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.

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.

Installation

Install the package from source via

python setup.py install

or via conda

conda install -c conda-forge -c cpape elf

Functionality