VolSeg Tools

A library used for processing of volumes and segmentations.

Instalation

If you cannot, or don't want to use the PyPi Package, you can install the project locally using uv:

    git clone https://github.com/DanielKriz/volseg-tools
    cd volseg-tools
    uv venv
    source .venv/bin/activate
    uv pip install .

Usage

The library is intended for definition of processing pipelines for volumetric data and segmentations.

Next to that a CLI preprocessing application is provided. After the installation you can run:

molstar-preprocessor --help

If you wish to be more informed about the processing you might add --verbose option.

Given that we have downloaded some volumetric data, e.g. EMD-53130, we can start the processing with some downsampling method:

molstar-preprocessor --vs EMD-53130.map --strategy tricubic --bundle mvsx --output-path out

This is going to create downsampled version of the provided dataset in directory out/ in the MVSX archive.

After this step it is possible to drop this archive into, e.g. Mol* Viewer for visualization.

To get the list of supported downsampling method you can run --list-strategies.

Current implementation is sensitive to the contents of the working directory. You might want to run --overwrite-tmp to ignore the data already stored in the working directory and run the processing again (effectively overwriting the contents of the working directory).

Support

Input Formats

• MRC
• NiBabel
• SFF
• Imaris Bitplane
• STL, OBJ, PLY
• VRML
• OME-TIFF
• OME-NGFF

Serialization Formats

• MRC
• BCIF

Bundling Formats

• MVSX
• Zip per resolution
• Zip

License

This project is licensed under the MIT. See the LICENSE for more information.