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Forward modeling of volume electron microscopy (vEM) of stained resin-embedded biological samples

Yu Yuan, Sabrina Clusiau, Raynald Gauvin, Christopher Bleck, Adrian Phoulady, Pouya Tavousi, Sina Shahbazmohamadi, Nicolas Piché, Mike Marsh
2021 Microscopy and Microanalysis  
The physics of electron-matter interaction has been described and modeled by MC-Xray in the past, although, only recently, has that modeling been integrated into a user-friendly software framework Dragonfly  ...  Image formation in the scanning electron microscope (SEM) is a complicated process that starts with interaction between the incident electron beam and the sample being imaged.  ...  Image formation in the scanning electron microscope (SEM) is a complicated process that starts with interaction between the incident electron beam and the sample being imaged.  ... 
doi:10.1017/s1431927621003093 fatcat:7j4qpgtmubbnbk5dlgyy5qsofu

From tissue to silicon to plastic: three-dimensional printing in comparative anatomy and physiology

Henrik Lauridsen, Kasper Hansen, Mathias Ørum Nørgård, Tobias Wang, Michael Pedersen
2016 Royal Society Open Science  
We have applied computed tomography and magnetic resonance imaging to produce digital models of animal anatomy well suited to be printed on low-cost 3D printers.  ...  One way to circumvent this problem is in the production of 3D-printed scale models.  ...  The interactive slider model is available as the electronic supplementary material, S1, and the ready-to-3D-print STL-file of the same model is available as the electronic supplementary material, S2. indistinguishable  ... 
doi:10.1098/rsos.150643 pmid:27069653 pmcid:PMC4821264 fatcat:zsx3ugqervd3diilrrnscpptl4

Informatics in Radiology (infoRAD)

Wieslaw L. Nowinski, A. Thirunavuukarasuu, Ihar Volkau, Rafail Baimuratov, Qingmao Hu, Aamer Aziz, Su Huang
2005 Radiographics  
Abbreviation: 3D ϭ three-dimensional RadioGraphics 2005; 25:263-271 • Published online 10.1148/rg.251045051 • Content Codes:  ...  The use of 3D polygonal models allows smooth navigation (rotation, zooming, panning) and interactive labeling of anatomic structures and vascular segments.  ...  Because Voxel-Man makes use of precalculated 3D and maximum-intensity-projection images, interaction with the 3D images is achieved with 3D Quick Time (Apple Computer, Cupertino, Calif) movies.  ... 
doi:10.1148/rg.251045051 pmid:15653601 fatcat:acvud3zgzbglbckm7ttye4mw3i

Model-enhanced neuroimaging: clinical, research, and educational applications

W. L. Nowinski
2002 IMIA Yearbook of Medical Informatics  
Key contributors to the development of applications described here include D. Belov, C. K. Chui, A. Fang, L. Jagannathan, R. A. Kockro, H. Ng, L Serra, A. Thirunavuukarasuu, Y. P. Wang, and G. L.  ...  is able to delineate the tumor completely; b) interactive segmentation of a brain tumor in a 2D case; c) interactive segmentation in a 3D case by using a customized 3D contour editor.  ...  VIVIAN provides 3D interactive segmentation tools to extract and model critical objects of a patient's anatomy and pathology.  ... 
doi:10.1055/s-0038-1638137 fatcat:qmhv3kdtuzc5tjssbalxp373mi

Incorporating 3D virtual anatomy into the medical curriculum

Celina Imielinska, Pat Molholt
2005 Communications of the ACM  
, illustrations, and interactive labeling; and • Formal evaluation of the electronic material in the classrooms to demonstrate the benefits of using this technology for teaching and learning.  ...  From this data, using proper imaging, 3D reconstruction, and modeling tools, one can extract 3D anatomical structures, texture them with photorealistic color of the fresh human tissue, and depict 3D spatial  ...  Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage  ... 
doi:10.1145/1042091.1042119 fatcat:lkvcapnjhnfolnlxuusb62qo2q

Continuous maximum flow segmentation method for nanoparticle interaction analysis

L. MARAK, O. TANKYEVYCH, H. TALBOT
2011 Journal of Microscopy  
Such images produced with a Transmission Electron Microscope (TEM) make it possible to image nanometerscale materials in 3D.  ...  In recent years, tomographic 3D reconstruction approaches using Electrons rather than X-Rays have become popular.  ...  used in 3D image segmentation.  ... 
doi:10.1111/j.1365-2818.2011.03507.x pmid:21707616 fatcat:hxbvuxjf6vd7tom2pa7hexs2ky

A 3D stereotactic atlas of the adult human skull base

Wieslaw L. Nowinski, Thant S. L. Thaung
2018 Brain Informatics  
Although many textbooks describe this region illustrated well with drawings, scans and photographs, a complete, 3D, electronic, interactive, realistic, fully segmented and labeled, and stereotactic atlas  ...  Our goal is to create a 3D electronic atlas of the adult human skull base along with interactive tools for structure manipulation, exploration, and quantification.  ...  The authors are grateful to numerous individuals (listed as the co-authors of the component atlases in the references) for their kind contribution.  ... 
doi:10.1186/s40708-018-0082-1 pmid:29881932 fatcat:xolj6nvjcvfctigruggt2e5gzi

Image processing for materials characterization: Issues, challenges and opportunities

