capture a series of low-spatial-resolution images at different wavelengths. Second, a new algorithm, combining hyperspectral resolution imaging using interpolation compensation and a phase retrieval algorithm, is proposed to reconstruct high-spatial-resolution, wide FOV, and hyperspectral resolution images. Finally, we verified the feasibility and effectiveness of our experimental setup and algorithm by both simulation and experiment. The results show that our method can not only reconstruct high-spatial-resolution and wide FOV images, but also has a spectral resolution of 5 nm.

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20

Katoh, Kazuo. "Software-Based Three-Dimensional Deconvolution Microscopy of Cytoskeletal Proteins in Cultured Fibroblast Using Open-Source Software and Open Hardware." Journal of Imaging 5, no. 12 (November 23, 2019): 88. http://dx.doi.org/10.3390/jimaging5120088.

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As conventional fluorescence microscopy and confocal laser scanning microscopy generally produce images with blurring at the upper and lower planes along the z-axis due to non-focal plane image information, the observation of biological images requires “deconvolution.” Therefore, a microscope system’s individual blur function (point spread function) is determined theoretically or by actual measurement of microbeads and processed mathematically to reduce noise and eliminate blurring as much as possible. Here the author describes the use of open-source software and open hardware design to build a deconvolution microscope at low cost, using readily available software and hardware. The advantage of this method is its cost-effectiveness and ability to construct a microscope system using commercially available optical components and open-source software. Although this system does not utilize expensive equipment, such as confocal and total internal reflection fluorescence microscopes, decent images can be obtained even without previous experience in electronics and optics.

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21

McMillan, William. "Laser Scanning Confocal Microscopy for Materials Science." Microscopy Today 6, no. 5 (July 1998): 20–23. http://dx.doi.org/10.1017/s1551929500067791.

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Confocal microscopy has gained great popularity in biology and medical research because of the ability to image three-dimensional objects at greater resolution than conventional optical microscopes. In a typical Laser Scanning Confocal Microscope (LSCM), the specimen stage is stepped up or down to collect a series of two-dimensional images (or slices) at each focal plane. Conventional light microscopes create images with a depth of field, at high power, of 2 to 3 μm. The depth of field of confocal microscopes ranges from 0.5 to 1.5 μm, which allows information to be collected from a well defined optical section rather than from most of the specimen. Therefore, due to this “thin” focal plane, out of focus light is virtually eliminated which results in an increase in contrast, clarity and detection.

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22

You, Yun-Wen, Hsun-Yun Chang, Hua-Yang Liao, Wei-Lun Kao, Guo-Ji Yen, Chi-Jen Chang, Meng-Hung Tsai, and Jing-Jong Shyue. "Electron Tomography of HEK293T Cells Using Scanning Electron Microscope–Based Scanning Transmission Electron Microscopy." Microscopy and Microanalysis 18, no. 5 (October 2012): 1037–42. http://dx.doi.org/10.1017/s1431927612001158.

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AbstractBased on a scanning electron microscope operated at 30 kV with a homemade specimen holder and a multiangle solid-state detector behind the sample, low-kV scanning transmission electron microscopy (STEM) is presented with subsequent electron tomography for three-dimensional (3D) volume structure. Because of the low acceleration voltage, the stronger electron-atom scattering leads to a stronger contrast in the resulting image than standard TEM, especially for light elements. Furthermore, the low-kV STEM yields less radiation damage to the specimen, hence the structure can be preserved. In this work, two-dimensional STEM images of a 1-μm-thick cell section with projection angles between ±50° were collected, and the 3D volume structure was reconstructed using the simultaneous iterative reconstructive technique algorithm with the TomoJ plugin for ImageJ, which are both public domain software. Furthermore, the cross-sectional structure was obtained with the Volume Viewer plugin in ImageJ. Although the tilting angle is constrained and limits the resulting structural resolution, slicing the reconstructed volume generated the depth profile of the thick specimen with sufficient resolution to examine cellular uptake of Au nanoparticles, and the final position of these nanoparticles inside the cell was imaged.

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23

Turner, JN, DP Barnard, DH Szarowski, JW Swann, and K. Smith. "Confocal laser scanned microscopy: Analog preprocessing." Proceedings, annual meeting, Electron Microscopy Society of America 47 (August 6, 1989): 150–51. http://dx.doi.org/10.1017/s0424820100152720.

