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Cut Detector

cut-detector

Automatic Cut Detector

License BSD-3 PyPI Python Version tests codecov napari hub

Automatic micro-tubules cut detector.


This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

Conda environment

It is highly recommended to create a dedicated conda environment, by following these few steps:

  1. Install an Anaconda distribution of Python. Note you might need to use an anaconda prompt if you did not add anaconda to the path.

  2. Open an Anaconda prompt as admin to create a new environment using conda. We advice to use python 3.10 and conda 23.10.0, to get conda-libmamba-solver as default solver. Note than openjdk is necessary to call Fiji from python, which is needed as you will see below.

conda create --name cut_detector python=3.10 conda=23.10.0
conda activate cut_detector
conda install -c conda-forge openjdk=8

Package installation

Once in a dedicated environment, our package can be installed via pip:

pip install cut_detector

Fiji

This package relies on Trackmate to perform cell tracking. Trackmate is called through Fiji, which has to be installed independently. Please follow the steps here to install it.

GPU

We highly recommend to use GPU to speed up segmentation. To use your NVIDIA GPU, the first step is to download the dedicated driver from NVIDIA.

Next we need to remove the CPU version of torch:

pip uninstall torch

The GPU version of torch to be installed can be found here. You may choose the CUDA version supported by your GPU, and install it with conda. This package has been developed with the version 11.6, installed with this command:

conda install numpy==1.25 pytorch==1.12.1 torchvision pytorch-cuda=11.6 -c pytorch -c nvidia

Note that we have added numpy here to prevent conda from installing a version higher than 1.25, which is not supported by numba.

Update

To update cut-detector to the latest version, open an Anaconda prompt and use the following commands:

conda activate cut_detector
pip install cut-detector --upgrade

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, "cut-detector" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.

Version:

  • 0.0.8

Last updated:

  • 01 December 2023

First released:

  • 17 October 2023

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

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

Python versions supported:

Operating system:

Requirements:

  • cellpose >=2.2.3
  • pyimagej
  • scyjava
  • numpy <=1.24
  • cnn-framework ==0.0.11
  • magicgui
  • pydantic ==1.10.12
  • xmltodict
  • shapely
  • aicsimageio
  • scikit-learn ==1.2.2
  • charset-normalizer ==3.3.0
  • napari[all]

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