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, which uses a lot of elf functionality internally.

It is used by several down-stream dependencies:

• cluster_tools
• paintera_tools
• pybdv
• ilastik
• mobie-python
• plantseg

Installation

Install the package from source and in development mode via

pip install -e .

or via conda

conda install -c conda-forge python-elf