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Histopathology in 3D: From three-dimensional reconstruction to multi-stain and multi-modal analysis
2015
Journal of Pathology Informatics
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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
2017
Journal of Pathology Informatics
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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
2006
Annals of the New York Academy of Sciences
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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
2015
Frontiers in Physiology
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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
2020
Cell
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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
2010
Medical Imaging 2010: Image Processing
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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
2018
Medical Image Analysis
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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]
2019
bioRxiv
pre-print
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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
2018
NeuroImage
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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
2021
NeuroImage
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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
2008
Journal of Biomedical Informatics
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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
2018
Molecular Imaging and Biology
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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]
2000
Brain Mapping: The Disorders
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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
2016
Journal of Comparative Neurology
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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
2016
Journal of Comparative Neurology
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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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