napari-AxonDeepSeg (Work in progress)

A (work in progress) plugin for napari that implements the AxonDeepSeg tools

Instructions to install the plugin

1. Clone the AxonDeepSeg repo.
2. In the AxonDeepSeg repo, open the environment.yml file and change the fsleyes requirement to napari. While you're here, you could change the name of the environment to ads_napari_env. Save the file.
3. Follow the instructions of the AxonDeepSeg installation documentation.
4. Clone this repo:

git clone https://github.com/axondeepseg/napari-plugin.git

5. Get to the napari-ADS folder:

cd napari-plugin
cd napari-ADS

6. While the conda environment in which you installed AxonDeepSeg is active, use this command to install the plugin:

pip install -e .

7. Open napari:

napari

8. The plugin should appear in the plugins tab