BacSEG

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

  • Piers Turner

License BSD-3 PyPI Python Version 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 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.

Version:

  • 1.1.2

Last updated:

  • 2024-11-13

First released:

  • 2023-02-24

License:

  • Unavailable

Supported data:

  • Information not submitted

Plugin type:

Open extension:

Save extension:

Python versions supported:

Operating system:

  • Information not submitted

Requirements:

  • napari[all]==0.5.0
  • torch
  • torchvision
  • cellpose==3.0.1
  • opencv-python
  • picassosr==0.7.3
  • bactfit>=0.1.6
  • numpy
  • pyqt5
  • pyqt6
  • qtpy
  • scipy
  • natsort
  • tqdm
  • imagecodecs
  • tifffile
  • pandas
  • mat4py
  • glob2
  • matplotlib
  • scikit-image
  • roifile
  • openpyxl
  • shapely
  • colicoords
  • psutil
  • xmltodict
  • astropy
  • tiler
  • imageio-ffmpeg
  • aicspylibczi
  • czifile
  • omnipose
  • h5py
  • pyqtgraph
  • tox; extra == "testing"
  • pytest; extra == "testing"
  • pytest-cov; extra == "testing"
  • pytest-qt; extra == "testing"
  • napari; extra == "testing"
  • pyqt5; extra == "testing"
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