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Blockface histology with optical coherence tomography: A comparison with Nissl staining

Caroline Magnain, Jean C. Augustinack, Martin Reuter, Christian Wachinger, Matthew P. Frosch, Timothy Ragan, Taner Akkin, Van J. Wedeen, David A. Boas, Bruce Fischl
2014 NeuroImage  
Spectral domain optical coherence tomography (SD-OCT) is a high resolution imaging technique that generates excellent contrast based on intrinsic optical properties of the tissue, such as neurons and fibers  ...  We compared blockface registration to SD-OCT and Nissl, respectively, and found that SD-OCT-blockface registration was significantly more accurate than Nissl-blockface registration.  ...  ., Blockface histology with optical coherence tomography: A comparison with Nissl staining, NeuroImage (2013), region revisited: cytoarchitecture  ... 
doi:10.1016/j.neuroimage.2013.08.072 pmid:24041872 pmcid:PMC4315235 fatcat:5iki4vpolvce3n7b5yoixvrsha

MRI parcellation of ex vivo medial temporal lobe

Jean C. Augustinack, Caroline Magnain, Martin Reuter, André J.W. van der Kouwe, David Boas, Bruce Fischl
2014 NeuroImage  
Based on our findings, both myelin and Nissl staining relate to contrast in ex vivo MRI.  ...  Localization of Brodmann areas 28 and 35 (entorhinal and perirhinal, respectively) demonstrates MRI based area boundaries validated with multiple methods and histological stains.  ...  Obtaining high quality histological images in 3D is an attractive alternative and optical coherence tomography may provide such a solution.  ... 
doi:10.1016/j.neuroimage.2013.05.053 pmid:23702414 pmcid:PMC3883990 fatcat:gtzhycjnzrgfdmioukf6ok646y

Colocalization of neurons in optical coherence microscopy and Nissl-stained histology in Brodmann's area 32 and area 21

Caroline Magnain, Jean C. Augustinack, Lee Tirrell, Morgan Fogarty, Matthew P. Frosch, David Boas, Bruce Fischl, Kathleen S. Rockland
2018 Brain Structure and Function  
In a previous report, we compared the correspondence of OCM acquired imaging of neurons with traditional Nissl stained histology in entorhinal cortex layer II.  ...  Optical coherence tomography (OCT) is an optical technique that uses backscattered light to highlight intrinsic structure, and when applied to brain tissue, it can resolve cortical layers and fiber bundles  ...  Acknowledgements The authors would like to thank the brain donors for their generous gift, Samantha Romano for help with histology and segmentation and Dr.  ... 
doi:10.1007/s00429-018-1777-z pmid:30328512 fatcat:4rv44v5ss5f6jd5i4dvs3342oa

A Review of Intrinsic Optical Imaging Serial Blockface Histology (ICI-SBH) for Whole Rodent Brain Imaging

Joël Lefebvre, Patrick Delafontaine-Martel, Frédéric Lesage
2019 Photonics  
These projects rely on the use of optical imaging to target neuronal structures with histological stains or fluorescent dyes that are either expressed by transgenic mice or injected at specific locations  ...  Serial blockface histology (SBH) systems using ICI modalities are then reported, followed by a review of some of their applications.  ...  For example, OCT and optical coherence microscopy (OCM) images measured in brain tissues were compared with adjacent slices labeled with Nissl staining.  ... 
doi:10.3390/photonics6020066 fatcat:qyfjrhymyndrzewigjrogxbbw4

A three-dimensional stereotaxic atlas of the gray short-tailed opossum (Monodelphis domestica) brain

