Cryo-FIB/SEM Image Stacks Post-Processing

A napari plugin for artifact removal, noise reduction, contrast enhancement and stack brightness correction of Cryo-FIB/SEM image stacks.

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

Installation¶

It is recommended to create a fresh [conda] environment with Python 3.12 and napari:

conda create -n imgproc-env -c conda-forge python=3.12.0 napari pyqt

You can install napari-cryofibsem-imgproc via pip:

pip install napari-cryofibsem-imgproc

To install latest development version :

pip install git+https://github.com/EMCRUMC/napari-cryofibsem-imgproc.git

Usage¶

Cryo-FIB/SEM Image Processing offers 5 functions: curtaining artifact removal, charging artifact removal, noise reduction, contrast enhancement, and stack brightness correction. Using the widgets, the user can choose the input image or stack, set the function parameters, and call the function. These functions can be used in sequence with each other or individually, depending on the image processing requirements.

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 Apache Software License 2.0 license, "napari-cryofibsem-imgproc" is free and open source software

Issues¶

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