I’ve inherited a problem whereby someone would like to add brightfield whole slide images (ndpi) to OMERO, but ensure that the slide label is completely omitted.
My proposed approach is to write an OME-TIFF of the image (perhaps cropping it in the process) and ensuring that only the main image is written. But I wanted to ask:
- is there a smarter way to do get rid of the label?
- is there a preferred format for OMERO, or or tips on optimizing performance (e.g. compression type, tile size)?
I recall there’s an OMERO pyramid format but I understand it pre-dates OME-TIFF’s pyramidal support, so wasn’t sure if there were any reasons to prefer it.
Since there will be a lot of images to convert, any advice to help us select the best approach early would be much appreciated!