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Journal articles on the topic 'Microscopy tools'

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Author: Grafiati

Published: 10 December 2022

Last updated: 28 January 2023

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1

Bracker, CE, and P. K. Hansma. "Scanning tunneling microscopy and atomic force microscopy: New tools for biology." Proceedings, annual meeting, Electron Microscopy Society of America 47 (August 6, 1989): 778–79. http://dx.doi.org/10.1017/s0424820100155864.

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A new family of scanning probe microscopes has emerged that is opening new horizons for investigating the fine structure of matter. The earliest and best known of these instruments is the scanning tunneling microscope (STM). First published in 1982, the STM earned the 1986 Nobel Prize in Physics for two of its inventors, G. Binnig and H. Rohrer. They shared the prize with E. Ruska for his work that had led to the development of the transmission electron microscope half a century earlier. It seems appropriate that the award embodied this particular blend of the old and the new because it demonstrated to the world a long overdue respect for the enormous contributions electron microscopy has made to the understanding of matter, and at the same time it signalled the dawn of a new age in microscopy. What we are seeing is a revolution in microscopy and a redefinition of the concept of a microscope.Several kinds of scanning probe microscopes now exist, and the number is increasing. What they share in common is a small probe that is scanned over the surface of a specimen and measures a physical property on a very small scale, at or near the surface. Scanning probes can measure temperature, magnetic fields, tunneling currents, voltage, force, and ion currents, among others.

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2

Carragher, Bridget, Clinton S. Potter, and Fred J. Sigworth. "Software tools for macromolecular microscopy." Journal of Structural Biology 157, no. 1 (January 2007): 1–2. http://dx.doi.org/10.1016/j.jsb.2006.11.001.

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3

Smith, Ross, and Bridget Carragher. "Software tools for molecular microscopy." Journal of Structural Biology 163, no. 3 (September 2008): 224–28. http://dx.doi.org/10.1016/j.jsb.2008.03.002.

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4

Prater, C. B. "New tools for Atomic Force Microscopy." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 716–17. http://dx.doi.org/10.1017/s0424820100139950.

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The Atomic Force Microscope (AFM) has been widely used in the physics, chemistry, and materials science communities, and is becoming more common in life sciences research. To better serve the biological community, new instruments have been developed recently that combine AFM and various forms of optical microscopy including EPI-fluorescence, DIC, and confocal microscopy. In addition, new techniques like fluid Tapping Mode™ have been developed to allow gentle, non-destructive imaging of biological samples, including live specimens in physiological conditions. Other new techniques can provide information about sample elasticity or molecular adhesion along with nanometerscale topography measurements.Until recently, most AFMs scanned the sample under a stationary probe using a small piezoelectric scanner. This arrangement placed serious limits on the size and type of sample that could be used as a sample substrate. Now instruments have been developed that scan the AFM probe over a fixed sample that then allows imaging of larger, more convenient sample substrates, including cover slips, slides, and even petri dishes.

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5

Ai, R. "A Microscope-Compatible Auger Electron Spectrometer." Proceedings, annual meeting, Electron Microscopy Society of America 49 (August 1991): 992–93. http://dx.doi.org/10.1017/s0424820100089275.

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With the recent development of ultra-high vacuum high resolution electron microscopes (UHV-HREM), electron microscopes have become valuable tools for surface studies. Techniques such as surface profile image, surface sensitive plane view, and reflection electron microscopy have been developed to take full advantage of the atomic resolution of HREM to study surface structures. However a complete surface study requires information on both the surface structure and surface chemistry. Therefore in order to turn an electron microscope into a real surface analytical tool, the challenge is to develop a microscopecompatible, surface sensitive tool for in-situ surface chemical analysis.

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6

Brama, Elisabeth, Christopher J. Peddie, Gary Wilkes, Yan Gu, Lucy M. Collinson, and Martin L. Jones. "ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy." Wellcome Open Research 1 (December 13, 2016): 26. http://dx.doi.org/10.12688/wellcomeopenres.10299.1.

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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.

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7

Graef, M. De, N. T. Nuhfer, and N. J. Cleary. "Implementation Of A Digital Microscopy Teaching Environment." Microscopy and Microanalysis 5, S2 (August 1999): 4–5. http://dx.doi.org/10.1017/s1431927600013349.

