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Journal articles on the topic 'Microscopy and tomography'

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Author: Grafiati

Published: 6 September 2023

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1

van der Krift, Theo, Ulrike Ziese, Willie Geerts, and Bram Koster. "Computer-Controlled Transmission Electron Microscopy: Automated Tomography." Microscopy and Microanalysis 7, S2 (August 2001): 968–69. http://dx.doi.org/10.1017/s1431927600030919.

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The integration of computers and transmission electron microscopes (TEM) in combination with the availability of computer networks evolves in various fields of computer-controlled electron microscopy. Three layers can be discriminated: control of electron-optical elements in the column, automation of specific microscope operation procedures and display of user interfaces. The first layer of development concerns the computer-control of the optical elements of the transmission electron microscope (TEM). Most of the TEM manufacturers have transformed their optical instruments into computer-controlled image capturing devices. Nowadays, the required controls for the currents through lenses and coils of the optical column can be accessed by computer software. The second layer of development is aimed toward further automation of instrument operation. For specific microscope applications, dedicated automated microscope-control procedures are carried out. in this paper, we will discuss our ongoing efforts on this second level towards fully automated electron tomography. The third layer of development concerns virtual- or telemicroscopy. Most telemicroscopy applications duplicate the computer-screen (with accessory controls) at the microscope-site to a computer-screen at another site. This approach allows sharing of equipment, monitoring of instruments by supervisors, as well as collaboration between experts at remote locations.Electron tomography is a three-dimensional (3D) imaging method with transmission electron microscopy (TEM) that provides high-resolution 3D images of structural arrangements. with electron tomography a series of images is acquired of a sample that is tilted over a large angular range (±70°) with small angular tilt increments.

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Wang, Xinkun, Kedi Xiong, Xin Jin, and Sihua Yang. "Tomography-assisted Doppler photoacoustic microscopy: proof of concept." Chinese Optics Letters 18, no. 10 (2020): 101702. http://dx.doi.org/10.3788/col202018.101702.

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3

Butz, T., D. Lehmann, T. Reinert, D. Spemann, and J. Vogt. "Ion Microscopy and Tomography." Acta Physica Polonica A 100, no. 5 (November 2001): 603–13. http://dx.doi.org/10.12693/aphyspola.100.603.

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4

Wang, Lihong V. "Photoacoustic Tomography and Microscopy." Optics and Photonics News 19, no. 7 (July 1, 2008): 36. http://dx.doi.org/10.1364/opn.19.7.000036.

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5

Xiu, Peng, Xin Zhou, Cuifang Kuang, Yingke Xu, and Xu Liu. "Controllable tomography phase microscopy." Optics and Lasers in Engineering 66 (March 2015): 301–6. http://dx.doi.org/10.1016/j.optlaseng.2014.10.001.

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6

Borg, Thomas K., James A. Stewart, and Michael A. Sutton. "Imaging the Cardiovascular System: Seeing Is Believing." Microscopy and Microanalysis 11, no. 3 (May 12, 2005): 189–99. http://dx.doi.org/10.1017/s1431927605050439.

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From the basic light microscope through high-end imaging systems such as multiphoton confocal microscopy and electron microscopes, microscopy has been and will continue to be an essential tool in developing an understanding of cardiovascular development, function, and disease. In this review we briefly touch on a number of studies that illustrate the importance of these forms of microscopy in studying cardiovascular biology. We also briefly review a number of imaging modalities such as computed tomography, (CT) Magnetic resonance imaging (MRI), ultrasound, and positron emission tomography (PET) that, although they do not fall under the realm of microscopy, are imaging modalities that greatly complement microscopy. Finally we examine the role of proper imaging system calibration and the potential importance of calibration in understanding biological tissues, such as the cardiovascular system, that continually undergo deformation in response to strain.

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Carlson, David B., Jeff Gelb, Vadim Palshin, and James E. Evans. "Laboratory-Based Cryogenic Soft X-Ray Tomography with Correlative Cryo-Light and Electron Microscopy." Microscopy and Microanalysis 19, no. 1 (January 18, 2013): 22–29. http://dx.doi.org/10.1017/s1431927612013827.

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AbstractHere we present a novel laboratory-based cryogenic soft X-ray microscope for whole cell tomography of frozen hydrated samples. We demonstrate the capabilities of this compact cryogenic microscope by visualizing internal subcellular structures of Saccharomyces cerevisiae cells. The microscope is shown to achieve better than 50 nm half-pitch spatial resolution with a Siemens star test sample. For whole biological cells, the microscope can image specimens up to 5 μm thick. Structures as small as 90 nm can be detected in tomographic reconstructions following a low cumulative radiation dose of only 7.2 MGy. Furthermore, the design of the specimen chamber utilizes a standard sample support that permits multimodal correlative imaging of the exact same unstained yeast cell via cryo-fluorescence light microscopy, cryo-soft X-ray microscopy, and cryo-transmission electron microscopy. This completely laboratory-based cryogenic soft X-ray microscope will enable greater access to three-dimensional ultrastructure determination of biological whole cells without chemical fixation or physical sectioning.

