napari-BacSEG

Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installing BacSeg from PyPi

Create a new conda environment:

conda create --name napari-bacseg python==3.9
conda activate napari-bacseg
conda install -c anaconda git
conda update --all

Install napari-bacseg via pip:

pip install napari-bacseg

Launch Napari:

napari

Install latest version of 'napri-bacseg' from pip:

pip install napari-bacseg --upgrade

Select napari-bacseg from the Plugins dropdown menu

Installing BacSeg From GitHub

conda create –-name napari-bacseg python==3.9
conda activate napari-bacseg
conda install -c anaconda git
conda update --all

pip install napari[all]

pip install git+https://github.com/piedrro/napari-bacseg.git

Updating BacSeg From Github

Once you have installed the plugin, you can update the plugin by running the following commands:

pip install git+https://github.com/piedrro/napari-bacseg.git

GPU Installation

Once you have installed the plugin, you can install the GPU version of the plugin by running the following commands:

pip uninstall torch torchvision torchaudio -y
pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu118

If the latest CUDA versions don't work, try an older version like cuda 11.3:

pip uninstall torch torchvision torchaudio -y
pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu113

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-bacseg" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.