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Confocal laser scanned images often have such a large dynamic range that interpretation is hampered. We employed analog preprocessing to overcome this limitation, using a homomorphic filter and a differentiator. Individual neurons in thick brain slices were injected with a fluorescent dye, and imaged as test objects. The dye density varied for different subcellular regions, and the specimen acted as an attenuater as a function of depth. Thus, each “optical section” had a large signal range that was extreme when the sections were stack to form projections or stereo pairs. Images of either the fine processes (low signal) with a saturated cell body, or a cell body (high signal) with loss of the fine processes resulted from standard methods, but the homomorphic filter and differentiator produced high quality images of both in the same field.

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24

Cakir, Serdar, Deniz Cansen Kahraman, Rengul Cetin-Atalay, and A. Enis Cetin. "Contrast Enhancement of Microscopy Images Using Image Phase Information." IEEE Access 6 (2018): 3839–50. http://dx.doi.org/10.1109/access.2018.2796646.

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25

Min, Tang, and Wang Hui-Nan. "Image Processing and Interactive Visualization of Confocal Microscopy Images." Journal of Algorithms & Computational Technology 2, no. 1 (March 2008): 165–74. http://dx.doi.org/10.1260/174830108784300330.

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26

Llavador, Anabel, Gabriele Scrofani, Genaro Saavedra, and Manuel Martinez-Corral. "Large Depth-of-Field Integral Microscopy by Use of a Liquid Lens." Sensors 18, no. 10 (October 10, 2018): 3383. http://dx.doi.org/10.3390/s18103383.

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Integral microscopy is a 3D imaging technique that permits the recording of spatial and angular information of microscopic samples. From this information it is possible to calculate a collection of orthographic views with full parallax and to refocus computationally, at will, through the 3D specimen. An important drawback of integral microscopy, especially when dealing with thick samples, is the limited depth of field (DOF) of the perspective views. This imposes a significant limitation on the depth range of computationally refocused images. To overcome this problem, we propose here a new method that is based on the insertion, at the pupil plane of the microscope objective, of an electrically controlled liquid lens (LL) whose optical power can be changed by simply tuning the voltage. This new apparatus has the advantage of controlling the axial position of the objective focal plane while keeping constant the essential parameters of the integral microscope, that is, the magnification, the numerical aperture and the amount of parallax. Thus, given a 3D sample, the new microscope can provide a stack of integral images with complementary depth ranges. The fusion of the set of refocused images permits to enlarge the reconstruction range, obtaining images in focus over the whole region.

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27

Máté, Gabriell, and Dieter W. Heermann. "A generalized Potts model for confocal microscopy images." International Journal of Modern Physics B 29, no. 08 (March 30, 2015): 1550048. http://dx.doi.org/10.1142/s0217979215500484.

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Much as being among the least invasive mainstream imaging technologies in life sciences, the resolution of confocal microscopy is limited. Imaged structures, e.g., chromatin-fiber loops, have diameters around or beyond the diffraction limit, and microscopy images show seemingly random spatial density distributions only. While such images are important because the organization of the chromosomes influences different cell mechanisms, many interesting questions can also be related to the observed patterns. These concern their spatial aspects, the role of randomness, the possibility of modeling these images with a random generative process, the interaction between the densities of adjacent loci, the length-scales of these influences, etc. We answer these questions by implementing a generalization of the Potts model. We show how to estimate the model parameters, test the performance of the estimation process and numerically prove that the obtained values converge to the ground truth. Finally, we generate images with a trained model and show that they compare well to real cell images.

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Greenberg, Gary L., and Alan Boyde. "A Transportable Multiple Oblique Illumination System which Retrofits to Conventional Optical Microscopes to Provide Highdefinition Real Time 3-Dimensional Imaging." Microscopy and Microanalysis 4, S2 (July 1998): 444–45. http://dx.doi.org/10.1017/s1431927600022340.

