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  4. Deep learning for classifying neuronal morphologies: combining topological data analysis and graph neural networks
 
preprint

Deep learning for classifying neuronal morphologies: combining topological data analysis and graph neural networks

Kanari, Lida  
•
Schmidt, Stanislav  
•
Casalegno, Francesco  
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September 15, 2024

The shape of neuronal morphologies plays a critical role in determining their dynamical properties and the functionality of the brain. With an abundance of neuronal morphology reconstructions, a robust definition of cell types is important to understand their role in brain functionality. However, an objective morphology classification scheme is hard to establish due to disagreements on the definition of cell types, on which subjective views of field experts show significant differences. The robust grouping of neurons based on their morphological shapes is important for generative models and for establishing a link between anatomical properties and other modalities, such as biophysical and transcriptomic information. We combine deep learning techniques with a variety of mathematical descriptions of neurons and evaluate the classification accuracy of different methods. We demonstrate that various methodologies, including graph neural networks, topological morphology descriptors, and morphometrics, consistently perform with the highest accuracy for a variety of datasets. Based on these methods, we present a robust classification of both inhibitory and excitatory cell types in the rodent cortex and propose a generalized scheme for a consistent classification of neurons into classes.

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Type
preprint
DOI
10.1101/2024.09.13.612635
Author(s)
Kanari, Lida  

EPFL

Schmidt, Stanislav  
Casalegno, Francesco  
Delattre, Emilie  

EPFL

Banjac, Jelena  
Negrello, Thomas
Shi, Ying  

EPFL

Meystre, Julie  

EPFL

Defferrard, Michaël  
Schürmann, Felix  
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Date Issued

2024-09-15

Publisher

bioRxiv

Subjects

machine learning

•

graph neural networks

•

algebraic topology

•

neuronal mor- phology classification

•

Topological Data Analysis

•

Artificial Intelligence

Written at

EPFL

EPFL units
BBP-CORE  
FunderFunding(s)Grant NumberGrant URL

Board of the Swiss Federal Institutes of Technology

Blue Brain Project

RelationRelated workURL/DOI

IsSupplementedBy

[dataset] Computational synthesis of cortical dendritic morphologies

https://zenodo.org/records/5909613

IsSupplementedBy

[code] Morphoclass

https://github.com/BlueBrain/morphoclass
Available on Infoscience
January 6, 2025
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/242549
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