TMD: Topological Morphology Descriptor

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

Details

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

Funding

The Blue Brain Project receives Swiss government funding from ETH Board of the ETH Domain (ETH = Swiss Federal Institutes of Technology) and receives support as a research center by the École polytechnique fédérale de Lausanne (EPFL).

Sotware description

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.

Supported OS

Ubuntu : 12.0, 14.04, 16.04

macOS: Sierra 10.13.3

Required Dependencies

Python : 2.7+

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

Optional Dependencies

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

Instalation instructions

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]

arnaudon/TMD