Organoid tiny dataset for stitching (SearchFirst, ome-zarr)

Ome-zarr dataset that is the output of raw tifs (doi 10.5281/zenodo.12795728) processed by Fractal task (see .json file). 

Dataset acquired on Yokogawa CV8000 on 2024.06.07 by Nicole Repina, Friedrich Miescher Institute for Biomedical Research

Dataset contains 11 fields of view (each 1000 x 1000 pix) acquired with SearchFirst*. Touching fields have 50 pix overlap. 

60x water objective, 2x2 binning, zyx spacing (6, 0.21667, 0.21667) um per pixel. Each field of view has 6 z-slices.

Mouse small intestinal organoids (day 4) immunostained with the following dyes (2 fluorescence channels):

Channel 1 (C01, 405nm) = DAPI nuclear stainChannel 2 (C02, 488nm) = B-catenin membrane stain

*In SearchFirst, the sample is first imaged with a first-pass low-magnification objective (e.g. 4x). An object detection algorithm is then used to identify object-containing regions. Next, the second-pass acquisition is performed with a higher magnification objective that only acquires object-containing regions. The objects are thus imaged not in a tiled grid. Further, some fields may be standalone, while others may have one or more touching fields that are acquired with the specified pixel overlap.