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The steady evolution of computer controlled electron microscopes is dramatically changing the way we teach microscopy. For today’s microscopy student, an electron microscope may be just another program on the desktop of whatever computer platform he or she uses. This is reflected in the use of the term Desktop Microscopy. The SEM in particular has become a mouse and keyboard controlled machine, and running the microscope is not very different from using a drawing program or a word processor. Transmission electron microscopes are headed in the same direction.While one can debate whether or not it is wise to treat an SEM or a TEM as just another black-box computer program, it is a fact that these machines are here to stay, which means that microscopy educators must adapt their traditional didactic tools and methods. One way to bring electron microscopes into the classroom is through the use of remote control software packages, such as Timbuktu Pro or PC-Anywhere. The remote user essentially opens a window containing the desktop of the microscope control computer and has all functions available. On microscopes with specialized graphics boards, integration of the image and control display for remote operation may not be straightforward, and often requires the purchase of additional graphics boards for the remote machine.

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8

Frigault, M. M., J. Lacoste, J. L. Swift, and C. M. Brown. "Live-cell microscopy - tips and tools." Journal of Cell Science 122, no. 6 (March 4, 2009): 753–67. http://dx.doi.org/10.1242/jcs.033837.

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9

Budich, Christian, Jonathan West, Peter Lampen, and Volker Deckert. "Force microscopy analysis using chemometric tools." Analytical and Bioanalytical Chemistry 390, no. 5 (December 24, 2007): 1253–60. http://dx.doi.org/10.1007/s00216-007-1722-0.

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10

Shri, D. N. Awang, J. Ramli, N. A. Alang, and M. M. Mahat. "Influence of Surface Pretreatment on Carbon Coating of Cutting Tools Using PVD." Applied Mechanics and Materials 236-237 (November 2012): 530–35. http://dx.doi.org/10.4028/www.scientific.net/amm.236-237.530.

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Alumina (Al2O3) cutting tools have been coated with carbon coating using physical vapor deposition (PVD) to improve its wear resistance. The cutting tools were subjected to surface pretreatments namely blasting and acid etching to improve the coating adhesion onto the substrates. The effects of pretreatments on the cutting tools topography prior to deposition were investigated using atomic force microscopy (AFM) while the surface morphology was investigated using scanning electron microscopy (SEM). The rake angle of the coated cutting tool and surface roughness of the cutting edge were investigated using infinite focus microscope. The adhesion strength of the carbon coating was investigated using microscratch. This study shows that although the coating were deposited evenly on all samples, the cutting tool that was blasted prior to deposition has better adhesion strength when compared to acid etching and no-pretreatment.

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11

O’Keefe, M. A., J. Taylor, D. Owen, B. Crowley, K. H. Westmacott, W. Johnston, and U. Dahmen. "Remote On-Line Control of a High-Voltage in situ Transmission Electron Microscope with A Rational User Interface." Proceedings, annual meeting, Electron Microscopy Society of America 54 (August 11, 1996): 384–85. http://dx.doi.org/10.1017/s0424820100164386.

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Remote on-line electron microscopy is rapidly becoming more available as improvements continue to be developed in the software and hardware of interfaces and networks. Scanning electron microscopes have been driven remotely across both wide and local area networks. Initial implementations with transmission electron microscopes have targeted unique facilities like an advanced analytical electron microscope, a biological 3-D IVEM and a HVEM capable of in situ materials science applications. As implementations of on-line transmission electron microscopy become more widespread, it is essential that suitable standards be developed and followed. Two such standards have been proposed for a high-level protocol language for on-line access, and we have proposed a rational graphical user interface. The user interface we present here is based on experience gained with a full-function materials science application providing users of the National Center for Electron Microscopy with remote on-line access to a 1.5MeV Kratos EM-1500 in situ high-voltage transmission electron microscope via existing wide area networks. We have developed and implemented, and are continuing to refine, a set of tools, protocols, and interfaces to run the Kratos EM-1500 on-line for collaborative research. Computer tools for capturing and manipulating real-time video signals are integrated into a standardized user interface that may be used for remote access to any transmission electron microscope equipped with a suitable control computer.

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12

Becker, John H. "Virtual Microscopes in Podiatric Medical Education." Journal of the American Podiatric Medical Association 96, no. 6 (November 1, 2006): 518–24. http://dx.doi.org/10.7547/0960518.

