diff --git a/README.md b/README.md index f4d98f3..8d3e143 100644 --- a/README.md +++ b/README.md @@ -41,6 +41,10 @@ Divisions are not supported at the moment. ## Usage Example +### Minimal example + +Minimal example using a track file following the convention described above. + ```python3 import napari import pandas as pd @@ -59,6 +63,30 @@ napari.view_tracks(tracks) napari.run() ``` +### Zebrahub example + +Zebrafish embryo tail example. This example requires the package `napari-ome-zarr`. + +```python3 +import napari +import pandas as pd +from in_silico_fate_mapping import FateMappingWidget + +image_path = "http://public.czbiohub.org/royerlab/zebrahub/imaging/single-objective/ZSNS001_tail.ome.zarr" +tracks_path = "http://public.czbiohub.org/royerlab/zebrahub/imaging/single-objective/ZSNS001_tail_tracks.csv" + +viewer = napari.Viewer() +viewer.window.add_dock_widget(FateMappingWidget(viewer)) + +viewer.open(image_path, plugin="napari-ome-zarr") + +tracks = pd.read_csv(tracks_path) +viewer.add_tracks(tracks[["TrackID", "t", "z", "y", "x"]]) +viewer.add_points(name="Markers") + +napari.run() +``` + ## Citing If used please cite: