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

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

./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.

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.

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.

>>> from morphoclass.models.coriander_net import CorianderNet
>>> help(CorianderNet)

Help on class CorianderNet in module morphoclass.models.coriander_net:

class CorianderNet(torch.nn.modules.module.Module)
 |  CorianderNet(n_classes=4, n_features=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.

BlueBrain / morphoclass

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