Sep 21 – 23, 2021
Europe/Berlin timezone

3D Reconstruction of BigBrain2: Challenges and Milestones

Sep 22, 2021, 5:15 PM


Board: 12
Talk Reconstruction Contributed Talks: Reconstruction


Dr Hartmut Mohlberg (Forschungszentrum Jülich)Dr Claude Lepage (McGill University)


The current state of reconstruction of BigBrain2 is presented, describing
the brain of a 30 year old anonymous male donor. As for the original BigBrain,
cell-body stained histological coronal sections were digitized and
reconstructed in 3D. Sections are first repaired at 20 microns in-plane
resolution to correct for manipulation artifacts, then aligned to the MRI
serving as the undistorted frame of reference. Given the time-consuming
nature of the manual aspects of the corrections, including provenance
tracking of the operations for reproducibility and variability assessment
in section repairs, every fifth section was initially repaired and a first
optically-balanced aligned volume at 100 microns isoptropic resolution was
obtained. This preliminary 3D alignment at 100 microns defines a transformation
to the MRI which can subsequently be used for the newly repaired sections being
added to the pipeline (25% completed). The transformations defined at 100 microns
will be applied at full resolution to obtain a 3D volume at 20 microns
isotropic resolution prior to performing non-linear section-to-section
alignment at finer resolution levels once all sections have been repaired.

This multi-resolution approach can be extended for future reconstructions
of BigBrain3 at full 1 micron resolution by first downsampling the 1 micron
sections to 20 microns. With provenance tracking, manual repair operations
carried at 20 microns can be reproduced at the 1 micron level.

Primary authors

Dr Hartmut Mohlberg (Forschungszentrum Jülich) Dr Claude Lepage (McGill University)


Prof. Katrin Amunts (Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich) Dr Alan C. Evans (Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada) Susanne Wenzel (Forschungszentrum Jülich GmbH) Dr Paule Joanne Toussaint (McGill University)

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