Piotr Majka, Natalia Chlodzinska, Krzysztof Turlejski, Tomasz Banasik, Ruzanna L. Djavadian, Władysław P. Węglarz, Daniel K. Wójcik
2017 Brain Structure and Function  
of sections stained with the Nissl method and for myelinated fibers.  ...  The stereotaxic coordinate system was defined using a set of cranial landmarks: interaural line, bregma, and lambda, which allows for easy expression of any location within the brain with respect to the  ...  The first series of 264 sections was stained with the standard Nissl method, and the second with the Gallyas (1971) stain for myelinated fibers.  ... 
doi:10.1007/s00429-017-1540-x pmid:29214509 pmcid:PMC5884921 fatcat:wnget3a2c5eopmatpqxvwqcnhi

as -PSOCT: Volumetric microscopic imaging of human brain architecture and connectivity

Hui Wang, Caroline Magnain, Ruopeng Wang, Jay Dubb, Ani Varjabedian, Lee S. Tirrell, Allison Stevens, Jean C. Augustinack, Ender Konukoglu, Iman Aganj, Matthew P. Frosch, Jeremy D. Schmahmann (+2 others)
2018 NeuroImage  
In this study, we developed a fully automatic serial sectioning polarization sensitive optical coherence tomography (as-PSOCT) system to enable volumetric reconstruction of human brain samples with unprecedented  ...  Polarization sensitive optical coherence tomography (PSOCT) with serial sectioning has enabled the investigation of 3D structures in mouse and human brain tissue samples.  ...  Acknowledgments We thank Vivina Siless and Anastasia Yendiki for helpful discussions about tractography analysis and comparison with dMRI.  ... 
doi:10.1016/j.neuroimage.2017.10.012 pmid:29017866 pmcid:PMC5732037 fatcat:tr6imkudzfbbrdkn5pfn2ugdtu

Scalable mapping of myelin and neuron density in the human brain with micrometer resolution [article]

Hui Wang, Shuaibin Chang, Divya Varadarajan, Jiarui Yang, Ichun Anderson Chen, Sreekanth Kura, Caroline Magnain, Jean C Augustinack, Bruce Fischl, Douglas N Greve, David A Boas
2021 bioRxiv   pre-print
Optical Coherence Tomography (OCT) is an emerging 3D imaging technique that allows quantification of intrinsic optical properties such as scattering coefficient and back-scattering coefficient, and has  ...  To date, histology remains the golden standard, which is prone to errors and can only work on a small number of subjects.  ...  Mental Health (R01 MH123195, R01 MH121885), the National Institute for Neurological Disorders and Stroke (R01NS0525851, R21NS072652, R01NS070963, R01NS083534, 5U01NS086625, 5U24NS10059103, R01NS105820), a  ... 
doi:10.1101/2021.05.13.444005 fatcat:heblzk2jsjhoxneurl6dxwey7q

A Survey of Methods for 3D Histology Reconstruction

Jonas Pichat, Juan Eugenio Iglesias, Tarek Yousry, Sébastien Ourselin, Marc Modat
2018 Medical Image Analysis  
Histology permits the observation of otherwise invisible structures of the internal topography of a specimen.  ...  We then successively describe methods for 3D histology recontruction without and with the help of 3D medical imaging.  ...  From left to right, a screenshot of a T2w ex vivo slice (0.1×0.1×0.4mm 3 ), a visually corresponding blockface photograph (tissue surrounded by wax) and a Nissl-stained histological section.  ... 
doi:10.1016/ pmid:29502034 fatcat:ta5hlvqjpzenxhltfwh6p4mhqq

Architectonic Mapping of the Human Brain beyond Brodmann

Katrin Amunts, Karl Zilles
2015 Neuron  
Criteria for defining a cortical area will be discussed, considering novel preparations, imaging and optical methods, 2D and 3D quantitative architectonics, as well as high-performance computing including  ...  A triple-scale concept is proposed that includes repetitive modular-like structures and micro-and meso-maps.  ...  Optical coherence tomography (OCT) is a method already used to analyze the microstructure of human brain tissue.  ... 
doi:10.1016/j.neuron.2015.12.001 pmid:26687219 fatcat:cyjyuzlk6jcn5c2hbqm5idhxb4