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Microscope specimens are 3-dimensional objects, but the images from conventional light microscopes are flat - they only show two dimensions. Multiple oblique illumination is a novel lighting technique for transmitted light microscopes that produces multiple (i.e. two or more) high definition 3-dimensional images using conventional microscope objective lenses. We have previously described its use in transmitted light. The same optical theory has now been expanded to include reflection microscopy. In the present paper, we describe a new development which will make this approach more widely available. It is a retrofit illumination system that will produce true 3-dimensional images directly through the eyepieces of conventional microscopes.By seeing z-axis information in real-time and in the context of a specimen's entire thickness, researchers can gain additional, unambiguous information about the interrelationships between structures, whereas critical information about 3-dimensional structures can be obscured, lost or misinterpreted when using 2-dimensional instruments. The importance of accurate z-axis information has popularized methods such as deconvolution and confocal microscopy.

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Jester, J. V., H. D. Cavanagh, and M. A. Lemp. "In vivo confocal imaging of the eye using tandem scanning confocal microscopy (TSCM)." Proceedings, annual meeting, Electron Microscopy Society of America 46 (1988): 56–57. http://dx.doi.org/10.1017/s0424820100102365.

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New developments in optical microscopy involving confocal imaging are now becoming available which dramatically increase resolution, contrast and depth of focus by optically sectioning through structures. The transparency of the anterior ocular structures, cornea and lens, make microscopic visualization and optical sectioning of the living intact eye an interesting possibility. Of the confocal microscopes available, the Tandem Scanning Reflected Light Microscope (referred to here as the Tandem Scanning Confocal Microscope), developed by Professors Petran and Hadravsky at Charles University in Pilzen, Czechoslovakia, permits real-time image acquisition and analysis facilitating in vivo studies of ocular structures.Currently, TSCM imaging is most successful for the cornea. The corneal epithelium, stroma, and endothelium have been studied in vivo and photographed in situ. Confocal scanning images of the superficial epithelium, similar to those obtained by scanning electron microscopy, show both light and dark surface epithelial cells.

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Antoniuk, Izabella, Artur Krupa, and Radosław Roszczyk. "Normal Patch Retinex robust algorithm for white balancing in digital microscopy." Machine Graphics and Vision 29, no. 1/4 (December 1, 2020): 79–94. http://dx.doi.org/10.22630/mgv.2020.29.1.5.

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The acquisition of accurately coloured, balanced images in an optical microscope can be a challenge even for experienced microscope operators. This article presents an entirely automatic mechanism for balancing the white level that allows the correction of the microscopic colour images adequately. The results of the algorithm have been confirmed experimentally on a set of two hundred microscopic images. The images contained scans of three microscopic specimens commonly used in pathomorphology. Also, the results achieved were compared with other commonly used white balance algorithms in digital photography. The algorithm applied in this work is more effective than the classical algorithms used in colour photography for microscopic images stained with hematoxylin-phloxine-saffron and for immunohistochemical staining images.

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31

Mansfield, John F. "Digital Imaging: When Should One Take The Plunge?" Microscopy Today 5, no. 4 (May 1997): 14–15. http://dx.doi.org/10.1017/s1551929500061393.

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The current imaging trend in optical microscopy, scanning electron microscopy (SEM) or transmission electron microscopy (TEM) is to record all data digitally. Most manufacturers currently market digital acquisition systems with their microscope packages. The advantages of digital acquisition include: almost instant viewing of the data as a high-quality positive image (a major benefit when compared to TEM images recorded onto film, where one must wait until after the microscope session to develop the images); the ability to readily quantify features in the images and measure intensities; and extremely compact storage (removable 5.25” storage devices which now can hold up to several gigabytes of data).

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32

Wang, Yuliang, Tongda Lu, Xiaolai Li, and Huimin Wang. "Automated image segmentation-assisted flattening of atomic force microscopy images." Beilstein Journal of Nanotechnology 9 (March 26, 2018): 975–85. http://dx.doi.org/10.3762/bjnano.9.91.

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Atomic force microscopy (AFM) images normally exhibit various artifacts. As a result, image flattening is required prior to image analysis. To obtain optimized flattening results, foreground features are generally manually excluded using rectangular masks in image flattening, which is time consuming and inaccurate. In this study, a two-step scheme was proposed to achieve optimized image flattening in an automated manner. In the first step, the convex and concave features in the foreground were automatically segmented with accurate boundary detection. The extracted foreground features were taken as exclusion masks. In the second step, data points in the background were fitted as polynomial curves/surfaces, which were then subtracted from raw images to get the flattened images. Moreover, sliding-window-based polynomial fitting was proposed to process images with complex background trends. The working principle of the two-step image flattening scheme were presented, followed by the investigation of the influence of a sliding-window size and polynomial fitting direction on the flattened images. Additionally, the role of image flattening on the morphological characterization and segmentation of AFM images were verified with the proposed method.

