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Histopathology in 3D: From three-dimensional reconstruction to multi-stain and multi-modal analysis

Derek Magee, Stephen Gilbert, Andrew Bulpitt, Yi Song, Nicholas Roberts, Nagitha Wijayathunga, Ruth Wilcox, Darren Treanor
2015 Journal of Pathology Informatics  
Our approach involves transforming dissimilar images into a multi-channel representation derived from co-occurrence statistics between roughly aligned images.  ...  Several authors, including the authors of this work, have extended the use of digital microscopy to three dimensions by stacking digital images of serial sections using image-based registration.  ...  However, such data are 2D only and as such, not suitable for use in building 3D models.  ... 
doi:10.4103/2153-3539.151890 pmid:25774317 pmcid:PMC4355830 fatcat:m47uklh7qza3rhuxt5w6iskhuu

Three-dimensional imaging and scanning: Current and future applications for pathology

Navid Farahani, Alex Braun, Dylan Jutt, Todd Huffman, Nick Reder, Zheng Liu, Yukako Yagi, Liron Pantanowitz
2017 Journal of Pathology Informatics  
Herein, we summarize current 3D imaging and 3D scanning methods, with an emphasis on techniques Imaging is vital for the assessment of physiologic and phenotypic details.  ...  These methods are capable of producing sets of two-dimensional (2D) images and three-dimensional (3D) reconstructions for interpretation. [2] [3] [4] 3D imagery provides a better way to visualize and accurately  ...  [71] Recent investigations into the use of 3D printing in anatomic pathology have driven the use of 3D scanners for gross surgical specimen capture.  ... 
doi:10.4103/jpi.jpi_32_17 pmid:28966836 pmcid:PMC5609355 fatcat:fanrcrebhvcytj2otpbrzdmhma

Three-Dimensional Models of Individual Cardiac Histoanatomy: Tools and Challenges

R. A.B BURTON, G. PLANK, J. E SCHNEIDER, V. GRAU, H. AHAMMER, S. L KEELING, J. LEE, N. P SMITH, D. GAVAGHAN, N. TRAYANOVA, P. KOHL
2006 Annals of the New York Academy of Sciences  
by reference to detailed atlases of serial histology obtained from representative samples.  ...  of histoanatomically detailed models of cardiac 3D 301 302 ANNALS NEW YORK ACADEMY OF SCIENCES structure and function at hitherto unprecedented resolution and accuracy (based on 26.4 × 26.4 × 24.4 m MRI  ...  3D anatomical MRI, see next section).  ... 
doi:10.1196/annals.1380.023 pmid:17132791 pmcid:PMC3313659 fatcat:hia7yl6f7zajfboxpnh6olseuq

The Open Physiology workflow: modeling processes over physiology circuitboards of interoperable tissue units

Bernard de Bono, Soroush Safaei, Pierre Grenon, David P. Nickerson, Samuel Alexander, Michiel Helvensteijn, Joost N. Kok, Natallia Kokash, Alan Wu, Tommy Yu, Peter Hunter, Richard A. Baldock
2015 Frontiers in Physiology  
A key challenge for the physiology modeling community is to enable the searching, objective comparison and, ultimately, re-use of models and associated data that are interoperable in terms of their physiological  ...  In particular, we show how, via this approach, we can systematically extract, parcellate and annotate tissue histology data to represent component units of tissue function.  ...  ACKNOWLEDGMENTS The authors gratefully acknowledge grants from the Innovative Medicines Initiative (IMI) grants 115156-2 (DDMoRe) and 115568 (AETIONOMY), as well as European Union FP7 grant agreement 600841  ... 
doi:10.3389/fphys.2015.00024 pmid:25759670 pmcid:PMC4338662 fatcat:tsrg5z4mafghpc2x3f5mpmbqei

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E Rood, Orr Ashenberg, Ethan Cerami, Robert J Coffey, Emek Demir, Li Ding, Edward D Esplin (+26 others)
2020 Cell  
treatments of cancer patients and those at risk for cancer.  ...  Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution.  ...  Toolbox Used for Building 3D Tumor Atlases across Scales The HTAN toolbox includes molecular, spatiomolecular, histological, and anatomical profiling.  ... 
doi:10.1016/j.cell.2020.03.053 pmid:32302568 pmcid:PMC7376497 fatcat:jlxyctmcfrewlnjzhxrckim5p4

A structural-functional MRI-based disease atlas: application to computer-aided-diagnosis of prostate cancer

