5th BigBrain Workshop - Insights from the BigBrain

Session

Contributed Talks: Reconstruction

Session2

22 Sept 2021, 17:15

Virtual

Conveners

Contributed Talks: Reconstruction

• Konrad Wagstyl (Wellcome Centre for Human Neuroimaging, University College London)

12. 3D Reconstruction of BigBrain2: Challenges and Milestones

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

22/09/2021, 17:15

Reconstruction

Talk

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...

24. Strategies and challenges for building a 1 micron brain from histology

Dr Timo Dickscheid (Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich), Marcel Huysegoms (Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich)

22/09/2021, 17:30

Reconstruction

Talk

Mapping the microscopical organization of the human brain provides an important basis for multimodal brain atlases, and is indispensable for linking functional, physiological, connectivity, molecular, or genetic properties to their cellular correlates. The BigBrain (Amunts et al., 2013) is a 3D model of a complete human brain at microscopic resolution, constructed from more than 7000...

10. 3D reconstruction of 20 neurotransmitter receptor atlases from 2D autoradiographs

Dr Thomas Funck (Institute of Neuroscience and Medicine INM-1, Research Centre Jülich, Jülich, Germany)

22/09/2021, 17:45

Reconstruction

Talk

We present a 3D reconstruction pipeline for 2D autoradiographs that will allow for the creation of the first ever set of ultra-high resolution (50𝜇m). The 3D atlases for 20 different neurotransmitter binding sites in the human brain. This pipeline was designed to overcome significant challenges in the data, including: non-linear deformations in the brain tissue, intensity variations between...

8. 3D reconstruction and analysis of the macaque brain from histological slices

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)

22/09/2021, 18:00

Reconstruction

Talk

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...

11. MRI guided hierarchical sectioning and stitching of brain blocks for alignment of digitized histology to corresponding MR images

Prof. Amir Shmuel (McGill University), Mr Sethu Boopathy Jegathambal (McGill University)

22/09/2021, 18:15

Reconstruction

Talk

Ex-vivo high-resolution MRI of brain tissue can provide morphological and microstructural information. MR images can also serve as undistorted references for the reconstruction of digitized histology, immunohistochemistry, or clearing techniques. Small-bore scanners, equipped with powerful gradients systems and operating at ultra-high magnetic fields present the optimal conditions for ex-vivo...