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Smallwood, R., P. Metherall, D. Hose, M. Delves, H. Pollock, A. Hammiche, C. Hodges, V. Mathot, and P. Willcocks. "Tomographic imaging and scanning thermal microscopy: thermal impedance tomography." Thermochimica Acta 385, no. 1-2 (March 2002): 19–32. http://dx.doi.org/10.1016/s0040-6031(01)00705-5.

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9

Ko, Dae-Sik. "Multiple-Transducer Scheme for Scanning Tomographic Acoustic Microscopy Using Transverse Waves." Ultrasonic Imaging 19, no. 4 (October 1997): 294–304. http://dx.doi.org/10.1177/016173469701900405.

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We propose a new type of multiple-transducer scheme with functions of multiple-angle and multiple-frequency tomography for scanning tomographic acoustic microscopy (STAM) using transverse waves. We review the data acquisition system and mode conversion of the acoustic waves for STAM and the multiple-angle and multiple-frequency tomography. Our multiple-transducer scheme has three insonification angles and three resonance frequencies in order to operate, in the transverse wave mode, multiple-angle and multiple frequency tomography for STAM. In order to evaluate the performance of our transducer scheme, we have simulated tomographic reconstruction with a back-and-forth propagation algorithm. Simulation results show that our multiple-transducer scheme is capable of obtaining good resolution with transverse wave mode and multiple-frequency tomography. We also show that our multiple-transducer scheme is an efficient rotation tool for a number of projections.

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Qin, Wei, Qian Chen, and Lei Xi. "A handheld microscope integrating photoacoustic microscopy and optical coherence tomography." Biomedical Optics Express 9, no. 5 (April 16, 2018): 2205. http://dx.doi.org/10.1364/boe.9.002205.

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11

Quinto, Eric Todd, and Ozan Öktem. "Local Tomography in Electron Microscopy." SIAM Journal on Applied Mathematics 68, no. 5 (January 2008): 1282–303. http://dx.doi.org/10.1137/07068326x.

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12

Bishara, Waheb, Serhan O. Isikman, and Aydogan Ozcan. "Lensfree Optofluidic Microscopy and Tomography." Annals of Biomedical Engineering 40, no. 2 (September 2, 2011): 251–62. http://dx.doi.org/10.1007/s10439-011-0385-3.

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13

Koster, A. J., H. Chen, J. W. Sedat, and D. A. Agard. "Automated microscopy for electron tomography." Ultramicroscopy 46, no. 1-4 (October 1992): 207–27. http://dx.doi.org/10.1016/0304-3991(92)90016-d.

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14

Schroer, Christian G., Peter Cloetens, Mark Rivers, Anatoly Snigirev, Akahisa Takeuchi, and Wenbing Yun. "High-Resolution 3D Imaging Microscopy Using Hard X-Rays." MRS Bulletin 29, no. 3 (March 2004): 157–65. http://dx.doi.org/10.1557/mrs2004.53.

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AbstractThe key strength of hard x-ray full-field microscopy is the large penetration depth of hard x-rays into matter, which allows one to image the interior of opaque objects. Combined with tomographic techniques, the three-dimensional inner structure of an object can be reconstructed without the need for difficult and destructive sample preparation. Projection microscopy and microtomography are now routinely available at synchrotron radiation sources. The resolution of these techniques is limited by that of the detector to 1 µm or slightly less. X-ray images and tomograms at higher spatial resolution can be obtained by x-ray optical magnification, for example, by using parabolic refractive x-ray lenses as a magnifying optic. Combining magnifying x-ray imaging with tomography allows one to reconstruct the three-dimensional structure of an object, such as a microprocessor chip, with resolution well below 1 µm. In x-ray scanning microscopy, the sample is scanned through a small-diameter beam. The great advantage of scanning microscopy is that x-ray analytical techniques such as fluorescence analysis, diffraction, and absorption spectroscopy can be used as contrast mechanisms in the microscope. In combination with tomography, fluorescence analysis makes it possible to reconstruct the distribution of different chemical elements inside an object (fluorescence microtomography), while combining absorption spectroscopy with tomography yields the distribution of different oxidation states of atomic species.

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Ellisman, Mark H., Stephen J. Young, G. Y. Fan, Guy Perkins, Steve Lamont, and Maryann E. Martone. "Highlights of Selected Microscopy Research Resource Activities at San Diego." Microscopy and Microanalysis 3, S2 (August 1997): 275–76. http://dx.doi.org/10.1017/s1431927600008266.