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In many medical schools, microscopes are being replaced as teaching tools by computers with software that emulates the use of a light microscope. This article chronicles the adoption of “virtual microscopes” by a podiatric medical school and presents the results of educational research on the effectiveness of this adoption in a histology course. If the trend toward virtual microscopy in education continues, many 21st-century physicians will not be trained to operate a light microscope. The replacement of old technologies by new is discussed. The fundamental question is whether all podiatric physicians should be trained in the use of a particular tool or only those who are likely to use it in their own practice. (J Am Podiatr Med Assoc 96(6): 518–524, 2006)

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13

Schorb, Martin, Isabella Haberbosch, Wim J. H. Hagen, Yannick Schwab, and David N. Mastronarde. "Software tools for automated transmission electron microscopy." Nature Methods 16, no. 6 (May 13, 2019): 471–77. http://dx.doi.org/10.1038/s41592-019-0396-9.

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14

Thomas, C., P. DeVries, J. Hardin, and J. G. White. "Software tools for 4D live cell microscopy." Proceedings, annual meeting, Electron Microscopy Society of America 54 (August 11, 1996): 620–21. http://dx.doi.org/10.1017/s0424820100165562.

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The Integrated Microscopy Resource has developed a trio of Macintosh-based software tools which allow the user to collect digital 4D microscopy (3D over time) of live cells. To demonstrate the program, high-resolution Nomarski DIC images were collected from an inverted microscope using a video camera. The output of the camera can be averaged and contrast-enhanced before the resulting signal is digitized using a framegrabber card installed in a Macintosh computer (Figure 1). Collection, subsequent processing, and analysis of the resulting data sets are handled by the following three software tools:4D Acquisition Software - This IMR-designed software system is based on the popular shareware image processing program “NIH-Image” (author Wayne Rasband, NIH) and controls the actual image acquisition through a series of graphic user interfaces. A framegrabber card, a stage drive motor, and an illumination shutter are manipulated to allow the imaging of either a single focal-plane of the specimen over time, or the acquisition of 3-dimensional volumes at each timepoint. After selecting the top and bottom of the sample, the user can specify the number of focal planes to acquire, the increment for the focus motor between focal planes, the number of timepoints to collect, and a file format in which to save the images. The software will automatically move through the sample from the top to the bottom gathering images of each focal plane as it goes. The result is a stack of images representing the 3D structure of the sample. The software will wait a defined amount of time and the process will be repeated for as many timepoints as the user has designated.

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15

Hunt, J. A., and C. Meyer. "Network Control and Tools for Electron Microscopy." Microscopy and Microanalysis 4, S2 (July 1998): 14–15. http://dx.doi.org/10.1017/s1431927600020195.

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Recently there has been great interest in creating Internet and Intranet tools for electron microscopy. We can somewhat arbitrarily divide the goals of these tools into three categories: (1) Service lab interaction, (2) Laboratory extension, (3) Teaching & outreach. The service lab wants to disseminate the results of experiments quickly to its customers. Sometimes it needs to do this during the experiments for verification that the experiments are being correctly performed, but most collaboration problems can be solved with a phone discussion while looking at the same image. This level of interactivity is not sufficient for the laboratory extension community that wants real time experimental results and perhaps even controls of the equipment projected to a remote location. Finally, several groups have expressed interest in bringing observation and control of instrumentation into the classroom to potentially many computers and potentially many different displays of the experiment in progress.

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16

Deschamps, Joran, Markus Mund, Daniel Schroeder, and Jonas Ries. "Open-Source Tools for Automated Localization Microscopy." Biophysical Journal 118, no. 3 (February 2020): 147a. http://dx.doi.org/10.1016/j.bpj.2019.11.924.

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17

Simok, Anna Alicia, Fazlina Kasim, Siti Nurma Hanim Hadie, Husnaida Abdul Manan@Sulong, Muhamad Saiful Bahri Yusoff, Nor Farid Mohd Noor, and Mohd Asnizam Asari. "Knowledge Acquisition and Satisfaction of Virtual Microscopy Usage Among Medical Students of Universiti Sains Malaysia." Education in Medicine Journal 13, no. 4 (December 30, 2021): 43–55. http://dx.doi.org/10.21315/eimj2021.13.4.4.