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33

Rostan, Julen, Nicolo Incardona, Emilio Sanchez-Ortiga, Manuel Martinez-Corral, and Pedro Latorre-Carmona. "Machine Learning-Based View Synthesis in Fourier Lightfield Microscopy." Sensors 22, no. 9 (May 3, 2022): 3487. http://dx.doi.org/10.3390/s22093487.

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Current interest in Fourier lightfield microscopy is increasing, due to its ability to acquire 3D images of thick dynamic samples. This technique is based on simultaneously capturing, in a single shot, and with a monocular setup, a number of orthographic perspective views of 3D microscopic samples. An essential feature of Fourier lightfield microscopy is that the number of acquired views is low, due to the trade-off relationship existing between the number of views and their corresponding lateral resolution. Therefore, it is important to have a tool for the generation of a high number of synthesized view images, without compromising their lateral resolution. In this context we investigate here the use of a neural radiance field view synthesis method, originally developed for its use with macroscopic scenes acquired with a moving (or an array of static) digital camera(s), for its application to the images acquired with a Fourier lightfield microscope. The results obtained and presented in this paper are analyzed in terms of lateral resolution and of continuous and realistic parallax. We show that, in terms of these requirements, the proposed technique works efficiently in the case of the epi-illumination microscopy mode.

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34

Madrid-Wolff, Jorge, and Manu Forero-Shelton. "Protocol for the Design and Assembly of a Light Sheet Light Field Microscope." Methods and Protocols 2, no. 3 (July 4, 2019): 56. http://dx.doi.org/10.3390/mps2030056.

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Light field microscopy is a recent development that makes it possible to obtain images of volumes with a single camera exposure, enabling studies of fast processes such as neural activity in zebrafish brains at high temporal resolution, at the expense of spatial resolution. Light sheet microscopy is also a recent method that reduces illumination intensity while increasing the signal-to-noise ratio with respect to confocal microscopes. While faster and gentler to samples than confocals for a similar resolution, light sheet microscopy is still slower than light field microscopy since it must collect volume slices sequentially. Nonetheless, the combination of the two methods, i.e., light field microscopes that have light sheet illumination, can help to improve the signal-to-noise ratio of light field microscopes and potentially improve their resolution. Building these microscopes requires much expertise, and the resources for doing so are limited. Here, we present a protocol to build a light field microscope with light sheet illumination. This protocol is also useful to build a light sheet microscope.

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35

Mayergoyz, I. D., A. A. Adly, R. D. Gomez, and E. R. Burke. "Magnetization image reconstruction from magnetic force scanning tunneling microscopy images." Journal of Applied Physics 73, no. 10 (May 15, 1993): 5799–801. http://dx.doi.org/10.1063/1.353581.

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Медведева, Ольга Александровна, Святослав Николаевич Простаков, Николай Николаевич Тупицын, and Александра Дмитриевна Палладина. "METHODOLOGY FOR FORMING A DATABASE OF REFERENCE IMAGES OF BONE MARROW CELLS FOR THE AUTOMATED DIAGNOSIS OF ACUTE LEUKEMIA IN ONCOHEMATOLOGY." СИСТЕМНЫЙ АНАЛИЗ И УПРАВЛЕНИЕ В БИОМЕДИЦИНСКИХ СИСТЕМАХ, no. 3 (December 2, 2021): 84–89. http://dx.doi.org/10.36622/vstu.2021.20.3.011.