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The intermediate high-voltage electron microscope (IVEM) located at the National Center for Microscopy and Imaging Research at San Diego (NCMIR) can image relatively thick specimens that contain substantial three-dimensional (3-D) structure. Electron tomography is an important tool used at NCMIR for deriving 3-D cellular and subcellular structure from IVEM images. Reconstruction algorithms commonly used in electron tomography include weighted back projection, and iterative algebraic reconstruction techniques such as ART and SIRT. Improvements in reconstruction quality are possible using the iterative algorithms. Because these algorithms are computationally intensive, we have ported them to massively parallel computers at the San Diego Supercomputer Center, reducing the computation time over that required with workstation level machines.The quality of tomographic data for the 3-D reconstruction of biological structures is also being enhanced by NCMIR projects to improve the microscope. We have designed and constructed special electron optics and microscope control systems for the JEOL 4000EX.

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Kuś, Arkadiusz, Wojciech Krauze, and Małgorzata Kujawińska. "From digital holographic microscopy to optical coherence tomography – separate past and a common goal." Photonics Letters of Poland 13, no. 4 (December 30, 2021): 91. http://dx.doi.org/10.4302/plp.v13i4.1130.

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In this paper we briefly present the history and outlook on the development of two seemingly distant techniques which may be brought close together with a unified theoretical model described as common k-space theory. This theory also known as the Fourier diffraction theorem is much less common in optical coherence tomography than its traditional mathematical model, but it has been extensively studied in digital holography and, more importantly, optical diffraction tomography. As demonstrated with several examples, this link is one of the important factors for future development of both techniques. Full Text: PDF ReferencesN. Leith, J. Upatnieks, "Reconstructed Wavefronts and Communication Theory", J. Opt. Soc. Am. 52(10), 1123 (1962). CrossRef Y. Park, C. Depeursinge, G. Popescu, "Quantitative phase imaging in biomedicine", Nat. Photonics 12, 578 (2018). CrossRef D. Huang et al., "Optical Coherence Tomography", Science 254(5035), 1178 (1991). CrossRef D. P. Popescu, C. Flueraru, S. Chang, J. Disano, S. Sherif, M.G. Sowa, "Optical coherence tomography: fundamental principles, instrumental designs and biomedical applications", Biophys. Rev. 3(3), 155 (2011). CrossRef M. Wojtkowski, V. Srinivasan, J.G. Fujimoto, T. Ko, J.S. Schuman, A. Kowalczyk, J.S. Duker, "Three-dimensional Retinal Imaging with High-Speed Ultrahigh-Resolution Optical Coherence Tomography", Ophthalmology 112(10), 1734 (2005). CrossRef K.C. Zhou, R. Qian, A.-H. Dhalla, S. Farsiu, J.A. Izatt, "Unified k-space theory of optical coherence tomography", Adv. Opt. Photon. 13(2), 462 (2021). CrossRef A.F. Fercher, C.K. Hitzenberger, G. Kamp, S.Y. El-Zaiat, "Measurement of intraocular distances by backscattering spectral interferometry", Opt. Comm. 117(1-2), 43 (1995). CrossRef E. Wolf, "Determination of the Amplitude and the Phase of Scattered Fields by Holography", J. Opt. Soc. Am. 60(1), 18 (1970). CrossRef E. Wolf, "Three-dimensional structure determination of semi-transparent objects from holographic data", Opt. Comm. 1(4), 153 (1969). CrossRef V. Balasubramani et al., "Roadmap on Digital Holography-Based Quantitative Phase Imaging", J. Imaging 7(12), 252 (2021). CrossRef A. Kuś, W. Krauze, P.L. Makowski, M. Kujawińska, "Holographic tomography: hardware and software solutions for 3D quantitative biomedical imaging (Invited paper)", ETRI J. 41(1), 61 (2019). CrossRef A. Kuś, M. Dudek, M. Kujawińska, B. Kemper, A. Vollmer, "Tomographic phase microscopy of living three-dimensional cell cultures", J. Biomed. Opt. 19(4), 46009 (2014). CrossRef O. Haeberlé, K. Belkebir, H. Giovaninni, A. Sentenac, "Tomographic diffractive microscopy: basics, techniques and perspectives", J. Mod. Opt. 57(9), 686 (2010). CrossRef B. Simon et al., "Tomographic diffractive microscopy with isotropic resolution", Optica 4(4), 460 (2017). CrossRef B.A. Roberts, A.C. Kak, "Reflection Mode Diffraction Tomography", Ultrason. Imag. 7, 300 (1985). CrossRef M. Sarmis et al., "High resolution reflection tomographic diffractive microscopy", J. Mod. Opt. 57(9), 740 (2010). CrossRef L. Foucault et al., "Versatile transmission/reflection tomographic diffractive microscopy approach", J. Opt. Soc. Am. A 36(11), C18 (2019). CrossRef W. Krauze, P. Ossowski, M. Nowakowski, M. Szkulmowski, M. Kujawińska, "Enhanced QPI functionality by combining OCT and ODT methods", Proc. SPIE 11653, 116530B (2021). CrossRef E. Mudry, P.C. Chaumet, K. Belkebir, G. Maire, A. Sentenac, "Mirror-assisted tomographic diffractive microscopy with isotropic resolution", Opt. Lett. 35(11), 1857 (2010). CrossRef P. Hosseini, Y. Sung, Y. Choi, N. Lue, Z. Yaqoob, P. So, "Scanning color optical tomography (SCOT)", Opt. Expr. 23(15), 19752 (2015). CrossRef J. Jung, K. Kim, J. Yoon, Y. Park, "Hyperspectral optical diffraction tomography", Opt. Expr. 24(3), 1881 (2016). CrossRef T. Zhang et al., Biomed. "Multi-wavelength multi-angle reflection tomography", Opt. Expr. 26(20), 26093 (2018). CrossRef R.A. Leitgeb, "En face optical coherence tomography: a technology review [Invited]", Biomed. Opt. Expr. 10(5), 2177 (2019). CrossRef J.F. de Boer, R. Leitgeb, M. Wojtkowski, "Twenty-five years of optical coherence tomography: the paradigm shift in sensitivity and speed provided by Fourier domain OCT [Invited]", Biomed. Opt. Expr. 8(7), 3248 (2017). CrossRef T. Anna, V. Srivastava, C. Shakher, "Transmission Mode Full-Field Swept-Source Optical Coherence Tomography for Simultaneous Amplitude and Quantitative Phase Imaging of Transparent Objects", IEEE Photon. Technol. Lett. 23(11), 899 (2011). CrossRef M.T. Rinehart, V. Jaedicke, A. Wax, "Quantitative phase microscopy with off-axis optical coherence tomography", Opt. Lett. 39(7), 1996 (2014). CrossRef C. Photiou, C. Pitris, "Dual-angle optical coherence tomography for index of refraction estimation using rigid registration and cross-correlation", J. Biomed. Opt. 24(10), 1 (2019). CrossRef Y. Zhou, K.K.H. Chan, T. Lai, S. Tang, "Characterizing refractive index and thickness of biological tissues using combined multiphoton microscopy and optical coherence tomography", Biomed. Opt. Expr. 4(1), 38 (2013). CrossRef K.C. Zhou, R. Qian, S. Degan, S. Farsiu, J.A. Izatt, "Optical coherence refraction tomography", Nat. Photon. 13, 794 (2019). CrossRef