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The virtual microscope has been employed as an adjunct tool to teach optical microscopy for histology learning in medical schools. However, there is no reliable evidence in the literature that virtual and optical microscopy impacts students’ learning. This study focuses on comparing two different methods in learning histology in Universiti Sains Malaysia, namely virtual microscopy and optical microscopy, with regard to medical students’ knowledge acquisition and satisfaction levels. A total number of 120 medical students, consisting of 53 first-year and 67 second-year students, were recruited. The students were divided into virtual microscopy and optical microscopy groups. During the one-day intervention, all students attended a pre-requisite lecture on “Histology of the Eye”, a slide demonstration and a hands-on session using a designated microscope. Students’ knowledge acquisition was evaluated through a pre- and post-practical evaluation and their satisfaction level on learning histology using respective learning tools was measured. The study revealed that the optical and virtual microscopy groups showed significant improvement from the pre- to post-practical tests scores with p < 0.001, respectively. However, the mean increment was higher in virtual microscopy (38.51%) than in optical microscopy (35.08%). Furthermore, the virtual microscopy group had a significantly higher satisfaction score towards the learning tool than the optical microscopy group, p = 0.008. The knowledge acquisition of the virtual microscopy group was equal to the optical microscopy group as they were shown to have a similar improvement in the test scores, comprehension level and learning ability. However, students were nonetheless satisfied with the usage of virtual microscopy as a learning tool.

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18

Rocha, Márcio S., and Oscar N. Mesquita. "New tools to study biophysical properties of single molecules and single cells." Anais da Academia Brasileira de Ciências 79, no. 1 (March 2007): 17–28. http://dx.doi.org/10.1590/s0001-37652007000100003.

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We present a review on two new tools to study biophysical properties of single molecules and single cells. A laser incident through a high numerical aperture microscope objective can trap small dielectric particles near the focus. This arrangement is named optical tweezers. This technique has the advantage to permit manipulation of a single individual object. We use optical tweezers to measure the entropic elasticity of a single DNA molecule and its interaction with the drug Psoralen. Optical tweezers are also used to hold a kidney cell MDCK away from the substrate to allow precise volume measurements of this single cell during an osmotic shock. This procedure allows us to obtain information about membrane water permeability and regulatory volume increase. Defocusing microscopy is a recent technique invented in our laboratory, which allows the observation of transparent objects, by simply defocusing the microscope in a controlled way. Our physical model of a defocused microscope shows that the image contrast observed in this case is proportional to the defocus distance and to the curvature of the transparent object. Defocusing microscopy is very useful to study motility and mechanical properties of cells. We show here the application of defocusing microscopy to measurements of macrophage surface fluctuations and their influence on phagocytosis.

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19

Klinger, Miloslav, and Aleš Jäger. "Crystallographic Tool Box(CrysTBox): automated tools for transmission electron microscopists and crystallographers." Journal of Applied Crystallography 48, no. 6 (October 21, 2015): 2012–18. http://dx.doi.org/10.1107/s1600576715017252.

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Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly,diffractGUIdetermines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly,ringGUIidentifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. BothdiffractGUIandringGUIemploy methods of computer vision for a fast, robust and accurate analysis. Thirdly,cellVieweris an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes.diffractGUIandcellViewercan be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly fromDigitalMicrograph(Gatan Inc.).

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20

Lee, Andrew K. "A Trend Towards Computer Aided Microscopy." Microscopy Today 5, no. 4 (May 1997): 10–11. http://dx.doi.org/10.1017/s1551929500061368.

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As the dawn of the next millennium approaches, the light microscope enters its fifth century of use, while the personal computer barely enters its third decade.When Antony van Leeuwenhoek peered through his self made hand crafted microscope and documented the first observations of bacteria and cells, much of microbiology and cell biology was born. When the personal computer became a tool in modern science, molecular cell biologists were well into the age of human genetic engineering.While the rise and acceptance into scientific importance of the microscope and the personal computer represent vastly different periods of sophistication in modem science, the combination of these two important scientific tools for computer aided microscopy (CAM) clearly provides bold uncharted potentials and opportunities for medicine, biomedical research, and industry in the future century to come.

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21

Barlow, Steven B. "CD-ROMs as Teaching Tools for Microscopy: A Survey of Microscopy-TutorTM Users." Microscopy and Microanalysis 9, S02 (July 24, 2003): 1264–65. http://dx.doi.org/10.1017/s1431927603446321.

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22

Dougherty, Matthew T. "3d Visualization Tools." Microscopy and Microanalysis 7, S2 (August 2001): 770–71. http://dx.doi.org/10.1017/s1431927600029925.

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The tutorial presents 3D visualization as implemented at NCMI: beginning with a brief overview of the history and philosophy of scientific visualization, proceeding to a description of general methodologies used throughout the field of visualization, and concluding with specific applications in electron microscopy, confocal microscopy and x-ray diffraction. The majority of the tutorial uses biological examples of visualization to demonstrate concepts and tools.History and Philosophy: Effective scientific visualization presents data in a simple, accurate conceptual formulation. Over the last one hundred years there has been a sea change in its economics caused by digital computers: beginning with calculated tables that were manually plotted, proceeding to two dimensional image graphics, and most recently multivariate 3D interactive graphics. The capability of scientific visualization has been greatly facilitated by the evolution of computers; particularly over the last ten years the 3D visualization of biological structures is quickly becoming a necessity for analysis, conceptualization, and presentations.

