OME-Zarr 3D hiPSCs with labels & measurements, 2x2 field of views

These are 2 small OME-Zarr files of the data from 10.5281/zenodo.7057076.

They have been processed using fractal-client 0.2.1, fractal-server 0.1.4 and fractal-tasks-core 0.1.9 using this workflow: https://github.com/fractal-analytics-platform/fractal/tree/main/examples/08_cardio_2x2_dataset_processing_zenodo

Both Zarr files are Zip-compressed to allow easier upload & download from Zenodo. 

20200812-CardiomyocyteDifferentiation14-Cycle1.zarr contains 3 3D channels and a table with regions of interest for the 4 field of views contained in this data.

20200812-CardiomyocyteDifferentiation14-Cycle1_mip.zarr contains the same 3 channels, but as maximum intensity projections. It contains nuclear segmentation through cellpose. It also contains 2 tables: The region of interests like in the 3D data, as well as measurements performed with napari-skimage-regionprops.

The tables are stored in the OME-Zarr file according to the proposed OME-NGFF table spec in AnnData.

The 3 channels are:

- 0: DAPI, nuclear stain

- 1: nanog, antibody staining with Bio-Techne AG, AF1997-SP, Lot KKJ0617121 for the stemness marker nanog

- 2: Lamin B1, antibody staining with Abcam, ab16048, Lot GR3244890-2 for the nuclear envelope marker Lamin B1

This updated version now passes the ngff schema validation. A version with 3D segmentation is available here: https://zenodo.org/record/7144919