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Add functionality overview to the README
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constantinpape committed Sep 13, 2023
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Expand Up @@ -11,6 +11,7 @@ This repository implements common functionality for (large-scale) bio-medical im
- **skeleton**: skeletonization
- **transformation**: helper functions for affine transformations
- **wrapper**: volume wrappers for on-the-fly transformations
- **tracking**: graph based tracking algorithms

and more.

Expand All @@ -34,3 +35,20 @@ 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
```

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