OME-Zarr 3D hiPSCs with 3D labels & 3D 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 0.2.3, fractal-server 0.2.0 and fractal-tasks-core 0.2.1 using this workflow: https://github.com/fractal-analytics-platform/fractal/tree/main/examples/13_zenodo_3D_Segmentation

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

20200812-CardiomyocyteDifferentiation14-Cycle1.zarr contains 3 3D channels, a nuclear segmentation produced by cellpose as labels and 2 tables: A region of interests table for the 4 field of views, as well as measurements performed with napari-skimage-regionprops.

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 OME-Zarr file is an extended version of https://zenodo.org/record/7120354, now with 3D segmentation and measurements for 3D objects.