The TMD performs the topological analysis of neuronal morphologies and extracts the persistence barcodes of trees.

©Blue Brain Project/EPFL 2005 – 2019. All rights reserved

Author: Lida Kanari

Contributors: Pawel Dlotko, Benoit Coste

Publication:

A Topological Representation of Branching Neuronal Morphologies

Cite this article as: Kanari, L., Dłotko, P., Scolamiero, M. et al. Neuroinform (2018) 16:3. DOI: https://doi.org/10.1007/s12021-017-9341-1

Related publications:

Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex.

Cite this article as: Deitcher Y., Eyal G., Kanari L., et al. Cerebral Cortex (2017) 27:11 DOI: https://doi.org/10.1093/cercor/bhx226

Objective Classification of Neocortical Pyramidal Cells DOI: http://dx.doi.org/10.1101/349977

Developed in Blue Brain Project

This project/research was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology.

This Python module includes:

• Basic loading of neuronal morphologies in swc and h5 file format.
• Extraction of the topological descriptors of tree morphologies.
• Visualization of neuronal trees and neurons.
• Ploting persistence diagrams, barcodes and images.

Ubuntu : 12.0, 14.04, 16.04

macOS: Sierra 10.13.3

Python : 2.7+

numpy : 1.8.1+, scipy : 0.13.3+, enum34 : 1.0.4+, scikit-learn : 0.19.1+, munkres: 1.0.12+

h5py : 2.8.0+ (optional), matplotlib : 1.3.1+ (required for viewer mode)

virtualenv test_tmd
source ./test_tmd/bin/activate
git clone https://github.com/BlueBrain/TMD
pip install ./TMD

For installation of viewers (only works in Python2)

pip install ./TMD[viewer]

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