Adding whole slide images to OMERO without slide label

Hi,

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!

Thanks,

Pete

I can reassure you that I don’t think you’re missing any important tricks here. Writing pyramidal OME-TIFFs client-side then importing them is a fine way to proceed. My guess would be that zlib compression would work well but it’s absolutely worth testing both file size and read speed on representative data as of course these things can vary and you want to be making a good choice at this stage.

Without recoding just the main series into OME-TIFFs, a disappointing but safe approach to ignoring WSI slide labels is simply to hide them off in some other dataset (or orphaned images), even though they must remain in the same group. Admittedly, there are cunning off-script tricks that could be attempted (like directly manipulating the database or customizing the GUI) but they probably push you rather further from officially supported OMERO behavior than is worth it.

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Great, thanks! The OME-TIFF route feels ‘safer’ to make sure the labels don’t reappear someday where they shouldn’t. I’ll try this and explore compression options.