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
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).
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 ./TMDFor installation of viewers (only works in Python2)
pip install ./TMD[viewer]