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bentaculum authored Jun 7, 2024
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![Overview](overview.png)

If you are using this code in your research, please cite our [preprint](https://arxiv.org/abs/2405.15700)
If you are using this code in your research, please cite our [preprint](https://arxiv.org/abs/2405.15700):
> Benjamin Gallusser and Martin Weigert<br>*Trackastra - Transformer-based cell tracking for live-cell microscopy*<br> arXiv, 2024
## Examples
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2. The [SCIP Optimizer](https://www.scipopt.org/), a free and open source solver. If `motile` does not find a valid Gurobi license, it will fall back to using SCIP.
- On MacOS, installing packages into the conda environment before installing `ilpy` can cause problems.
- 2024-06-07: On Apple M3 chips, you might have to use the nightly build of `torch` and `torchvision`, or worst case build them yourself.

## Usage

The input to *Trackastra* is a sequence of images and their corresponding cell (instance) segmentations.
The input to Trackastra is a sequence of images and their corresponding cell (instance) segmentations.

### Napari plugin

For a quick try of Trackastra on your data, please use our [napari plugin](https://github.com/weigertlab/napari-trackastra/), which already comes with pretrained models included.

![demo](https://github.com/weigertlab/napari-trackastra/assets/8866751/097eb82d-0fef-423e-9275-3fb528c20f7d)


### Tracking with a pretrained model

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v.add_tracks(data=napari_tracks, graph=napari_tracks_graph)
```

### Napari plugin

We additionally provide a [napari plugin](https://github.com/weigertlab/napari-trackastra/) which allows one to quickly apply pretrained and custom models on custom timeseries.

### Training a model on your own data

To run an example
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