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В статье представлено описание факторов, влияющих на качество формирования базы эталонных изображений клеток костного мозга для диагностики острых лейкозов с применением методов компьютерной микроскопии. Отмечена важность контроля качества подготовки препаратов и микроскопа для применения в автоматизированных системах анализа изображений. Рассмотрены особенности регистрации цифровых микроскопических изображений клеток костного мозга в системах компьютерной микроскопии. Исследовано влияние фокусировки оптической системы микроскопа и уровня освещения препарата на формирование цифровых изображений клеток костного мозга. Установлены требования к условиям регистрации цифровых изображений, используемых в автоматизированных системах микроскопического анализа препаратов костного мозга. Предложена концептуальная модель базы эталонных изображений костного мозга, являющаяся основой для разработки инструментов эффективного распознавания клеток костного мозга в системах компьютерной микроскопии. Следование указанным требованиям к регистрации изображений призвано обеспечить надлежащее качество эталонной базы, что имеет непосредственной влияние на повышение точности и достоверности медицинской диагностики с применением методов компьютерной микроскопии. Результаты работы могут быть использованы в системах поддержки принятия врачебных решений при диагностике острых лейкозов The article describes the factors affecting the quality of the formation of a database of reference images of bone marrow cells for the diagnosis of acute leukemia using computer microscopy methods. The importance of quality control of specimen and microscope preparation for use in automated image analysis systems is noted. The features of registration of digital microscopic images of bone marrow cells in computer microscopy systems are considered. The effect of focusing of the optical system of the microscope and the level of illumination of the specimen on the formation of digital images of bone marrow cells is investigated. The requirements for the conditions of registration of digital images used in automated systems of microscopic analysis of bone marrow preparations have been established. A conceptual model of the base of reference images of bone marrow is proposed. It is the basis for the development of tools for effective recognition of bone marrow cells in computer microscopy systems. Following the specified requirements for image registration is designed to ensure the proper quality of the reference base of images, which has a direct impact on improving the accuracy and reliability of medical diagnostics using computer microscopy. The results of the work can be used in medical decision support systems for the diagnosis of acute leukemia

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37

Bradley, C., and J. Mancuso. "Securing and Authenticating Images with On-Image Metadata." Microscopy and Microanalysis 15, S2 (July 2009): 802–3. http://dx.doi.org/10.1017/s1431927609093040.

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38

Sijbrandij, S. J., K. F. Russell, R. C. Thomson, and M. K. Miller. "Digital Field Ion Microscopy." Microscopy and Microanalysis 4, S2 (July 1998): 88–89. http://dx.doi.org/10.1017/s1431927600020560.

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Due to environmental concerns, there is a trend to avoid the use of chemicals needed to develop negatives and to process photographic paper, and to use digital technologies instead. Digital technology also offers the advantages that it is convenient, as it enables quick access to the endresult, allows image storage and processing on computer, allows rapid hard copy output, and simplifies electronic publishing. Recently significant improvements have been made to the performance and cost of camera-sensors and printers. In this paper, field ion images recorded with two digital cameras of different resolution are compared to images recorded on standard 35 mm negative film. It should be noted that field ion images exhibit low light intensity and high contrast.Field ion images were recorded from a standard microchannel plate and a phosphor screen and had acceptance angles of ∼60°.

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39

Govil, Anurag, David M. Pallister, Li-Heng Chen, and Michael D. Morris. "Optical Sectioning Raman Microscopy." Applied Spectroscopy 45, no. 10 (December 1991): 1604–6. http://dx.doi.org/10.1366/0003702914335201.

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We describe the use of Hadamard transform Raman microscopy to acquire optically sectioned images of crystals of benzoic acid. Nearest-neighbor deblurring is used to reject out-of-focus information and sharpen the Raman images obtained from the crystal.

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40

Prabhakar, Neeraj, Markus Peurla, Olga Shenderova, and Jessica M. Rosenholm. "Fluorescent and Electron-Dense Green Color Emitting Nanodiamonds for Single-Cell Correlative Microscopy." Molecules 25, no. 24 (December 13, 2020): 5897. http://dx.doi.org/10.3390/molecules25245897.

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Correlative light and electron microscopy (CLEM) is revolutionizing how cell samples are studied. CLEM provides a combination of the molecular and ultrastructural information about a cell. For the execution of CLEM experiments, multimodal fiducial landmarks are applied to precisely overlay light and electron microscopy images. Currently applied fiducials such as quantum dots and organic dye-labeled nanoparticles can be irreversibly quenched by electron beam exposure during electron microscopy. Generally, the sample is therefore investigated with a light microscope first and later with an electron microscope. A versatile fiducial landmark should offer to switch back from electron microscopy to light microscopy while preserving its fluorescent properties. Here, we evaluated green fluorescent and electron dense nanodiamonds for the execution of CLEM experiments and precisely correlated light microscopy and electron microscopy images. We demonstrated that green color emitting fluorescent nanodiamonds withstand electron beam exposure, harsh chemical treatments, heavy metal straining, and, importantly, their fluorescent properties remained intact for light microscopy.

