OME-Zarr 3D hiPSCs with labels & measurements, 2x2 field of views
Authors/Creators
Description
These are 2 small OME-Zarr files of the data from 10.5281/zenodo.7057076.
They have been processed using fractal-client 0.1.2, fractal-server 0.1.2 and fractal-tasks-core 0.1.3 using this workflow: https://github.com/fractal-analytics-platform/fractal/commit/71686abecf153cdea0defb559a973035e11b8ce6
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 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