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17

Natterer, Frank. "Numerical methods in tomography." Acta Numerica 8 (January 1999): 107–41. http://dx.doi.org/10.1017/s0962492900002907.

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In this article we review the image reconstruction algorithms used in tomography. We restrict ourselves to the standard problems in the reconstruction of function from line or plane integrals as they occur in X-ray tomography, nuclear medicine, magnetic resonance imaging, and electron microscopy. Nonstandard situations, such as incomplete data, unknown orientations, local tomography, and discrete tomography are not dealt with. Nor do we treat nonlinear tomographic techniques such as impedance, ultrasound, and near-infrared imaging.

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18

Sorzano, C. O. S., J. Vargas, J. Otón, J. M. de la Rosa-Trevín, J. L. Vilas, M. Kazemi, R. Melero, et al. "A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy." BioMed Research International 2017 (2017): 1–17. http://dx.doi.org/10.1155/2017/6482567.

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One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy. We cover their use in Single Particle Analysis (SPA) as well as in Electron Tomography (ET).

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19

SCHNEIDER, G., E. ANDERSON, S. VOGT, C. KNÖCHEL, D. WEISS, M. LEGROS, and C. LARABELL. "COMPUTED TOMOGRAPHY OF CRYOGENIC CELLS." Surface Review and Letters 09, no. 01 (February 2002): 177–83. http://dx.doi.org/10.1142/s0218625x02001914.

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Soft X-ray microscopy has resolved 30 nm structures in biological cells. To protect the cells from radiation damage caused by X-rays, imaging of the samples has to be performed at cryogenic temperatures, which makes it possible to take multiple images of a single cell. Due to the small numerical aperture of zone plates, X-ray objectives have a depth of focus on the order of several microns. By treating the X-ray microscopic images as projections of the sample absorption, computed tomography (CT) can be performed. Since cryogenic biological samples are resistant to radiation damage, it is possible to reconstruct frozen-hydrated cells imaged with a full-field X-ray microscope. This approach is used to obtain three-dimensional information about the location of specific proteins in cells. To localize proteins in cells, immunolabeling with strongly X-ray absorbing nanoparticles was performed. With the new tomography setup developed for the X-ray microscope XM-1 installed at the ALS, we have performed tomography of immunolabeled frozen-hydrated cells to detect protein distributions inside of cells. As a first example, the distribution of the nuclear protein male-specific lethal 1 (MSL-1) in the Drosophila melanogaster cell was studied.

