Cut Detector

Automatic micro-tubules cut detector.

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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.

conda create --name cut_detector python=3.10 conda=23.10.0
conda activate cut_detector

Package installation¶

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

pip install cut_detector

Alternatively, you can clone the github repo to access to playground scripts.

git clone https://github.com/15bonte/cut-detector.git
cd cut-detector
pip install -e .

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.

Next, install openjdk which is necessary to call Fiji from python.

conda install -c conda-forge openjdk=8

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.