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.
1 maintainer
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