G. Xiao, B. Bloch, J. Chappelow, E. Genega, N. Rofsky, R. Lenkinski, A. Madabhushi, Benoit M. Dawant, David R. Haynor
2010 Medical Imaging 2010: Image Processing  
In this paper, we present a novel framework for the construction of a multi-parametric MRI-based data-driven disease atlas consisting of multi-modal and multi-protocol data from across multiple patient  ...  Preliminary investigation in quantitatively correlating the disease signatures from across the spatial and data driven atlases suggests that our quantitative atlas framework could emerge as a powerful  ...  The authors would like to acknowledge Johnson Henry from Teleradiology Solutions, Bangalore, India for his assistance in providing the expert segmentations.  ... 
doi:10.1117/12.845554 dblp:conf/miip/XiaoBCGRLM10 fatcat:iw6r2n7q2nhvrcfvejfoh74x6e

A Survey of Methods for 3D Histology Reconstruction

Jonas Pichat, Juan Eugenio Iglesias, Tarek Yousry, Sébastien Ourselin, Marc Modat
2018 Medical Image Analysis  
This paper reviews almost three decades of methods for 3D reconstruction from serial sections, used in the study of many different types of tissue.  ...  We then successively describe methods for 3D histology recontruction without and with the help of 3D medical imaging.  ...  Smriti Patodia, from UCL Institute of Neurology (Department of Neuropathology), for her comments on Section 2 and the images used in Figures  ... 
doi:10.1016/j.media.2018.02.004 pmid:29502034 fatcat:ta5hlvqjpzenxhltfwh6p4mhqq

Comprehensive Integrated Anatomical and Molecular Atlas of Rodent Intrinsic Cardiac Nervous System [article]

Achanta Sirisha, Gorky Jonathan, Leung Clara, Moss Alison, Robbins Shaina, Eisenman Leonard, Chen Jin, Tappan Susan, Maci Heal, Farhani Navid, Huffman Todd, Cheng Zixi (+2 others)
2019 bioRxiv   pre-print
We present a comprehensive 3D mapping of rat ICN in the overall histological and ontological context of the heart and demonstrating anatomically specific single-neuron transcriptional gradients.  ...  The development of the approaches needed to acquire these data have produced methods pipelines which can achieve the goals of the NIH Directors Initiative Stimulating Peripheral Activity to Relieve Conditions  ...  The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.  ... 
doi:10.1101/661033 fatcat:56v54dkiifc2ffgpfl5hyc4che

Validation strategies for the interpretation of microstructure imaging using diffusion MRI

Tim B. Dyrby, Giorgio M. Innocenti, Martin Bech, Henrik Lundell
2018 NeuroImage  
A number of mathematical models already suggest microstructural interpretations of diffusion MRI (dMRI) data.  ...  Here, we review current literature in this field and highlight the integrative work across anatomical length scales that is needed to validate and trust a new dMRI method.  ...  Acknowledgement TD was supported by the Capital Region Research Foundation (grant number: A5657), HL was supported by the Danish Council for Independent Research (4093-00280A and 4093-00280B).  ... 
doi:10.1016/j.neuroimage.2018.06.049 pmid:29920374 fatcat:n3t7t6gcuvf25psofwpo4cfcey

A High-Resolution Interactive Atlas of the Human Brainstem Using Magnetic Resonance Imaging

Syed M Adil, Evan Calabrese, Lefko T Charalambous, James J Cook, Shervin Rahimpour, Ahmet F Atik, Gary P Cofer, Beth A Parente, G Allan Johnson, Shivanand P Lad, Leonard E White
2021 NeuroImage  
Conventional atlases of the human brainstem are limited by the inflexible, sparsely-sampled, two-dimensional nature of histology, or the low spatial resolution of conventional magnetic resonance imaging  ...  A single human brainstem specimen extending from the rostral diencephalon through the caudal medulla was prepared for imaging after the brain was removed from a 65-year-old male within 24 hours of death  ...  Acknowledgments We thank Lucy Upchurch for her essential role in developing and maintaining the computer architecture and Steve Noh for his assistance in segmentation.  ... 
doi:10.1016/j.neuroimage.2021.118135 pmid:33951517 pmcid:PMC8480283 fatcat:526uqwqwbfdclfulb5tqjekk54

An imaging workflow for characterizing phenotypical change in large histological mouse model datasets