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41

Wan, Meixiang, Jiang Yang, Chuanfeng Zhu, and Chunli Bai. "Scanning tunnelling microscopy images of polyaniline." Thin Solid Films 208, no. 2 (February 1992): 153–55. http://dx.doi.org/10.1016/0040-6090(92)90633-m.

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42

Bailey, Jessica. "Converting Microscopy Images Into Other Formats." Microscopy Today 2, no. 5 (August 1994): 6–7. http://dx.doi.org/10.1017/s1551929500066190.

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In recent years, microscopy systems have become more capable of capturing, transferring, and manipulating electronic images. In the last issue of this publication, there was a summary of different image format types and their flexibility for use with microscopy. This article will briefly discuss converting images among different formats, which often becomes necessary when transferring images from one software application to another or creating hardcopy of the image. In order to transfer the image, either the original software has to save the image to a format which the new software or output device can read, or that new software or device has to read a format which is native to the image generating software.Sometimes (happy days), this all works out straightforwardly. Other times, transferring an image is impossible. The user then has the choice of writing his own conversion software, finding freeware, or purchasing a commercial conversion utility.

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43

Golan, G., A. J. Kenyon, C. W. Pitt, and G. Griffel. "High resolution images in acoustic microscopy." Journal of the Acoustical Society of America 95, no. 5 (May 1994): 2893–94. http://dx.doi.org/10.1121/1.409337.

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44

Yano, Fumiko, and Setsuo Nomura. "Deconvolution of scanning electron microscopy images." Scanning 15, no. 1 (1993): 19–24. http://dx.doi.org/10.1002/sca.4950150103.

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Zucker, Robert M., and Owen T. Price. "Statistical evaluation of confocal microscopy images." Cytometry 44, no. 4 (2001): 295–308. http://dx.doi.org/10.1002/1097-0320(20010801)44:4<295::aid-cyto1121>3.0.co;2-c.

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46

Strassburg, E., A. Boag, and Y. Rosenwaks. "Reconstruction of electrostatic force microscopy images." Review of Scientific Instruments 76, no. 8 (August 2005): 083705. http://dx.doi.org/10.1063/1.1988089.

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47

Vicente, Nathalie B., Javier E. Diaz Zamboni, Javier F. Adur, Enrique V. Paravani, and Víctor H. Casco. "Photobleaching correction in fluorescence microscopy images." Journal of Physics: Conference Series 90 (November 1, 2007): 012068. http://dx.doi.org/10.1088/1742-6596/90/1/012068.

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48

Brinatti Vazquez, Guillermo D., Axel M. Lacapmesure, Micaela Toscani, Sandra Martínez, and Oscar E. Martínez. "Super-Resolution Microscopy from Standard Images." Optics and Photonics News 31, no. 12 (December 1, 2020): 58. http://dx.doi.org/10.1364/opn.31.12.000058.

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49

Baker, L. R. "Measurement of Images by Comparison Microscopy." Journal of Photographic Science 38, no. 4-5 (July 1989): 127–29. http://dx.doi.org/10.1080/00223638.1989.11737089.

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Jacquemet, Guillaume. "Deep learning to analyse microscopy images." Biochemist 43, no. 5 (August 30, 2021): 60–64. http://dx.doi.org/10.1042/bio_2021_167.

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Artificial intelligence (AI)-powered algorithms are now influencing many aspects of our day-to-day life, from providing movies/music recommendations to controlling self-driving cars. These algorithms are also increasingly used in the lab to aid biomedical research. In particular, the ability to analyse and process images using AI is slowly revolutionizing the quality and quantity of data we collect from microscopy images. In fact, AI-based algorithms can now be applied to perform virtually any high-performance image analysis tasks such as classifying images, detecting and segmenting objects, aligning images or improving image quality by removing noise or increasing image resolution. This short feature article briefly underlies the principles behind using AI algorithms to analyse microscopy images with a specific focus on segmentation and denoising.

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