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Arslan, I., EA Marquis, M. Homer, MA Hekmaty, and NC Bartelt. "Correlating Electron Tomography and Atom Probe Tomography." Microscopy and Microanalysis 14, S2 (August 2008): 1044–45. http://dx.doi.org/10.1017/s1431927608087746.

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21

Oldenburg, Amy L., Chenyang Xu, and Stephen A. Boppart. "Spectroscopic Optical Coherence Tomography and Microscopy." IEEE Journal of Selected Topics in Quantum Electronics 13, no. 6 (2007): 1629–40. http://dx.doi.org/10.1109/jstqe.2007.910292.

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22

Roduit, Charles, Serguei Sekatski, Giovanni Dietler, Stefan Catsicas, Frank Lafont, and Sandor Kasas. "Stiffness Tomography by Atomic Force Microscopy." Biophysical Journal 97, no. 2 (July 2009): 674–77. http://dx.doi.org/10.1016/j.bpj.2009.05.010.

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23

Wang, Lihong V. "Multiscale photoacoustic microscopy and computed tomography." Nature Photonics 3, no. 9 (August 28, 2009): 503–9. http://dx.doi.org/10.1038/nphoton.2009.157.

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Liang, Chia-Pin, Chao-Wei Chen, Jeremiah Wierwille, Jaydev Desai, Rao Gullapalli, Reuben Mezrich, Cha-Min Tang, and Yu Chen. "Endoscopic Microscopy Using Optical Coherence Tomography." Current Medical Imaging Reviews 8, no. 3 (October 1, 2012): 174–93. http://dx.doi.org/10.2174/157340512803759910.

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Staehelin, L. Andrew, and Dominick J. Paolillo. "A brief history of how microscopic studies led to the elucidation of the 3D architecture and macromolecular organization of higher plant thylakoids." Photosynthesis Research 145, no. 3 (September 2020): 237–58. http://dx.doi.org/10.1007/s11120-020-00782-3.

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Abstract Microscopic studies of chloroplasts can be traced back to the year 1678 when Antonie van Leeuwenhoek reported to the Royal Society in London that he saw green globules in grass leaf cells with his single-lens microscope. Since then, microscopic studies have continued to contribute critical insights into the complex architecture of chloroplast membranes and how their structure relates to function. This review is organized into three chronological sections: During the classic light microscope period (1678–1940), the development of improved microscopes led to the identification of green grana, a colorless stroma, and a membrane envelope. More recent (1990–2020) chloroplast dynamic studies have benefited from laser confocal and 3D-structured illumination microscopy. The development of the transmission electron microscope (1940–2000) and thin sectioning techniques demonstrated that grana consist of stacks of closely appressed grana thylakoids interconnected by non-appressed stroma thylakoids. When the stroma thylakoids were shown to spiral around the grana stacks as multiple right-handed helices, it was confirmed that the membranes of a chloroplast are all interconnected. Freeze-fracture and freeze-etch methods verified the helical nature of the stroma thylakoids, while also providing precise information on how the electron transport chain and ATP synthase complexes are non-randomly distributed between grana and stroma membrane regions. The last section (2000–2020) focuses on the most recent discoveries made possible by atomic force microscopy of hydrated membranes, and electron tomography and cryo-electron tomography of cryofixed thylakoids. These investigations have provided novel insights into thylakoid architecture and plastoglobules (summarized in a new thylakoid model), while also producing molecular-scale views of grana and stroma thylakoids in which individual functional complexes can be identified.

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Durkin, James W. "Computer Graphics Challenges in Electron Microscope Tomography Visualization." Microscopy and Microanalysis 3, S2 (August 1997): 1127–28. http://dx.doi.org/10.1017/s1431927600012526.

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We are developing a collaborative research environment, the Collaboratory for Microscopic Digital Anatomy (CMDA), to provide remote access to the sophisticated instrumentation located at the Na-tional Center for Microscopy and Imaging Research (NCMIR). The project’s initial focus is the col-lection and analysis of data from NCMIR’s unique intermediate-high voltage transmission electron microscope (HVEM), an instrument expressly designed to obtain images from thick specimens con-taining substantial 3-D structure. Because of the electron optical characteristics of the microscope, its images represent a 2-D projection of the specimen’s 3-D structure. 3-D data is derived, using axial tomography, from a series of projections acquired as the specimen is successively tilted in small angu-lar increments. Visualizing the 3-D volume data generated by this procedure is a key challenge facing the project. Our experience suggests that existing visualization mechanisms are limited in their ability to fully access the data’s biologically interesting information.

