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Phase-contrast zoom tomography reveals precise locations of macrophages in mouse lungs

Martin Krenkel, Andrea Markus, Matthias Bartels, Christian Dullin, Frauke Alves, Tim Salditt
2015 Scientific Reports  
The zoom capability and, in particular, the high dose efficiency are enabled by the near-perfect exit wavefront of an optimized x-ray waveguide channel.  ...  Using a divergent x-ray beam generated by nanoscale focusing, we used zoom tomography to produce three-dimensional reconstructions with selectable magnification, resolution, and field of view.  ...  Funding provided by the DFG collaborative research centre SFB 755 'Nanoscale Photonic Imaging' and  ... 
doi:10.1038/srep09973 pmid:25966338 pmcid:PMC4428069 fatcat:5zrmzd5robdbdlh2clhmzp5y6y

Toward Routine Use of 3D Histopathology as a Research Tool

Nicholas Roberts, Derek Magee, Yi Song, Keeran Brabazon, Mike Shires, Doreen Crellin, Nicolas M. Orsi, Richard Quirke, Philip Quirke, Darren Treanor
2012 American Journal of Pathology  
We describe a novel system for 3D histological reconstruction, integrating whole-slide imaging (virtual slides), image serving, registration, and visualization into one user-friendly package.  ...  It produces high-resolution 3D reconstructions with minimal user interaction and can be used in a histopathological laboratory without input from computing specialists.  ...  Acknowledgments We thank Mike Hale, Martin Waterhouse, David Turner, and Alex Wright (Leeds Institute of Molecular Medicine Digital Pathology Group) for scanning and computing assistance.  ... 
doi:10.1016/j.ajpath.2012.01.033 pmid:22490922 pmcid:PMC3538002 fatcat:vhudcw3eqvhcxpso7or5fzt7ne

Three-dimensional digital reconstruction of human placental villus architecture in normal and complicated pregnancies

R. McCarthy, N.M. Orsi, D. Treanor, O. Moran, M. Vernooij, D.R. Magee, N. Roberts, J. Stahlschmidt, N.A.B. Simpson
2016 European Journal of Obstetrics, Gynecology, and Reproductive Biology  
Slides were then scanned and the digitised images reconstructed using customised software.  ...  Objective This study aimed to examine the use of digital technology in the three-dimensional reconstruction of human placentas.  ...  Recent developments in imaging software and computational power have proved amenable to being harnessed for the creation of high-resolution 3D tissue images (15) .  ... 
doi:10.1016/j.ejogrb.2015.12.015 pmid:26745392 fatcat:7v5ezubmrvhirjnkw5jmcqg26q

Interactive Visualization of 3D Histopathology in Native Resolution

2018 IEEE Transactions on Visualization and Computer Graphics  
We present a visualization application that enables effective interactive visual analysis of large-scale 3D histopathology, that is, high-resolution 3D microscopy data of human tissue.  ...  Despite this, our developed application supports interactive study of 3D histology datasets at native resolution.  ...  The liver cirrhosis data, the healthy liver data, and the mouse embryo data are courtesy of University of Leeds, UK. The image slides of the colorectal polyp were provided by Prof.  ... 
doi:10.1109/tvcg.2018.2864816 pmid:30130214 fatcat:tiup5byainbqda6oxmygg5srs4

Histopathology: ditch the slides, because digital and 3D are on show

Ilaria Jansen, Marit Lucas, C. Dilara Savci-Heijink, Sybren L. Meijer, Henk A. Marquering, Daniel M. de Bruin, Patricia J. Zondervan
2018 World journal of urology  
WSI Whole slide image * Ilaria Jansen  ...  Due to the growing field of digital pathology, more and more digital histology slides are becoming available.  ...  By optically scanning the histologic glass slide, a 2D ultra-high-resolution digital image is created, a so-called whole slide image (WSI).  ... 
doi:10.1007/s00345-018-2202-1 pmid:29396786 pmcid:PMC5871638 fatcat:u44jncdeffg3hcipurx4iic5mm