Towards multimodal atlases of the human brain

Arthur W. Toga, Paul M. Thompson, Susumu Mori, Katrin Amunts, Karl Zilles
2006 Nature Reviews Neuroscience  
Comprehensive maps of brain structure have been created, at a variety of spatial scales, from anatomical specimens2 -5 and various histological preparations that reveal regional cytoarchitecture6 , 7,  ...  Cartographic approaches have been used for centuries to identify and target specific regions in the brain and to establish spatial relationships between a coordinate and a structure.  ...  These types of architecture were studied by visual inspection of Nissl-or myelin-stained histological sections in single brains.  ... 
doi:10.1038/nrn2012 pmid:17115077 pmcid:PMC3113553 fatcat:vb3kvw2wrjbahd67546jgvxtky

Automatic Segmentation of Human Cortical Layer-Complexes and Architectural Areas Using Ex vivo Diffusion MRI and Its Validation

Matteo Bastiani, Ana-Maria Oros-Peusquens, Arne Seehaus, Daniel Brenner, Klaus Möllenhoff, Avdo Celik, Jörg Felder, Hansjürgen Bratzke, Nadim J. Shah, Ralf Galuske, Rainer Goebel, Alard Roebroeck
2016 Frontiers in Neuroscience  
We validate our clustering results by histological analysis of the same tissue.  ...  We then used the signature of diffusion MRI signals along cortical depth as a criterion to detect area boundaries and find borders at which the signature changes abruptly.  ...  coherence tomography (Wang et al., 2011; Magnain et al., 2015) .  ... 
doi:10.3389/fnins.2016.00487 pmid:27891069 pmcid:PMC5102896 fatcat:isrov2tvbngb7b7fabguqjyz2e

Joint registration and synthesis using a probabilistic model for alignment of MRI and histological sections

Juan Eugenio Iglesias, Marc Modat, Loïc Peter, Allison Stevens, Roberto Annunziata, Tom Vercauteren, Ed Lein, Bruce Fischl, Sebastien Ourselin
2018 Medical Image Analysis  
Nonlinear registration of 2D histological sections with corresponding slices of MRI data is a critical step of 3D histology reconstruction.  ...  In our model, the MRI slice is assumed to be a contrast-warped, spatially deformed version of the histological section.  ...  In addition, BF has a financial interest in Cortico-Metrics, a company whose medical pursuits focus on brain imaging and measurement technologies.  ... 
doi:10.1016/ pmid:30282061 fatcat:gwxmcrob4zb4dk36xgqikrxjoi

Hard X-ray microtomography for virtual histology of the brain with cellular resolution

Griffin Rodgers
Contributions 2 Optimizing spatial and density resolution for X-ray virtual histology 3 Impact of fixation and paraffin embedding on mouse brain morphology and X-ray contrast Part 1: Data acquisition,  ...  The authors thank A. Rack and the staff at beamline ID19 of ESRF for support during the beamtime.  ...  Wanelik, and A. Bodey, Diamond Light Source I13-2, for their support during the beam time. The authors thank C. Bikis, University of Basel, and S.  ... 
doi:10.5451/unibas-ep85651 fatcat:7btknvr5lzhevdxgcyyj6sz23m

Association for Chemoreception Sciences (AChemS), 37th Annual Meeting, Bonita Springs, Florida, 22–25 April 2015:

2015 Chemical Senses  
By providing a critical review of the literature linking use of NNS with metabolic disturbances, and closely examining Downloaded from by  ...  One explanation for such a counterintuitive result is that consuming sweet tastes without typical post-ingestive outcomes could interfere with basic learning processes that normally operate to regulate  ...  The present work is an examination of the pig brain with Nissl, Golgi, and fluorescence-immunostained sections.  ... 
doi:10.1093/chemse/bjv029 fatcat:nf3ixsnfwfd5zcig6j3aagrura