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.
A napari plugin for artifact removal, noise reduction, contrast enhancement and stack brightness correction of Cryo-FIB/SEM image stacks.
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.
Version:
- 0.0.3
Last updated:
- 2024-11-19
First released:
- 2024-09-20
License:
- Apache License ...
Supported data:
- Information not submitted
Plugin type:
Open extension:
Save extension:
Operating system:
- Information not submitted
Requirements:
- numpy==1.26.4
- magicgui
- scikit-image==0.24.0
- PyWavelets==1.6.0
- opencv-python==4.10.0.84
- tox; extra == "testing"
- pytest; extra == "testing"
- pytest-cov; extra == "testing"
- pytest-qt; extra == "testing"
- napari; extra == "testing"
- pyqt5; extra == "testing"