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BacSeg

napari-bacseg

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

    License BSD-3 PyPI Python Version tests codecov napari hub

    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.

    Version:

    • 1.0.16

    Last updated:

    • 11 January 2024

    First released:

    • 24 February 2023

    License:

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 3
    • Forks: 2
    • Issues + PRs: 0

    Python versions supported:

    Operating system:

    Requirements:

    • napari>=0.4.17
    • opencv-python
    • picassosr==0.6.5
    • numpy
    • pyqt5
    • pyqt6
    • qtpy
    • cellpose[all]>=2.1.1
    • scipy
    • torch
    • natsort
    • tqdm
    • imagecodecs
    • tifffile
    • pandas
    • mat4py
    • glob2
    • matplotlib
    • scikit-image
    • roifile
    • openpyxl
    • shapely
    • colicoords
    • psutil
    • xmltodict
    • astropy
    • tiler
    • imageio-ffmpeg
    • aicspylibczi
    • czifile
    • omnipose
    • h5py

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