elf

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.

See examples for some usage examples.. For processing large data on a cluster, check out cluster_tools.

It is used by several down-stream dependencies:

Installation

Install the package from source via

python setup.py install

or via conda

conda install -c conda-forge -c cpape elf