Three-dimensional histopathological reconstruction of bladder tumours

Ilaria Jansen, Marit Lucas, C. Dilara Savci-Heijink, Sybren L. Meijer, Esmee I. M. L. Liem, Onno J. de Boer, Ton G. van Leeuwen, Henk A. Marquering, Daniel M. de Bruin
2019 Diagnostic Pathology  
The aim of this study is to present three-dimensional (3D) reconstructions of histology images.  ...  Conclusion: Digital scanning of en-bloc resected specimens allows a full-fledged 3D reconstruction and analysis and has a potential role to support pathologists in the staging of BCa.  ...  Whole slide image (WSI) systems provide pathologists histopathologic glass slides as digital high resolution images with magnifications similar to conventional microscopy.  ... 
doi:10.1186/s13000-019-0803-7 fatcat:bmsjzhqhvjhodkpbj2ir4raeem

Deep Learning Based Large-scale Histological Tau Protein Mapping for Neuroimaging Biomarker Validation in Alzheimer's Disease [article]

Maryana Alegro, Yuheng Chen, Dulce Ovando, Helmut Heinsen, Rana Eser, Duygu Tosun, Lea Grinberg
2019 bioRxiv   pre-print
Our dataset is composed of histological slices stained for AT100, AT8. Each slide was imaged in our in-house built slide scanner at 1.22um resolution. Each image is about 82000x37000 pixel wide.  ...  Manually locating and segmenting Tau in such images is unfeasible since a whole human brain slice, at the adequate resolution, spans several Gigabytes of data and carries thousands of inclusions.  ...  created 3D maps of three different forms of abnormal tau protein in each case and registered each 3D histological map to the MRI volume.  ... 
doi:10.1101/698902 fatcat:ftrobwopezcjrm3uqc64zuslje

System for combined three-dimensional morphological and molecular analysis of thick tissue specimens

Rodrigo Fernandez-Gonzalez, Arthur Jones, Enrique Garcia-Rodriguez, Ping Yuan Chen, Adam Idica, Stephen J. Lockett, Mary Helen Barcellos-Hoff, Carlos Ortiz-De-Solorzano
2002 Microscopy research and technique (Print)  
We describe the system in detail and illustrate its use by imaging, reconstructing and analyzing two complete tissue blocks which were differently processed and stained.  ...  The second block contained a fully sectioned mammary gland of a mouse, stained for Histology with H&E.  ...  Gray for their support and advice regarding the selection of the tissue and A. Harris for her help with tissue imaging and annotation.  ... 
doi:10.1002/jemt.10233 pmid:12467029 fatcat:2aoh6yw2dzfivmadbqcuteduni

Acquisition, Visualization, and Potential Applications of 3D Data in Anatomic Pathology

Shyam Prajapati, Emilio Madrigal, Mark T. Friedman
2016 Discoveries  
Although these technologies are yet to be adopted in routine surgical pathology, forensic pathology has embraced 3D scanning and model reconstruction.  ...  Accompanying these advances are novel clinical and non-clinical applications of 3D data in pathology.  ...  Acknowledgments We thank to the Mount Sinai Health System, the Department of Diagnostic Pathology and Laboratory, for support.  ... 
doi:10.15190/d.2016.15 pmid:32309587 pmcid:PMC6941555 fatcat:xiww6okr4befxpscmaibmx3rhy

Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus

Peizhen Sun, Prasanna Parvathaneni, Bennett A. Landman, Adam M. Anderson, Kurt G. Schilling, Yurui Gao, Vaibhav A. Janve, Robert C. Molthen, Barjor Gimi
2015 Medical Imaging 2015: Biomedical Applications in Molecular, Structural, and Functional Imaging  
The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while  ...  In vivo MRI acquisitions include high resolution T2 structural imaging (300 µm isotropic) and low resolution diffusion tensor imaging (600 um isotropic).  ...  This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University, Nashville, TN.  ... 
doi:10.1117/12.2081443 pmid:25914510 pmcid:PMC4405811 dblp:conf/mibam/SunPSGJAL15 fatcat:ut543nqo65dlzpoq6ekbco4ycq

Sub-micrometer morphology of human atherosclerotic plaque revealed by synchrotron radiation-based μCT—A comparison with histology

