OME-Zarr hiPSC 3D immunofluorescence images, tiny test set

This dataset is intended to be used for automated testing of OME-Zarr processing.

Example dataset of human induced pluripotent stem cells, imaged at 40x magnification with a Yokogawa CV7000. This is a tiny subset of a larger experiment intended as a test dataset for the Fractal platform and others experimenting with OME-Zarrs.

1 Channel is included:

• C01: DAPI, nuclear stain

It is generated from this raw data: https://zenodo.org/records/8287221

This dataset contains 2 Z levels for 2 field of views for this 1 channel, as well as (manually adjusted) metadata files from the Yokogawa CV7000. The data was acquired in the Pelkmans lab in August 2020.

The images have been processed using Fractal, the workflow is attached as a json file. It ran with fractal-server==2.3.6, fractal-client==2.0.1, fractal-web==1.4.0 and fractal-tasks-core==1.2.1.

Two versions of the OME-Zarr are added here: A 3D version with both Z planes. And a 2D version (MIP of the Z-planes) which also contains label images from cellpose segmentation, measurements and output ROI tables.