Conference Presentation (After Call)

FZJ-2021-04674

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png 3D reconstruction and analysis of the macaque brain from histological slices

Morales-Gregorio, A. (Corresponding author)FZJ* ; Bakker, R. (Corresponding author)FZJ* ; van Albada, S.FZJ*

2021

Please use a persistent id in citations: http://hdl.handle.net/2128/29261

Abstract: Given the usefulness of the BigBrain high resolution histological volume, it would be very valuable to have a similar public domain resource for the macaque. Isotropic high resolution data to build such a resource is not currently available, but as an initial step we present a histological volume based on the NIH Blueprint Non-Human Primate (NHP) Atlas [1], acquired by the Allen Institute and funded by the NIH. Our contribution is to take the set of Nissl stained slices (50 μm thick, 250 μm apart) and to create a smooth volume by calculating the optimal alignment. We used open tools [2, 3] for processing, modernized the code of the poSSum three-dimensional reconstruction toolbox [4] and extended the deformable registration method thereof, using the an MRI-based macaque atlas [5] as a reference template. We will use the reconstructed volume to estimate neuron densities across all cortical areas used in the core-nets.org macaque connectivity database [6]. Besides adding to the body of knowledge on the cytoarchitecture [7] and geometry of the macaque cortex, this work will provide tools to further analyze histological data and support large-scale dynamical modeling studies.[1] NIH Blueprint NHP Atlas, www.blueprintnhpatlas.org[2] Bakker et al. Neuroinformatics, 2015[3] Microdraw, microdraw.pasteur.fr[4] Majka et al. Journal of Comparative Neurology, 2016[5] Calabrese et al. NeuroImage, 2015[6] Markov et al. Cerebral Cortex, 2012[7] Beul and Hilgetag. NeuroImage, 2019

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Contributing Institute(s):

1. Computational and Systems Neuroscience (INM-6)
2. Theoretical Neuroscience (IAS-6)
3. Jara-Institut Brain structure-function relationships (INM-10)

Research Program(s):

1. 5231 - Neuroscientific Foundations (POF4-523) (POF4-523)
2. HBP SGA3 - Human Brain Project Specific Grant Agreement 3 (945539) (945539)
3. DFG project 347572269 - Heterogenität von Zytoarchitektur, Chemoarchitektur und Konnektivität in einem großskaligen Computermodell der menschlichen Großhirnrinde (347572269) (347572269)

Appears in the scientific report 2021

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Database coverage:

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