BaSiCpy shadow correction in napari

BaSiCPy illumination correction for napari

Example¶

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Installation¶

Recommended Installation Method¶

We highly recommend using a conda virtual environment to install and operate this plugin.

To use Python 3.9, for example:

conda create -n basicpy -c conda-forge python=3.9 napari pyqt && \
conda activate basicpy && \
pip install napari-basicpy

For further instructions on installing napari, visit their install guide.

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IMPORTANT NOTE FOR APPLE SILICON AND WINDOWS USERS:

If the above instructions fail with Apple silicon (e.g., M1/M2 chip) or Windows, you may need to install the jax and jaxlib following the instruction here.

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Other Installation Methods¶

You can also install napari-basicpy via pip:

pip install napari-basicpy

To install latest development version:

pip install git+https://github.com/peng-lab/napari-basicpy.git

or

pip install git+https://github.com/tdmorello/napari-basicpy.git

Usage¶

General Usage¶

This plugin expects a stack of tiles as input. Mosaic images should be deconstructed into their tiled components before processing. Individual tiles should be two-dimensional.

There are many options to customize the performance of BaSiCPy. Please refer to the BaSiCPy documentation on parameters here for details.

Batch Processing¶

Coming soon...

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-basicpy" is free and open source software

Issues¶

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