Lecture (Invited)

FZJ-2025-04893

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Working with quantitative cortical cell densities using siibra

Dickscheid, T.FZJ* ; Bludau, S.FZJ*

2025

Abstract: The regional microstructure of cortical brain areas, along with their connectivity to other regions, is linked to their functional profile. Consequently, microstructure varies significantly between different brain region. Along with modern image analysis methods, the BigBrain provides a unique resource for quantifying microstructure in terms of numbers, densities, and distributions of cell bodies at different locations in the brain. In this tutorial, we demonstrate how the siibra toolsuite can be used to access micrometer resolution BigBrain image data and extract cortical image patches for custom regions of interest. We will show how locations can be specified or sampled in interactive and scripted workflows, and demonstrate how state of the art AI models can be used to extract and quantify cell instances from extracted image patches in a reproducible fashion. We will present a dataset of layer-specific cell densities for areas defined in the Julich-Brain cytoarchitectonic atlas, which has been created on the basis of these ideas and is available through siibra.

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Contributing Institute(s):

1. Strukturelle und funktionelle Organisation des Gehirns (INM-1)

Research Program(s):

1. 5254 - Neuroscientific Data Analytics and AI (POF4-525) (POF4-525)
2. 5251 - Multilevel Brain Organization and Variability (POF4-525) (POF4-525)
3. HIBALL - Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) (InterLabs-0015) (InterLabs-0015)
4. EBRAINS 2.0 - EBRAINS 2.0: A Research Infrastructure to Advance Neuroscience and Brain Health (101147319) (101147319)

Appears in the scientific report 2025

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