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Takamatsu, Tetsurou, and Setsuya Fujita. "Microscopic tomography by laser scanning microscopy and its three-dimensional reconstruction." Journal of Microscopy 149, no. 3 (March 1988): 167–74. http://dx.doi.org/10.1111/j.1365-2818.1988.tb04574.x.

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Martone, Maryann E., Andrea Thor, Stephen J. Young, and Mark H. Ellisman. "Correlated 3D Light and Electron Microscopy of Large, Complex Structures: Analysis of Transverse Tubules in Heart Failure." Microscopy and Microanalysis 4, S2 (July 1998): 440–41. http://dx.doi.org/10.1017/s1431927600022327.

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Light microscopic imaging has experienced a renaissance in the past decade or so, as new techniques for high resolution 3D light microscopy have become readily available. Light microscopic (LM) analysis of cellular details is desirable in many cases because of the flexibility of staining protocols, the ease of specimen preparation and the relatively large sample size that can be obtained compared to electron microscopic (EM) analysis. Despite these advantages, many light microscopic investigations require additional analysis at the electron microscopic level to resolve fine structural features.High voltage electron microscopy allows the use of relatively thick sections compared to conventional EM and provides the basis for excellent new methods to bridge the gap between microanatomical details revealed by LM and EM methods. When combined with electron tomography, investigators can derive accurate 3D data from these thicker specimens. Through the use of correlated light and electron microscopy, 3D reconstructions of large cellular or subcellular structures can be obtained with the confocal microscope,

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Larabell, C., and M. Le Gros. "Correlated Cryo Confocal Tomography and X-ray Tomography." Microscopy and Microanalysis 18, S2 (July 2012): 200–201. http://dx.doi.org/10.1017/s1431927612002851.

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Levine, Zachary H. "An X-Ray Tomography Primer." EDFA Technical Articles 7, no. 1 (February 1, 2005): 26–32. http://dx.doi.org/10.31399/asm.edfa.2005-1.p026.

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Abstract X-ray tomography has been rapidly gaining acceptance in the semiconductor industry since the first demonstration of its use on IC interconnect in 1999. As failure analysts are discovering, X-ray imaging is more powerful than visible light microscopy and can be used to analyze larger samples than those that fit in an electron microscope. This article provides an introduction to the physics, signal processing, and algorithms involved in X-ray imaging and tomography and the factors that affect resolution.

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Miller, M. K., and J. A. Panitz. "Microscopy Milestones: Field Ion Microscopy, Atom Probe Field Ion Microscopy and Atom Probe Tomography." Microscopy and Microanalysis 6, S2 (August 2000): 1190–91. http://dx.doi.org/10.1017/s1431927600038447.

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Two of the most significant microscopy milestones that were achieved in the last century were the imaging of individual atoms and the identification of individual atoms. Both these remarkable achievements were due to Prof. E. W. Miiller and members of his group at Pennsylvania State University. Almost fifty years ago, Miiller introduced a new type of microscope in which a sharp needle-shaped specimen was pointed at a fluorescent screen, Fig. 1. By applying an appropriately high positive voltage to the specimen, image gas atoms near the apex of the specimen could be ionized and radially projected towards the screen where they produced highly magnified images of the specimen surface, Fig. 2. By cryogenically cooling the specimen and using helium as the image gas, the first images of individual atoms were obtained in a field ion microscope by Bahadur and Müller on October 11th, 1955.

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Mekhantseva, Tamara, Oleg Voitenko, Ilya Smirnov, Evgeny Pustovalov, Vladimir Plotnikov, Boris Grudin, and Alexey Kirillov. "TEM and STEM Electron Tomography Analysis of Amorphous Alloys CoP-CoNiP System." Advanced Materials Research 590 (November 2012): 9–12. http://dx.doi.org/10.4028/www.scientific.net/amr.590.9.

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This paper covers the analysis of amorphous alloys CoP-CoNiP system by means of high-resolution transmission electron microscopy (HRTEM), scanning transmission electron microscopy and electron tomography. The last years have seen a sufficient progress in the analysis of nanomaterials structure with the help of high resolution tomography. This progress was motivated by the development of microscopes equipped with aberration correctors and specialized sample holders which allow reaching the tilts angles up to ±80°. The opportunities delivered by the method of electron tomography sufficiently grow when producing high resolution images and using chemical analysis, such as X-Ray energy-dispersive microanalysis and electron energy loss spectroscopy (EELS).

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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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Bell, D. C., C. J. Barrelet, Yue Wu, and C. M. Lieber. "Nano-Tomography: Tomography to Understand the Full Structure of Nanowire." Microscopy and Microanalysis 10, S02 (August 2004): 1202–3. http://dx.doi.org/10.1017/s1431927604886434.

