https://github.com/bluebrain/morphoclass
Neuronal morphology preparation and classification using Machine Learning.
https://github.com/bluebrain/morphoclass
classification-models morphologies
Last synced: 12 months ago
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Neuronal morphology preparation and classification using Machine Learning.
- Host: GitHub
- URL: https://github.com/bluebrain/morphoclass
- Owner: BlueBrain
- License: apache-2.0
- Created: 2022-04-01T08:28:27.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2024-07-05T12:57:51.000Z (almost 2 years ago)
- Last Synced: 2024-11-13T01:03:04.811Z (over 1 year ago)
- Topics: classification-models, morphologies
- Language: Python
- Homepage: https://morphoclass.readthedocs.io
- Size: 1.53 MB
- Stars: 8
- Watchers: 4
- Forks: 4
- Open Issues: 23
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
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README
# 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.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.
Copyright © 2022-2022 Blue Brain Project/EPFL