Kishore Mosaliganti, Tony Pan, Randall Ridgway, Richard Sharp, Lee Cooper, Alex Gulacy, Ashish Sharma, Okan Irfanoglu, Raghu Machiraju, Tahsin Kurc, Alain de Bruin, Pamela Wenzel (+3 others)
2008 Journal of Biomedical Informatics  
Additional confidence stem from agreement in the 3D visualization and the quantitative results generated. Availability: The source code is available upon request.  ...  Result: This workflow includes four major components: (i) serial section image acquisition, (ii) image preprocessing, (iii) image analysis involving 2D pair-wise registration, 2D segmentation and 3D reconstruction  ...  Acknowledgments This work was supported in part by funding from the National Institutes of Health NIBIB BISTI P20-EB000591, and The National Science Foundation (Grants CNS-0615155 and CNS-0509326).  ... 
doi:10.1016/j.jbi.2008.03.013 pmid:18502696 pmcid:PMC2657595 fatcat:manfzwyk5vag3kjhy7ykpgntei

Mass Spectrometry Imaging and Integration with Other Imaging Modalities for Greater Molecular Understanding of Biological Tissues

Tiffany Porta Siegel, Gregory Hamm, Josephine Bunch, Jo Cappell, John S. Fletcher, Kristina Schwamborn
2018 Molecular Imaging and Biology  
IMC is a multiplexed method for tissue phenotyping, imaging signalling pathway or cell marker assessment, at sub-cellular resolution (1 μm).  ...  ., increased spatial resolution, increased detection sensitivity especially for large molecules, higher throughput analysis and data management.  ...  J.S.F. acknowledges financial support from the Swedish Research Council (VR).  ... 
doi:10.1007/s11307-018-1267-y pmid:30167993 fatcat:ei3xvuzlcvhfljbxxqwq6yf6aa

Disease-Specific Brain Atlases [chapter]

Paul M. Thompson, Michael S. Mega, Arthur W. Toga
2000 Brain Mapping: The Disorders  
Acknowledgments This work was supported by research grants from the National Center for Research Resources (P41 RR13642 and RR05956), the National Institute of Neurological Disorders and Stroke and the  ...  National Institute of Mental Health (NINDS/NIMH NS38753), and by a Human Brain Project grant to the International Consortium for Brain Mapping, funded jointly by NIMH and NIDA (P20 MH/DA52176).  ...  They first build large systems of anatomical models in the atlas and patient's scan .  ... 
doi:10.1016/b978-012481460-8/50009-3 fatcat:63fa3fvfdbbf3hq6qm4dy5nwny

Comprehensive cellular-resolution atlas of the adult human brain

Song-Lin Ding, Joshua J. Royall, Susan M. Sunkin, Lydia Ng, Benjamin A.C. Facer, Phil Lesnar, Angie Guillozet-Bongaarts, Bergen McMurray, Aaron Szafer, Tim A. Dolbeare, Allison Stevens, Lee Tirrell (+28 others)
2016 Journal of Comparative Neurology  
Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains.  ...  Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations.  ...  MATERIALS AND METHODS Specimen 2 Only a small portion of the superior colliculus regions was available. 3 BigBrain (Amunts et al., 2013) from this group is a whole brain 3D model based on silver stain  ... 
doi:10.1002/cne.24097 fatcat:dycahbnkzrhihkiyaf3qdkv75e

Comprehensive cellular-resolution atlas of the adult human brain

Song-Lin Ding, Joshua J. Royall, Susan M. Sunkin, Lydia Ng, Benjamin A.C. Facer, Phil Lesnar, Angie Guillozet-Bongaarts, Bergen McMurray, Aaron Szafer, Tim A. Dolbeare, Allison Stevens, Lee Tirrell (+28 others)
2016 Journal of Comparative Neurology  
Correlated neuroimaging and histological structural delineation allowed fine feature identification in MRI data and subsequent structural identification in MRI data from other brains.  ...  Neocortical delineations were done for sulci, gyri, and modified Brodmann areas to link macroscopic anatomical and microscopic cytoarchitectural parcellations.  ...  MATERIALS AND METHODS Specimen 2 Only a small portion of the superior colliculus regions was available. 3 BigBrain (Amunts et al., 2013) from this group is a whole brain 3D model based on silver stain  ... 
doi:10.1002/cne.24080 pmid:27418273 pmcid:PMC5054943 fatcat:qsm5sbg7rvbsjntpsqzz64e7h4
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