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Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
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.
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
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
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
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
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.
Distributed under the terms of the BSD-3 license, "napari-bacseg" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.
FAQs
Bacterial segmentation and analysis platform than can inport/export files in multiple formats. Integrating many tools such as Cellpose, ColiCoords, Oufti/MicrobeTracker.
We found that napari-bacseg demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
Did you know?
Socket for GitHub automatically highlights issues in each pull request and monitors the health of all your open source dependencies. Discover the contents of your packages and block harmful activity before you install or update your dependencies.
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