https://github.com/constantinpape/elf
Utils and convenience functions for large-scale bio-image analysis.
https://github.com/constantinpape/elf
3d-segmentation affine-transformation bio-image-analysis image-analysis lifted-multicut microscopy-images multicut mutex-watershed segmentation
Last synced: 3 months ago
JSON representation
Utils and convenience functions for large-scale bio-image analysis.
- Host: GitHub
- URL: https://github.com/constantinpape/elf
- Owner: constantinpape
- License: mit
- Created: 2019-08-05T22:22:58.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2025-12-16T12:21:33.000Z (6 months ago)
- Last Synced: 2025-12-20T02:07:49.348Z (6 months ago)
- Topics: 3d-segmentation, affine-transformation, bio-image-analysis, image-analysis, lifted-multicut, microscopy-images, multicut, mutex-watershed, segmentation
- Language: Python
- Size: 903 KB
- Stars: 58
- Watchers: 6
- Forks: 20
- Open Issues: 21
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# elf
This repository implements common functionality for biomedical 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
- **tracking**: graph based tracking algorithms
and more. See [the documentation](https://constantinpape.github.io/elf/elf.html) for how to use elf.
See `examples` for some usage examples. For processing large data on a cluster, check out [cluster_tools](https://github.com/constantinpape/cluster_tools), which uses a lot of `elf` functionality internally.
It is used by several down-stream dependencies:
- [cluster_tools](https://github.com/constantinpape/cluster_tools)
- [paintera_tools](https://github.com/constantinpape/paintera_tools)
- [pybdv](https://github.com/constantinpape/pybdv)
- [ilastik](https://github.com/ilastik/ilastik)
- [mobie-python](https://github.com/mobie/mobie-utils-python)
- [plantseg](https://github.com/hci-unihd/plant-seg)
## Installation
Install the package from source and in development mode via
```
pip install -e .
```
or via conda
```
conda install -c conda-forge python-elf
```
## Functionality overview
**Segmentation:** `elf` implements graph-based segmentation using the implementations of multict, lifted multicut and other graph partitioning approaches from [nifty](https://github.com/DerThorsten/nifty).
Check out [the examples](https://github.com/constantinpape/elf/tree/master/example/segmentation) to see how to use this functionality for segmenting your data.
**Tracking:** `elf` implements graph-based tracking using the implementations from [motile](https://github.com/funkelab/motile).
Checkout [the examples](https://github.com/constantinpape/elf/tree/master/example/tracking) to see how to use this functionality to track your data.
In order to use this functionality you will need to install `motile`. You can do this via
```
conda install -c conda-forge -c funkelab -c gurobi ilpy
```
and then
```
pip install motile
```