Pyramidal tiff in Omero

@joshmoore

  1. When saving data in pyramidal Tiff and uploading them to IDR and viewing them in OMERO, would your viewer make use of the pyramids?
  2. Does the OMERO viewer always make use of pyramids, given it finds them in the file format? Example: .czi?
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In pyramidal OME-TIFF, yes. i.e. there are other ways one could attempt to same multiple resolutions in a TIFF. Not all of them would be detected. If they are detected, though, the viewer will use them.

For any file reader which supports pyramids. See the last column on https://docs.openmicroscopy.org/bio-formats/6.3.0/supported-formats.html (or for future readers, latest). Currently:

~Josh

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Dear @joshmoore thanks for the message. Quick question about this. Does this mean that OMERO can support uploading VSI files natively without having to convert them?

Really really hoping that this is the case :slight_smile:

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That’s certainly the intent, @oburri. Do let us know if you have any issues.

~Josh

Cool thanks! How would I go about uploading a VSI file into OMERO since it’s a combination of the VSI file itself and a companion folder that contains the actual pyramids (like IDS/ICS)?

Best

Assuming that the filenames and folders are as written by the acquisition software then Bio-Formats should recognize that arrangement: select to import the VSI and the pyramid files should come right along with it. Do let us know if that turns out not to be the case.

Similarly, when you use Bio-Formats’ showinf command-line tool on the file you should see that one of the first things it reports is a list of “Used files” that includes the pyramids.