Morphology-Classification

MorphoClass is a toolbox for neuronal morphologies processing and classification using machine learning.

Documentation
License
Static Typing
Code Style
CI

Installation

Clone the repository and set up the virtual environment sh git clone git@github.com:BlueBrain/morphoclass.git cd morphoclass python --version # should be 3.8 python -m venv venv . venv/bin/activate

Install morphoclass sh ./install.sh

Open the file docs/build/html/index.html to view the documentation.

Examples

MorphoClass functionalities can be accessed using either a command line interface or by importing morphoclass as a Python module and using it as a library.

Command-Line Interface

By installing MorphoClass, we get access to a command line interface with a main entrypoint morphoclass and various sub-commands. sh morphoclass --help ``` Usage: morphoclass [OPTIONS] COMMAND [ARGS]...

Welcome to the command line application for morphoclass.

All functionality is provided through respective sub-commands. To learn more about their functionality call the corresponding sub-command with the --help flag to see a detailed description.

Options: ...

Commands: ... ```

For instance, to train a model for classifying neuronal morphologies, we can check the help of the corresponding sub-command. sh morphoclass train --help ``` Usage: morphoclass train [OPTIONS]

Train a morphology classification model.

Options: ... ```

Python Interface

MorphoClass is a pure Python package, and can be used as any other module once it is installed.

For instance, we can load a PersLay-based model for morphology classification and check its documentation as follows. ```py

from morphoclass.models.coriandernet import CorianderNet help(CorianderNet) Help on class CorianderNet in module morphoclass.models.coriandernet:

class CorianderNet(torch.nn.modules.module.Module) | CorianderNet(nclasses=4, nfeatures=64, dropout=False) | | A PersLay-based neural network for neuron m-type classification. | | Parameters | ---------- ... ```

Documentation

For more examples and details on the installation, development setup, docker, the command line interface, and the python API please see the extended documentation on https://morphoclass.readthedocs.io

Funding & Acknowledgment

The development of this software 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.

Copyright © 2022-2022 Blue Brain Project/EPFL