Seitenhistorie

In case of field images from the Operetta CLS, do NOT select the individual images for upload but the "index.idx.xml" file in the "Images" folder. OMERO will automatically extract the image information from this file and upload all images into a plate-well-field hierarchy and visualize it in a plate frame.

If you want to upload continuous images recorded at the Operetta, such as tissues on slides, then you first have to stitch the images before uploading (e.g. by using the Fiji plugin "Operetta importer"). The same accounts for whole well imaging – stitch the data before uploading to OMERO. The mentioned Fiji plugin provides a script to stitch individual objects (e.g. wells in a plate or tissue samples on a slide) automatically in batch processing. If you want to visualize stitched whole well images in a plate layout in OMERO, then a further processing step after upload is necessary in OMERO (Dataset to Plate transformation).