Reimport / repopulate image data


in our OMERO repository we have some files that Bioformats for which Bioformats could not parse some data (missing metadata) or didn’t interpret it correctly (slices and channels swapped). I believe that updates in Bioformats have addressed these issues as they open correctly in Fiji with more recent versions.

After an update to bioformats in OMERO, is it possible to trigger reimportation of the raw image file to update the metadata in OMERO?

I’ve had a look though the docs but I could find anything, probably because I don’t the correct phrasing for this issue.



Hi Chris,

the general answer to this question is: no, there is no generic reimport solution, although there might be solutions depending on what type of updates you are looking into.

Being a bit more specific, there are a few Bio-Formats APIs which are called dynamically by OMERO and will benefit automatically from fixes in the upgraded library. More specifically, I am thinking of the reading of the OriginalMetadata table as well as the reading of the pixel data.

However, the problem becomes more complex for any metadata that has been stored in the database at import time. This includes changes to the number of images per fileset/HCS layout, the image dimensionality or any OME metadata (physical size, instrument).

For these cases, updates to the database will be necessary and there is no generic solution that handles all cases. For specific types of updates e.g. “update all physical sizes”, some people have been writing scripts allowing to repopulate the database using the metadata from the latest version of library and might be able to share their experience/code.