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23

Opazo, Felipe, Matthew Levy, Michelle Byrom, Christina Schäfer, Claudia Geisler, Teja W. Groemer, Andrew D. Ellington, and Silvio O. Rizzoli. "Aptamers as potential tools for super-resolution microscopy." Nature Methods 9, no. 10 (September 27, 2012): 938–39. http://dx.doi.org/10.1038/nmeth.2179.

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24

Carragher, Bridget, and Pawel A. Penczek. "Analytical Methods and Software Tools for Macromolecular Microscopy." Journal of Structural Biology 144, no. 1-2 (October 2003): 1–3. http://dx.doi.org/10.1016/j.jsb.2003.10.018.

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25

Langhorst, M., A. Yakushevska, and B. Lich. "New Tools for Correlative Light and Electron Microscopy." Microscopy and Microanalysis 19, S2 (August 2013): 1344–45. http://dx.doi.org/10.1017/s1431927613008714.

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26

Rodriguez, Erik A., John T. Ngo, Sakina F. Palida, Stephen R. Adams, Mason R. Mackey, Ranjan Ramachandra, Mark H. Ellisman, and Roger Y. Tsien. "New Molecular Tools for Light and Electron Microscopy." Microscopy and Microanalysis 21, S3 (August 2015): 1–2. http://dx.doi.org/10.1017/s143192761500080x.

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27

Tsien, Roger Y. "New Molecular Tools for Light and Electron Microscopy." Microscopy and Microanalysis 21, S2 (August 2015): 40–41. http://dx.doi.org/10.1017/s1431927615014567.

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28

Mitchell, D. R. G., and B. Schaffer. "Scripting-customised microscopy tools for Digital Micrograph™." Ultramicroscopy 103, no. 4 (July 2005): 319–32. http://dx.doi.org/10.1016/j.ultramic.2005.02.003.

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29

Wait, Eric C., Michael A. Reiche, and Teng-Leong Chew. "Hypothesis-driven quantitative fluorescence microscopy – the importance of reverse-thinking in experimental design." Journal of Cell Science 133, no. 21 (November 1, 2020): jcs250027. http://dx.doi.org/10.1242/jcs.250027.

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ABSTRACTOne of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.

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Yang, Pucheng, Zheng Li, Yi Yang, Rui Li, Lufei Qin, and Yunhao Zou. "Effects of Electron Microscope Parameters and Sample Thickness on High Angle Annular Dark Field Imaging." Scanning 2022 (March 20, 2022): 1–9. http://dx.doi.org/10.1155/2022/8503314.

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Scanning transmission electron microscopy (STEM) developed into a very important characterization tool for atomic analysis of crystalline specimens. High-angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) has become one of the most powerful tools to visualize material structures at atomic resolution. However, the parameter of electron microscope and sample thickness is the important influence factors on HAADF-STEM imaging. The effect of convergence angle, spherical aberration, and defocus to HAADF imaging process has been analyzed through simulation. The applicability of two HAADF simulation software has been compared, and suggestions for their usage have been given.

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Flores, Daniela P., and Timothy C. Marzullo. "The construction of high-magnification homemade lenses for a simple microscope: an easy “DIY” tool for biological and interdisciplinary education." Advances in Physiology Education 45, no. 1 (March 1, 2021): 134–44. http://dx.doi.org/10.1152/advan.00127.2020.

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The rise of microscopy in the seventeenth century allowed scientists to discover a new world of microorganisms and achieve great physiological advances. One of the first microscopes of the epoch was Antonie van Leeuwenhoek’s microscope, a deceptively simple device that contains a single ball lens housed in a metal plate allowing the observation of samples at up to ×250 magnification. Such magnification was much greater than that achieved by rudimentary compound microscopes of the era, allowing for the discovery of microscopic, single-celled life, an achievement that marked the study of biology up to the nineteenth century. Since Leeuwenhoek’s design uses a single ball lens, it is possible to fabricate variations for educational activities in physics and biology university and high school classrooms. A fundamental problem, however, with home-built microscopes is that it is difficult to work with glass. We developed a simple protocol to make ball lenses of glass and gelatin with high magnification that can be done in a university/high school classroom, and we designed an optimized support for focusing and taking photographs with a smartphone. The protocol details a simple, easily accessible, low-cost, and effective tool for the observation of microscopic samples, possible to perform anywhere without the need for a laboratory or complex tools. Our protocol has been implemented in classrooms in Chile to a favorable reception.

