Sep 21 – 23, 2021
Virtual
Europe/Berlin timezone

3D reconstruction and analysis of the macaque brain from histological slices

Sep 22, 2021, 6:00 PM
15m
Virtual

Virtual

Talk Reconstruction Contributed Talks: Reconstruction

Speakers

Aitor Morales-Gregorio (Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany and Institute of Zoology, University of Cologne, Cologne, Germany)Dr Rembrandt Bakker (Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany and Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, Netherlands)

Description

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 $\mu m$ thick, 250 $\mu m$ 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.

Figure 1

[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

Primary authors

Aitor Morales-Gregorio (Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany and Institute of Zoology, University of Cologne, Cologne, Germany) Dr Rembrandt Bakker (Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany and Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, Netherlands) Prof. Sacha van Albada (Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institut Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany and Institute of Zoology, University of Cologne, Cologne, Germany)

Presentation materials

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