Segment Any Confocal Images

Segment Any Confocal Images is a flexible and high-performance plugin designed for segmentation of confocal microscopy data. It supports both 2D and 3D image stacks, enabling users to identify and extract cellular or subcellular structures with minimal manual effort.

Supported inputs

The widget currently supports standard image formats only:

• *.tif, *.tiff
• *.png
• *.jpg, *.jpeg

Microscope-specific container formats such as czi, nd2, lif, and lsm are not loaded by the widget anymore.

Loaded images are normalized into the widget's internal TCZYX layout:

• 2D grayscale images become 1 x 1 x 1 x Y x X
• grayscale stacks become 1 x 1 x Z x Y x X
• RGB/RGBA images become 1 x 3 x 1 x Y x X
• RGB/RGBA stacks become 1 x 3 x Z x Y x X

Physical pixel size metadata is no longer auto-imported from source files. Standard images default to pixel size 1.0.

This napari plugin was generated with copier using the napari-plugin-template (None).

Installation

You can install segment-any-confocal-images via pip:

pip install segment-any-confocal-images

If napari is not already installed, you can install segment-any-confocal-images with napari and Qt via:

pip install "segment-any-confocal-images[all]"

Core runtime dependencies include numpy, qtpy, magicgui, superqt, and scikit-image.

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 MIT license, "segment-any-confocal-images" is free and open source software

Issues

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