L. Duval, M. Moreaud, C. Couprie, D. Jeulin, H. Talbot, J. Angulo
2014 2014 IEEE International Conference on Image Processing (ICIP)  
This introductory paper aims at summarizing some problems and state-of-the-art techniques encountered in image processing for material analysis and design.  ...  Developing generic methods for this purpose is a complex task given the variability of the different image acquisition modalities (optical, scanning or transmission electron microscopy; surface analysis  ...  Microstructure stochastic modeling This step (Fig. 5 , with 3D modeling from 2D images) may use input characteristic data either from segmentation or analysis.  ... 
doi:10.1109/icip.2014.7025985 dblp:conf/icip/DuvalMCJTA14 fatcat:ydsfborvq5hbrlqfti3vley2i4

Effectively incorporating selected multimedia content into medical publications

Alexander Ziegler, Daniel Mietchen, Cornelius Faber, Wolfram von Hausen, Christoph Schöbel, Markus Sellerer, Andreas Ziegler
2011 BMC Medicine  
Fully interactive threedimensional models of a face and a schematic representation of a human brain are also part of this publication.  ...  We discuss the potential of this approach and its impact on the communication of scientific medical data, particularly with regard to electronic and open access publications.  ...  Critical comments by Jacopo Annese (University of California, San Diego, CA, USA) and Sameer Antani (National Library of Medicine, Bethesda, MD, USA) have helped to improve the manuscript.  ... 
doi:10.1186/1741-7015-9-17 pmid:21329532 pmcid:PMC3040697 fatcat:7f3oyk42wjhhhfx56dmajvikom

Nano-Tomography of Porous Geological Materials Using Focused Ion Beam-Scanning Electron Microscopy

Yang Liu, Helen King, Marijn van Huis, Martyn Drury, Oliver Plümper
2016 Minerals  
Tomographic analysis using focused ion beam-scanning electron microscopy (FIB-SEM) provides three-dimensional information about solid materials with a resolution of a few nanometres and thus bridges the  ...  We then focus on image processing procedures, including image alignment, correction, and segmentation to finally result in a three-dimensional, quantified pore network representation of the two example  ...  King and Oliver Plümper provided sample material and contributed to the interpretation.  ... 
doi:10.3390/min6040104 fatcat:kzheiu2ywzepveh5zzntan3qjm

Automating material image analysis for material discovery

Chiwoo Park, Yu Ding
2019 MRS Communications  
Analysis of all these images is time-consuming and labor intensive, creating a bottleneck in material discovery that needs to be overcome.  ...  Advancements in temporal and spatial resolutions of microscopes promise to expand the frontiers of understanding in materials science.  ...  Should the same 2d models be used for 3d objects, a much greater degree of freedom would have to be used, but then, the models would become too complex to be practical.  ... 
doi:10.1557/mrc.2019.48 fatcat:gnc5cma5lvg4tek5gyyzknzq4u

Functional foregut anatomy of the blue–green sharpshooter illustrated using a 3D model

Daniel White, Elaine A. Backus, Ian M. Marcus, Sharon L. Walker, M. Caroline Roper
2021 Scientific Reports  
Herein, a 3D model of the blue–green sharpshooter functional foregut is derived from a meta-analysis of published microscopy images.  ...  The 3D model can also be used in future fluid dynamic simulations to better understand acquisition, retention, and inoculation of X. fastidiosa.  ...  (c) Epipharynx electron microscope image (left) and 3D model segment (right, concave, internal) for comparison.  ... 
doi:10.1038/s41598-021-85954-4 pmid:33753809 fatcat:xukkenjmn5dkvgnlxihkcun5pm

Advanced tomography techniques for inorganic, organic, and biological materials

James E. Evans, Heiner Friedrich
2016 MRS bulletin  
The rendering of a 3D model usually involves volume segmentation, a process by which the 3D intensity map is partitioned into multiple segments (i.e., phases, components, compartments, materials).  ...  Segmentation can be performed by manual methods; 20 -22 using automated operator-independent algorithms, for instance, based on intensity differences; 23 -25 or by using models of the structures to be  ...  Macromolecular protein complexes of known structure (a) are used for computational 3D template matching within a solved 3D electron tomogram (b) to create a detailed map/model of (c) protein localization  ... 
doi:10.1557/mrs.2016.134 fatcat:4j2u47sqxfdmfieuxib557me54

Some trends in microscope image processing

N BONNET
2004 Bioorganic & Medicinal Chemistry  
The present review tries to identify some trends among the multitude of ways followed by image processing developments in the field of microscopy. Nine topics were selected.  ...  A specific topic is dedicated to a trend towards semi-automation instead of full automation in image processing. q  ...  Acknowledgements I thank the referees for their helpful comments on the first version of the manuscript.  ... 
doi:10.1016/s0968-4328(04)00095-2 fatcat:y4xfvtgncfglbg4moqpsnwl34u

Some trends in microscope image processing

Noël Bonnet
2004 Micron  
The present review tries to identify some trends among the multitude of ways followed by image processing developments in the field of microscopy. Nine topics were selected.  ...  A specific topic is dedicated to a trend towards semi-automation instead of full automation in image processing. q  ...  Acknowledgements I thank the referees for their helpful comments on the first version of the manuscript.  ... 
doi:10.1016/j.micron.2004.04.006 pmid:15288643 fatcat:i62hiuaw75gtbenwsponfrqh7i
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