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:

  • 1.0.6

Last updated:

  • 06 May 2023

First released:

  • 24 February 2023

License:

  • BSD-3-Clause

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 2
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • napari (>=0.4.17)
  • numpy (==1.23.5)
  • qtpy
  • cellpose[all] (>=2.1.1)
  • numba (>=0.43.1)
  • scipy
  • torch
  • opencv-python-headless
  • natsort
  • tqdm
  • imagecodecs
  • tifffile
  • pandas
  • mat4py
  • glob2
  • matplotlib
  • scikit-image
  • roifile
  • openpyxl
  • shapely
  • colicoords
  • psutil
  • xmltodict
  • astropy
  • tiler
  • imageio-ffmpeg

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