Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
Project description
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
Create a virtual environment and then activate it:
conda create –-name napari-bacseg python==3.9
conda activate napari-bacseg
Install napari-bacseg
via pip:
pip install napari-bacseg
Launch Napari:
Napari
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
conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia
If the latest CUDA versions don't work, try an older version like cuda 11.3:
pip uninstall torch
conda install pytorch torchvision torchaudio cudatoolkit=11.3 -c pytorch -c nvidia
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.
Project details
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