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[!WARNING]\n\u003e The Blue Brain Project concluded in December 2024, so development has ceased under the BlueBrain GitHub organization.\n\u003e Future development will take place at: https://github.com/openbraininstitute/TMD\n\n# TMD\n\n[![Run all tox jobs using Python3](https://github.com/BlueBrain/TMD/actions/workflows/run-tox.yml/badge.svg)](https://github.com/BlueBrain/TMD/actions/workflows/run-tox.yml)\n[![license](https://img.shields.io/pypi/l/tmd.svg)](https://github.com/BlueBrain/TMD/blob/master/LICENSE-LGPL.txt)\n[![codecov.io](https://codecov.io/github/BlueBrain/TMD/coverage.svg?branch=master)](https://codecov.io/github/BlueBrain/TMD?branch=master)\n[![Documentation Status](https://readthedocs.org/projects/tmd/badge/?version=latest)](http://tmd.readthedocs.io/en/latest/?badge=latest)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10678146.svg)](https://doi.org/10.5281/zenodo.10678146)\n\nA python package for the topological analysis of neurons.\n\nThe TMD performs the topological analysis of neuronal morphologies and extracts the persistence\nbarcodes of trees.\n\nThis Python module includes:\n\n* Basic loading of neuronal morphologies in swc and h5 file format.\n* Extraction of the topological descriptors of tree morphologies.\n* Visualization of neuronal trees and neurons.\n* Plotting persistence diagrams, barcodes and images.\n\n\n## Installation\n\nThis package should be installed using pip:\n\n```bash\npip install TMD\n```\n\nFor installation of optional viewers:\n\n```bash\npip install TMD[viewer]\n```\n\n\n## Usage\n\n```python\n# Import the TMD toolkit in IPython\nimport tmd\n\n# Load a neuron\nneuron = tmd.io.load_neuron('input_path_to_file/input_file.swc')\n\n# Extract the tmd of a neurite, i.e., neuronal tree\npd = tmd.methods.get_persistence_diagram(neuron.neurites[0])\n```\n\n## Citation\n\nIf you use this software or method for your research, we kindly ask you to cite the following publication associated to this repository:\n\n**A Topological Representation of Branching Neuronal Morphologies**\n\n_Cite this article as:_\n\nKanari, L., Dłotko P., Scolamiero M., et al., A Topological Representation of Branching Neuronal Morphologies, Neuroinformatics 16, nᵒ 1 (2018): 3‑13. https://doi.org/10.1007/s12021-017-9341-1.\n\n\n## Related publications\n\n**Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex, Cerebral Cortex**\n\n_Cite this article as:_\n\nDeitcher Y., Eyal G., Kanari L., et al., Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex, Cerebral Cortex, Volume 27, Issue 11, November 2017, Pages 5398–5414, https://doi.org/10.1093/cercor/bhx226\n\n**Objective Morphological Classification of Neocortical Pyramidal Cells**:\n\n_Cite this article as:_\n\nLida Kanari, Srikanth Ramaswamy, Ying Shi, Sebastien Morand, Julie Meystre, Rodrigo Perin, Marwan Abdellah, Yun Wang, Kathryn Hess, Henry Markram, Objective Morphological Classification of Neocortical Pyramidal Cells, Cerebral Cortex, Volume 29, Issue 4, April 2019, Pages 1719-1735, https://doi.org/10.1093/cercor/bhy339\n\nDeveloped in Blue Brain Project.\n\n## Funding \u0026 Acknowledgment\n\nThe development of this software was supported by funding to the Blue Brain Project, a research\ncenter of the École polytechnique fédérale de Lausanne (EPFL), from the Swiss government’s ETH\nBoard of the Swiss Federal Institutes of Technology.\n\nFor license and authors, see `LICENSE.txt` and `AUTHORS.md` respectively.\n\nCopyright © 2021-2022 Blue Brain Project/EPFL\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Ftmd","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbluebrain%2Ftmd","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbluebrain%2Ftmd/lists"}