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Shoeib, Mahmoud. "THE RECENT ELECTRON MICROSCOPY APPLICATIONS (ELECTRON TOMOGRAPHY)." Mansoura Veterinary Medical Journal 18, no. 1 (December 12, 2017): 587–90. http://dx.doi.org/10.21608/mvmj.2017.127987.

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Wang, Lihong V. "Tutorial on Photoacoustic Microscopy and Computed Tomography." IEEE Journal of Selected Topics in Quantum Electronics 14, no. 1 (2008): 171–79. http://dx.doi.org/10.1109/jstqe.2007.913398.

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Mujat, Mircea, Kristyn Greco, Kristin L. Galbally-Kinney, Daniel X. Hammer, R. Daniel Ferguson, Nicusor Iftimia, Phillip Mulhall, Puneet Sharma, Michael J. Pikal, and William J. Kessler. "Optical coherence tomography-based freeze-drying microscopy." Biomedical Optics Express 3, no. 1 (December 7, 2011): 55. http://dx.doi.org/10.1364/boe.3.000055.

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Richter, Verena, Sarah Bruns, Thomas Bruns, Petra Weber, Michael Wagner, Christoph Cremer, and Herbert Schneckenburger. "Axial tomography in live cell laser microscopy." Journal of Biomedical Optics 22, no. 9 (January 25, 2017): 091505. http://dx.doi.org/10.1117/1.jbo.22.9.091505.

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Butz, Tilman. "Ion microscopy and tomography in medical research." Zeitschrift für Medizinische Physik 19, no. 4 (December 2009): 221. http://dx.doi.org/10.1016/j.zemedi.2009.09.005.

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Kizilyaprak, Caroline, York-Dieter Stierhof, and Bruno M. Humbel. "Volume microscopy in biology: FIB-SEM tomography." Tissue and Cell 57 (April 2019): 123–28. http://dx.doi.org/10.1016/j.tice.2018.09.006.

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Elliott, J. C., and S. D. Dover. "X-ray microscopy using computerized axial tomography." Journal of Microscopy 138, no. 3 (June 1985): 329–31. http://dx.doi.org/10.1111/j.1365-2818.1985.tb02627.x.

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Remacha, Clément, Brenden Scott Nickerson, and Hans Jürgen Kreuzer. "Tomography by point source digital holographic microscopy." Applied Optics 53, no. 16 (May 30, 2014): 3520. http://dx.doi.org/10.1364/ao.53.003520.

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Takeuchi, Akihisa, and Yoshio Suzuki. "Recent progress in synchrotron radiation 3D–4D nano-imaging based on X-ray full-field microscopy." Microscopy 69, no. 5 (May 6, 2020): 259–79. http://dx.doi.org/10.1093/jmicro/dfaa022.

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Abstract The advent of high-flux, high-brilliance synchrotron radiation (SR) has prompted the development of high-resolution X-ray imaging techniques such as full-field microscopy, holography, coherent diffraction imaging and ptychography. These techniques have strong potential to establish non-destructive three- and four-dimensional nano-imaging when combined with computed tomography (CT), called nano-tomography (nano-CT). X-ray nano-CTs based on full-field microscopy are now routinely available and widely used. Here we discuss the current status and some applications of nano-CT using a Fresnel zone plate as an objective. Optical properties of full-field microscopy, such as spatial resolution and off-axis aberration, which determine the effective field of view, are also discussed, especially in relation to 3D tomographic imaging.

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Batenburg, KJ, S. Bals, J. Sijbers, and G. Van Tendeloo. "Discrete tomography: exploiting various forms of discreteness in electron tomography." Microscopy and Microanalysis 14, S2 (August 2008): 1050–51. http://dx.doi.org/10.1017/s1431927608083803.

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Perkins, G. A., C. W. Renken, S. J. Young, S. Lindsey, M. H. Ellisman, and T. G. Frey. "Use of High-Performance Computing Algorithms in Combination With Parallel Computing for Tomography." Microscopy and Microanalysis 3, S2 (August 1997): 1123–24. http://dx.doi.org/10.1017/s1431927600012502.

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The electron microscope is essential for resolving complex biological structures, such as mitochondria, which are too small to be viewed in detail with the light microscope. In contrast to a conventional instrument, the High-Voltage Electron Microscope (HVEM) located at the National Center for Microscopy and Imaging Research (NCMIR) can obtain images from relatively thick specimens that contain substantial three-dimensional structure. Though a single image acquired with the HVEM represents a projection through the specimen, tomographic methods can be applied to a set of images acquired from different orientations to derive a three-dimensional representation of its biological structure. Tomography requires extensive computation and considerable processing time on conventional workstations in order to reconstruct the typically large HVEM volumes from the tilt series.In order to expedite tomographic processing, we have implemented both the commonly used singleaxis tilt, R-weighted backprojection algorithm and two iterative reconstruction methods, algebraic reconstruction (ART) and simultaneous iterative reconstruction (SIRT) on the massively parallel Intel Paragon at the San Diego Supercompter Center.

