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.

The images have been processed using Fractal a workflow like the example in fractal_workflow_2x2.json above (with full paths to some helper files, use this script to create it in your setup). It ran with fractal-server==1.4.0, fractal-client==1.4.0 and fractal-tasks-core==0.14.0a0 (this exact commit).

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 3 tables: A ROI table for the whole well, 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, as well as 3 more labels generated by napari workflows (different thresholds, less accurate segmentations). It also contains 6 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.