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

<p>Ome-zarr dataset that is the output of raw tifs (doi <a href="../doi/10.5281/zenodo.12795728">10.5281/zenodo.12795728</a>) processed by Fractal task (see .json file).&nbsp;</p> <p>Dataset acquired on Yokogawa CV8000 on 2024.06.07 by Nicole Repina, Friedrich Miescher Institute for Biomedical Research</p> <p>Dataset contains 11 fields of view (each 1000 x 1000 pix) acquired with SearchFirst*. Touching fields have 50 pix overlap.&nbsp;</p> <p>60x water objective, 2x2 binning, zyx spacing (6, 0.21667, 0.21667) um per pixel. Each field of view has 6 z-slices.</p> <p>Mouse small intestinal organoids (day 4) immunostained with the following dyes (2 fluorescence channels):</p> <p>Channel 1 (C01, 405nm) = DAPI nuclear stain<br>Channel 2 (C02, 488nm) = B-catenin membrane stain</p> <p>*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.</p>