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ivadomed Overview

DOI Coverage Status test status publish package Documentation Status License: MIT Twitter Follow

ivadomed is an integrated framework for medical image analysis with deep learning.

The technical documentation is available here. The more detailed installation instruction is available there

Installation

ivadomed requires Python >= 3.7 and < 3.10 as well as PyTorch == 1.8. We recommend working under a virtual environment, which could be set as follows:

python -m venv ivadomed_env
source ivadomed_env/bin/activate

Install from release (recommended)

Install ivadomed and its requirements from Pypi <https://pypi.org/project/ivadomed/>__:

pip install --upgrade pip
pip install ivadomed

Install from source

Bleeding-edge developments builds are available on the project's master branch on Github. Installation procedure is the following:

git clone https://github.com/neuropoly/ivadomed.git
cd ivadomed
pip install -e .

Contributors

This project results from a collaboration between the NeuroPoly Lab and the Mila. The main funding source is IVADO.

List of contributors

Consult our Wiki(https://github.com/ivadomed/ivadomed/wiki) here for more help

ivadomed's Projects

anima-bin icon anima-bin

pip version of https://anima.readthedocs.io

brainstorm3 icon brainstorm3

Brainstorm software: MEG, EEG, fNIRS, ECoG, sEEG and electrophysiology

canproco icon canproco

Code for preprocessing the CanProCo brain and spinal cord dataset

data_example_spinegeneric icon data_example_spinegeneric

Dataset generated from the spine-generic dataset. For each subject, all contrasts are registered on the GRE-T1w contrast.

doc-figures icon doc-figures

Repository that contains most figures for ivadomed documentation.

ivadomed icon ivadomed

Repository on the collaborative IVADO medical imaging project between the Mila and NeuroPoly labs.

meeg-brainstorm icon meeg-brainstorm

Repository for training MEEG datasets with the ivadomed framework in Brainstorm

model-seg-dcm icon model-seg-dcm

Segmentation of lesions on MRI scans in patients with Degenerative Cervical Myelopathy (DCM)

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