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Vamvakeros, Antonios, Simon D. M. Jacques, Marco Di Michiel, Pierre Senecal, Vesna Middelkoop, Robert J. Cernik, and Andrew M. Beale. "Interlaced X-ray diffraction computed tomography." Journal of Applied Crystallography 49, no. 2 (March 1, 2016): 485–96. http://dx.doi.org/10.1107/s160057671600131x.

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An X-ray diffraction computed tomography data-collection strategy that allows, post experiment, a choice between temporal and spatial resolution is reported. This strategy enables time-resolved studies on comparatively short timescales, or alternatively allows for improved spatial resolution if the system under study, or components within it, appear to be unchanging. The application of the method for studying an Mn–Na–W/SiO2 fixed-bed reactor in situ is demonstrated. Additionally, the opportunities to improve the data-collection strategy further, enabling post-collection tuning between statistical, temporal and spatial resolutions, are discussed. In principle, the interlaced scanning approach can also be applied to other pencil-beam tomographic techniques, like X-ray fluorescence computed tomography, X-ray absorption fine structure computed tomography, pair distribution function computed tomography and tomographic scanning transmission X-ray microscopy.

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Schneider, Jan Philipp, Jan Hegermann, and Christoph Wrede. "Volume electron microscopy: analyzing the lung." Histochemistry and Cell Biology 155, no. 2 (September 17, 2020): 241–60. http://dx.doi.org/10.1007/s00418-020-01916-3.

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AbstractSince its entry into biomedical research in the first half of the twentieth century, electron microscopy has been a valuable tool for lung researchers to explore the lung’s delicate ultrastructure. Among others, it proved the existence of a continuous alveolar epithelium and demonstrated the surfactant lining layer. With the establishment of serial sectioning transmission electron microscopy, as the first “volume electron microscopic” technique, electron microscopy entered the third dimension and investigations of the lung’s three-dimensional ultrastructure became possible. Over the years, further techniques, ranging from electron tomography over serial block-face and focused ion beam scanning electron microscopy to array tomography became available. All techniques cover different volumes and resolutions, and, thus, different scientific questions. This review gives an overview of these techniques and their application in lung research, focusing on their fields of application and practical implementation. Furthermore, an introduction is given how the output raw data are processed and the final three-dimensional models can be generated.

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Giannuzzi, Lucille A. "FIB Lift-Out and Milling of Cylindrical Specimens for Electron Tomography (or Atom Probe Field Ion Microscopy)." Microscopy Today 12, no. 6 (November 2004): 34–35. http://dx.doi.org/10.1017/s1551929500065950.

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Electron tomography using transmission electron microscopy (TEM) and related techniques (e.g., scanning transmission electron microscopy (STEM) or energy filtered TEM (EFTEM)) allow for 3-D microstructural and elemental mapping of specimens, and has been used successfully in the biological sciences where mass-thickness contrast dominates these mostly amorphous materials. Z-contrast STEM imaging via high angle annular dark field (HAADF) tomography has also been used successfully in the physical sciences. STEM, EFTEM, and holography tomography are more useful techniques for crystalline materials, since diffraction contrast in conventional TEM images can hinder image reconstruction. Typical tomography routines utilize conventional electron transparent foils, whereby the dimensions of the specimen perpendicular to the electron beam may be orders of magnitude greater than the specimen thickness parallel to the electron beam. Using this conventional specimen geometry, the effective specimen thickness increases as the specimen is tilted through the ± 70 degrees necessary for the tomographic acquisition process.

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Haberfehlner, G., R. Serra, D. Cooper, G. Audoit, S. Barraud, and P. Bleuet. "Optimizing Sampling Schemes for Electron Tomography: Dual- and Multiple-Axis Tomography." Microscopy and Microanalysis 19, S2 (August 2013): 574–75. http://dx.doi.org/10.1017/s1431927613004868.

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Kelly, Thomas F., Michael K. Miller, Krishna Rajan, and Simon P. Ringer. "Atomic-Scale Tomography: A 2020 Vision." Microscopy and Microanalysis 19, no. 3 (May 13, 2013): 652–64. http://dx.doi.org/10.1017/s1431927613000494.

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AbstractAtomic-scale tomography (AST) is defined and its place in microscopy is considered. Arguments are made that AST, as defined, would be the ultimate microscopy. The available pathways for achieving AST are examined and we conclude that atom probe tomography (APT) may be a viable basis for AST on its own and that APT in conjunction with transmission electron microscopy is a likely path as well. Some possible configurations of instrumentation for achieving AST are described. The concept of metaimages is introduced where data from multiple techniques are melded to create synergies in a multidimensional data structure. When coupled with integrated computational materials engineering, structure–properties microscopy is envisioned. The implications of AST for science and technology are explored.

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