Topology of the mesoscale connectome of the mouse brain

DOI10.1515/CMB-2020-0106MaRDI QIDQ2236680zbMATH OpenOpenAlexFDO

Authors Pascal Grange

Publication date 26 October 2021

Published in Computational and Mathematical Biophysics (Search for Journal in Brave)

Copyright license Creative Commons Attribution 4.0 International

Full work available at URL https://arxiv.org/abs/1811.04698

zbMATH Keywords

computational topologyconnectomemouse neuroanatomy

Mathematics Subject Classification ID

Simplicial sets and complexes in algebraic topology (55U10) Neural networks for/in biological studies, artificial life and related topics (92B20) Computational methods for problems pertaining to biology (92-08) Computational methods for problems pertaining to algebraic topology (55-08)

Abstract: The wiring diagram of the mouse brain has recently been mapped at a mesoscopic scale in the Allen Mouse Brain Connectivity Atlas. Axonal projections from brain regions were traced using green fluoresent proteins. The resulting data were registered to a common three-dimensional reference space. They yielded a matrix of connection strengths between 213 brain regions. Global features such as closed loops formed by connections of similar intensity can be inferred using tools from persistent homology. We map the wiring diagram of the mouse brain to a simplicial complex (filtered by connection strengths). We work out generators of the first homology group. Some regions, including nucleus accumbens, are connected to the entire brain by loops, whereas no region has non-zero connection strength to all brain regions. Thousands of loops go through the isocortex, the striatum and the thalamus. On the other hand, medulla is the only major brain compartment that contains more than 100 loops.

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Cites work

• A functorial Dowker theorem and persistent homology of asymmetric networks
• Clique topology reveals intrinsic geometric structure in neural correlations
• Cliques and cavities in the human connectome
• Collective dynamics of `small-world' networks
• Computational topology. An introduction
• Computing persistent homology
• Emergence of Scaling in Random Networks
• Javaplex: a research software package for persistent (co)homology
• Topological persistence and simplification
• Topology of viral evolution

Cited in

(4)

• Simplex closing probabilities in directed graphs
• Cliques and cavities in the human connectome
• Brain chains as topological signatures for Alzheimer's disease
• Topological adventures in neuroscience

Describes a project that uses

Uses Software

• javaPlex
• CliqueTop

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