My Truong, Till Dreier, Johan Wassélius, Lena Sundius, Ana Persson, Goran Lovric, Anne Bonnin, Isabel Goncalves, Martin Bech, Alessandra Giuliani
2022 PLoS ONE  
In total, nine different regions with typical pathologic structures were identified and imaged with high-resolution SRμCT.  ...  The tomography datasets were reconstructed with additional 3D volume rendering and compared to histology.  ...  Acknowledgments We acknowledge the Paul Scherrer Institute, Villigen, Switzerland, for the provision of synchrotron radiation beamtime at beamline TOMCAT of the SLS.  ... 
doi:10.1371/journal.pone.0265598 pmid:35471989 pmcid:PMC9041845 fatcat:zifg3cauhnfc7clmqmlzjp6ta4

High-resolution episcopic microscopy: a rapid technique for high detailed 3D analysis of gene activity in the context of tissue architecture and morphology

Wolfgang J. Weninger, Stefan H. Geyer, Timothy J. Mohun, Diego Rasskin-Gutman, Takaaki Matsui, Ines Ribeiro, Luciano da F. Costa, Juan Carlos Izpisúa-Belmonte, Gerd B. Müller
2006 Anatomy and Embryology  
The quality of the episcopic images resembles the quality of digital images of true histological sections with respect to resolution and contrast.  ...  We describe a new methodology for rapid 2D and 3D computer analysis and visualisation of gene expression and gene product pattern in the context of anatomy and tissue architecture.  ...  The optical axis of a Fig. 2 2 Images in different resolution, obtained with HREM using GFP filter sets.  ... 
doi:10.1007/s00429-005-0073-x pmid:16429276 fatcat:sjd4a7wpojel5caxspailoglx4

Sensory epithelia of the fish inner ear in 3D: studied with high-resolution contrast enhanced microCT

Tanja Schulz-Mirbach, Martin Heß, Brian D Metscher
2013 Frontiers in Zoology  
Comparison with maculae that have been 3D reconstructed based on histological serial sections and phalloidin-stained maculae showed high congruence in overall shape of the maculae studied here.  ...  Results: High-resolution microCT imaging of black mollies Poecilia sp.  ...  Ladich (Department of Behavioural Biology, Vienna, Austria) for providing the specimens of S. tinanti. This study was funded by the German Academic Exchange Service (TSM).  ... 
doi:10.1186/1742-9994-10-63 pmid:24160754 pmcid:PMC4177137 fatcat:rhbauxsv3rhl7aqbrgmmedpgri

A correlative imaging based methodology for accurate quantitative assessment of bone formation in additive manufactured implants

Hua Geng, Naomi M. Todd, Aine Devlin-Mullin, Gowsihan Poologasundarampillai, Taek Bo Kim, Kamel Madi, Sarah Cartmell, Christopher A. Mitchell, Julian R. Jones, Peter D. Lee
2016 Journal of materials science. Materials in medicine  
This semi-automatic methodology registered each modality using a coarse graining technique to speed the registration of 2D histology sections to high resolution 3D lCT datasets.  ...  A correlative imaging methodology was developed to accurately quantify bone formation in the complex lattice structure of additive manufactured implants.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://crea, which permits unrestricted use, distribution  ... 
doi:10.1007/s10856-016-5721-6 pmid:27153828 pmcid:PMC4859838 fatcat:olvyxsmxyzb6beelj3snfvhljm

Three-dimensional image reconstruction of distribution of Pnmt+ cell-derived cells in murine heart

Haibo Ni, Yange Wang, William Crawford, Shanzhuo Zhang, Longxian Cheng, Henggui Zhang, Ming Lei
2017 Scientific Data  
The final reconstructed 3D volume was 561 × 866 × 48 pixels (corresponding to spatial resolutions of 5.8, 8.9 and 2.5 mm in the x-, y-and z-direction respectively), and visualised in Paraview.  ...  In this dataset, a 3D reconstruction was carried out to visualise the distribution of PdCMs throughout the murine heart.  ...  In a previous study, Osuala et al. 9 showed a distinctive distribution of adrenergic-derived cells in murine heart through 3D reconstruction of stained histological images.  ... 
doi:10.1038/sdata.2017.134 pmid:28949324 pmcid:PMC5613735 fatcat:ocxh5whaczfjrkiil7urjmwmnq
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