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Utils and convenience functions for large-scale bio-image analysis.

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constantinpape/elf

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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:

Installation

Install the package from source and in development mode via

pip install -e .

or via conda

conda install -c conda-forge python-elf