This repository implements common functionality for (large-scale) bio-medical image analysis:
- evaluation: evaluation of partitions via rand index and variation of information
- io: common interface for different libraries / formats
- parallel: parallel / larger than memory implementation of common numpy functions
- segmentation: graph-partition based segmentation
- skeleton: skeletonization
- transformation: helper functions for affine transformations
- wrapper: volume wrappers for on-the-fly transformations
and more.
It is used by several down-stream dependencies: cluster_tools, heimdall, skeletor, paintera_tools, pybdv and ilastik.
Of course, the functionality implemented here can also be used stand-alone, see the examples.
For workflows implemented for big data runnable on a compute cluster, check out cluster_tools.
Install the package from source via
python setup.py install
or via conda
conda install -c conda-forge -c cpape elf