Annotated datasets for cell segmentation from the RNA2seg study

Annotations from the RNA2seg study

# Annotation

This folder contains the manual annotation along the corresponding staining and RNA position
of the different datasets used in the RNA2seg paper.
the bounds.json indicate the coordiante of the crop in the original dataset.

the shape folders contain the annotation in a "geopandas shape" format to be integrated in a spataildata. Each segmentation shape can be load with :

```
    import geopandas as gpd
    gdf = gpd.read_file(path2save_shape_organ / "shape.shp")
```

All datasets staining images and transcripts come from https://vizgen.com/data-release-program/ (MERSCOPE FFPE Human Immuno-Oncology Data Release) except the mouse ileum dataset that come from :
Petukhov, V., Xu, R.J., Soldatov, R.A. et al.
Cell segmentation in imaging-based spatial transcriptomics.
Nat Biotechnol 40, 345–354 (2022). https://doi.org/10.1038/s41587-021-01044-w

contact : alice.blondel@minesparis.psl.eu, thomas.defard@minesparis.psl.eu

RNA2seg Code : https://github.com/fish-quant/rna2seg