Add more sample data

[jo-mueller]

Currently, the plugin comes with a (somewhat heavy) collection of multiple labels and their repective images from the BBBC0 dataset. TO make interactive testing of all the new functionalities easier, we should add more sample data for the suported layer types. It would be nice if the sample data also highlighted a (biological) use case.

Data to be added

• [ ] Points layer data: LIDAR, spatial genomics?
• [ ] Vectors data: Surface vector traces (see napari-stress)
• [x] Surface data: Organoid surfaces with some metrics computed on their surface - maybe @maleehahassan has some data at the ready for this? --> See #391
• [x] Shapes: A bunch of YOLO detections on a sample image? Maybe @tsmejkal has something for that? https://github.com/BiAPoL/napari-clusters-plotter/pull/424
• [x] Tracks: WIP with @stefanhahmann here https://github.com/BiAPoL/napari-clusters-plotter/pull/385

TODO

• [x] Point out sample data resources in new documentation (#389 )

[jo-mueller]

@ClementCaporal - would you, by any chance, have some point cloud sample data you'd contribute here as sample data? I could add some stuff from other scientific domains than biology - but it only looks cool and is not so interesting to play with.

[zoccoler]

@jo-mueller why not getting data from here?

[jo-mueller]

For the tracks layer that's what I just did with @stefanhahmann :)

For the other layer types I've seen the sample data but I was hoping for some real-life applications...

[ClementCaporal]

Hello @jo-mueller, Thank you for tagging me!

My lab has real life applications of brainbow labelling, but the dataset are not published yet. They will be available on zenedo (or other) at one point (months scale) but not right now... I am sorry!

As soon as I see an interesting available point cloud I will contact you!

[tsmejkal]

Hi @jo-mueller ,

here is the annotated data which I used for training the YOLO model. Since Louis has generated and annotated it, I guess you should ask him if you want to use it. https://omero-web.biotec.tu-dresden.de/webclient/?show=dataset-318

Best, Tina

[maleehahassan]

Hi @jo-mueller, I do have some surface data ready for this.

[haesleinhuepf]

There is also this dataset from Veenvliet lab, where usage rights / copyright are clear: https://zenodo.org/records/7603081

[jo-mueller]

There is also this dataset from Veenvliet lab, where usage rights / copyright are clear: https://zenodo.org/records/7603081

Completely forgot about this one - will convert to surface, compute some features and add :)