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32

Ulfig, Robert M., David J. Larson, David A. Reinhard, and Thomas F. Kelly. "Atom-Probe Tomography – Different Analysis Tools for Three-Dimensional Atomic-Resolution Data." Microscopy Today 16, no. 6 (November 2008): 10–13. http://dx.doi.org/10.1017/s1551929500062301.

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Like no other microscopy technique, atom-probe tomography (APT) requires detailed data analysis algorithms specific to the knowledge desired, as the data are both complex due to their three-dimensional nature and can only be collected in a digital format. With recent increases in speed and field of view available in contemporary instruments like the Imago Scientific Instruments LEAP™ microscopes, these challenges and significant benefits are exacerbated. In practice, ‘data collection’ in APT, as understood in complementary techniques like scanning electron microscopy (SEM) or transmission electron microscopy (TEM), does not even begin until after the atom-probe experiment is over and the microscopist leaves the laboratory. The sample is prepared into the appropriate needle-shaped geometry, field evaporated atom by atom, and the ‘experiment’ part of the specimen analysis is over as soon as the ions are detected and stored in a digital file.

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33

Cellucci, Thomas A. "Tools for Nanomanipulation and Nanometrology." Microscopy and Microanalysis 10, S02 (August 2004): 538–39. http://dx.doi.org/10.1017/s1431927604887488.

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34

Isikman, Serhan O., Alon Greenbaum, Myungjun Lee, Waheb Bishara, Onur Mudanyali, Ting-Wei Su, and Aydogan Ozcan. "Modern Trends in Imaging VIII: Lensfree Computational Microscopy Tools for Cell and Tissue Imaging at the Point-of-Care and in Low-Resource Settings." Analytical Cellular Pathology 35, no. 4 (2012): 229–47. http://dx.doi.org/10.1155/2012/842407.

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The recent revolution in digital technologies and information processing methods present important opportunities to transform the way optical imaging is performed, particularly toward improving the throughput of microscopes while at the same time reducing their relative cost and complexity. Lensfree computational microscopy is rapidly emerging toward this end, and by discarding lenses and other bulky optical components of conventional imaging systems, and relying on digital computation instead, it can achieve both reflection and transmission mode microscopy over a large field-of-view within compact, cost-effective and mechanically robust architectures. Such high throughput and miniaturized imaging devices can provide a complementary toolset for telemedicine applications and point-of-care diagnostics by facilitating complex and critical tasks such as cytometry and microscopic analysis of e.g., blood smears, Pap tests and tissue samples. In this article, the basics of these lensfree microscopy modalities will be reviewed, and their clinically relevant applications will be discussed.

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35

Lambin, Philippe. "Featuring the State of the Art of Nanosciences in Belgium." Applied Sciences 10, no. 16 (August 6, 2020): 5427. http://dx.doi.org/10.3390/app10165427.

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36

Ekstrom, James. "Digital Imaging in K-12 Biology." Microscopy Today 10, no. 6 (November 2002): 32–35. http://dx.doi.org/10.1017/s1551929500058508.

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K-12 instruction in biology has traditionally taken a very descriptive approach. This is in marked contrast to quantitative as well as qualitative way of looking at things in physics and chemistry. This qualitative/descriptive approach even extends into the iaboratory portion of the biological course. One way to introduce a more quantitative approach is in the microscopy portion of the biology curriculum. Because cellular structure is primarily a microscopic province It makes sense to introduce students to the different microscopic tools such as TEM and SEM, as well as the light microscope that are used to investigate cell structure.

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Etheridge, Thomas J., Antony M. Carr, and Alex D. Herbert. "GDSC SMLM: Single-molecule localisation microscopy software for ImageJ." Wellcome Open Research 7 (September 29, 2022): 241. http://dx.doi.org/10.12688/wellcomeopenres.18327.1.

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Single-molecule localisation microscopy (SMLM) uses software to extract super-resolved positions from microscope images of fluorescent molecules. These localisations can then be used to render super-resolution images or analysed to extract information about molecular behaviour. The GDSC SMLM software provides a set of tools for analysing SMLM data in a single cross-platform environment. The software identifies fluorescent molecules in raw microscope images and localises their positions using stages of spot detection, spot fitting and spot rejection. The resulting localisation data set can then be visualised, cropped and filtered. A suite of downstream analysis tools enable the user to perform single-particle tracking, cluster analysis and drift correction. In addition, GDSC SMLM also provides utility tools that enable modelling of EM-CCD and sCMOS cameras as well as point spread functions (PSFs) for data simulation. The software is written in Java and runs as a collection of plugins for the ImageJ software.

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HERNÁNDEZ-HERNÁNDEZ, H. M., J. J. CHANONA-PÉREZ, E. TERRÉS, A. VEGA, P. LIGERO, R. R. FARRERA-REBOLLO, and S. VILLANUEVA. "MICROSCOPY AND SPECTROSCOPY TOOLS FOR THE DESCRIPTION OF DELIGNIFICATION." Cellulose Chemistry and Technology 53, no. 1-2 (February 28, 2019): 87–97. http://dx.doi.org/10.35812/cellulosechemtechnol.2019.53.10.

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Shukla, Alpesh. "New electron microscopy tools for characterizing air-sensitive samples." Microscopy and Microanalysis 27, S1 (July 30, 2021): 1340–41. http://dx.doi.org/10.1017/s1431927621004992.

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Evans, Conor L. "Nonlinear Optical Microscopy for Melanoma: Challenges, Tools and Opportunities." Photochemistry and Photobiology 94, no. 4 (April 24, 2018): 624–32. http://dx.doi.org/10.1111/php.12916.

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Okada, Darren H., Scott W. Binder, Christopher L. Felten, Jonathan S. Strauss, and Alberto M. Marchevsky. "“Virtual Microscopy” and the Internet as Telepathology Consultation Tools." American Journal of Dermatopathology 21, no. 6 (December 1999): 525. http://dx.doi.org/10.1097/00000372-199912000-00004.

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Dolman, Nick J., Kevin M. Chambers, Bhaskar Mandavilli, Robert H. Batchelor, and Michael S. Janes. "Tools and techniques to measure mitophagy using fluorescence microscopy." Autophagy 9, no. 11 (November 3, 2013): 1653–62. http://dx.doi.org/10.4161/auto.24001.

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Johnson, Merrell A. "Exploring the cantilever: teaching tools for atomic force microscopy." European Journal of Physics 41, no. 4 (June 16, 2020): 045807. http://dx.doi.org/10.1088/1361-6404/ab92d4.

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Sutriyono, Widodo, and Retno Suryandari. "Addition of Illuminator Fiber Optic to Produce 3 Dimension Effects in Micrographic Observation Using Upright Microscope." Proceeding International Conference on Science and Engineering 3 (April 30, 2020): 493–96. http://dx.doi.org/10.14421/icse.v3.551.

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Microscope is one of the tools used in practicums with high intensity. The use of a microscope adjusts to the object to be observed in order to obtain optimal micrographic results. Stereo microscopes are used to observe three-dimensional objects. Upright microscopes are used to observe two-dimensional objects. This study aims to combine the two advantages of stereo microscopy that can produce three-dimensional micrography with the advantages of an upright microscope that has a high total magnification. The method used in this study is an experimental method by adding an optical fiber illuminator in the use of an upright microscope and then applying it in various observations. The conclusion of this research is the addition of an optical fiber illuminator in observations using an upright microscope can replace the function of a stereo microscope; can produce three-dimensional effects and increase magnification in Daphnia magna micrographic observations.

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Simard-Normandin, M., L. Weaver, D. Vacca, D. Rogers, A. Vitkin, and T. Tiedje. "Analytical microscopy of titanium nitride." Canadian Journal of Physics 69, no. 3-4 (March 1, 1991): 290–97. http://dx.doi.org/10.1139/p91-049.

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We report on microscopy tools for the in-situ analysis of TiN in microelectronic devices. Scanning tunnelling microscopy and Raman microprobe spectroscopy are compared with scanning and transmission electron microscopy.

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Bright, David S. "Software Tools for Examination of Microanalytical Images." Proceedings, annual meeting, Electron Microscopy Society of America 48, no. 2 (August 12, 1990): 116–17. http://dx.doi.org/10.1017/s042482010013417x.

