diff --git a/README.md b/README.md index b98a14e..3c3d00d 100644 --- a/README.md +++ b/README.md @@ -9,7 +9,7 @@ ![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
*Trackastra - Transformer-based cell tracking for live-cell microscopy*
arXiv, 2024 ## Examples @@ -42,9 +42,18 @@ Notes: 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 @@ -107,10 +116,6 @@ v.add_labels(masks_tracked) 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