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Image processing for enhancement and interpretation is a powerful tool for microscopy and microanalysis. Digital images are arrays of picture elements or pixels each having a coordinate (location) and a value. Two dimensional arrays with single intensity value (monochrome) or triple intensity values (color) pixels are in common use. Software tools and techniques are now available for desk top computers at reasonable cost that allow visualization of higher dimensional arrays and multivalued pixels. The following examples illustrate the application of these tools to microanalysis.Short image sequences (movies) are useful for showing dynamic effects such as the drift of an electron microscope stage with time or the interior of a sample eroded by sputtering on an ion microscope.The values of the pixels of registered images or x-ray maps can be accumulated in a multidimensional histogram (Concentration Histogram Image or CHI). The number of registered maps determines the dimensionality of the histogram.

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Burdíková, Z., M. Čapek, P. Ostasou, EAD Mitchell, J. Machač, and L. Kubínová. "Confocal Laser Scanning Microscopy and Two Photon Excitation Microscopy as Tools to Study Testate Amoebae." Microscopy and Microanalysis 16, S2 (July 2010): 1142–43. http://dx.doi.org/10.1017/s1431927610060897.

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Krishnamurthy, Savitri, Jonathan Quincy Brown, Nicusor Iftimia, Richard M. Levenson, and Milind Rajadhyaksha. "Ex Vivo Microscopy: A Promising Next-Generation Digital Microscopy Tool for Surgical Pathology Practice." Archives of Pathology & Laboratory Medicine 143, no. 9 (July 11, 2019): 1058–68. http://dx.doi.org/10.5858/arpa.2019-0058-ra.

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Context.— The rapid evolution of optical imaging modalities in recent years has opened the opportunity for ex vivo tissue imaging, which has significant implications for surgical pathology practice. These modalities have promising potential to be used as next-generation digital microscopy tools for examination of fresh tissue, with or without labeling with contrast agents. Objective.— To review the literature regarding various types of ex vivo optical imaging platforms that can generate digital images for tissue recognition with potential for utilization in anatomic pathology clinical practices. Data Sources.— Literature relevant to ex vivo tissue imaging obtained from the PubMed database. Conclusions.— Ex vivo imaging of tissues can be performed by using various types of optical imaging techniques. These next-generation digital microscopy tools have a promising potential for utilization in surgical pathology practice.

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Parvin, B., D. Agarwal, D. Owen, M. A. O'Keefe, K. H. Westmacott, U. Dahmen, and R. Gronsky. "A project for on-line remote control of a high-voltage TEM." Proceedings, annual meeting, Electron Microscopy Society of America 53 (August 13, 1995): 82–83. http://dx.doi.org/10.1017/s0424820100136787.

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On-line microscopy commenced with demonstrations for biological and SEM applications. For materials science, a project has recently been established to provide users of the NCEM with remote online access to a 1.5MeV Kratos EM-1500 high-voltage transmission electron microscope via existing wide area networks. Within this project we are developing and implementing a set of tools, protocols, and interfaces to bring transmission electron microscopy on-line for collaborative research. Initially applied to the Kratos, the project will provide increased utilization of this unique instrument with its heretofore restricted access due to its sensitive components and demand for sophisticated operator skills. Additionally, the project will provide computer tools for capturing and manipulating real-time audio and video signals. These tools will be integrated into a standardized user interface that may be used for remote access to any transmission electron microscope equipped with a suitable control computer.Dynamic study of a specimen in an electron microscope requires continuous adjustment of specimen position and orientation under the beam, illumination conditions, focus adjustments, and corrections for aberrations, all based upon the video signal coming from the imaging system.

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Mabaso, Matsilele Aubrey, Daniel James Withey, and Bhekisipho Twala. "SPOT DETECTION METHODS IN FLUORESCENCE MICROSCOPY IMAGING: A REVIEW." Image Analysis & Stereology 37, no. 3 (December 6, 2018): 173. http://dx.doi.org/10.5566/ias.1690.

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Fluorescence microscopy imaging has become one of the essential tools used by biologists to visualize and study intracellular particles within a cell. Studying these particles is a long-term research effort in the field of microscopy image analysis, consisting of discovering the relationship between the dynamics of particles and their functions. However, biologists are faced with challenges such as the counting and tracking of these intracellular particles. To overcome the issues faced by biologists, tools which can extract the location and motion of these particles are essential. One of the most important steps in these analyses is to accurately detect particle positions in an image, termed spot detection. The detection of spots in microscopy imaging is seen as a critical step for further quantitative analysis. However, the evaluation of these microscopic images is mainly conducted manually, with automated methods becoming popular. This work presents some advances in fluorescence microscopy image analysis, focusing on the detection methods needed for quantifying the location of these spots. We review several existing detection methods in microscopy imaging, along with existing synthetic benchmark datasets and evaluation metrics.

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