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PreibischLab / BigStitcher

ImgLib2/BDV implementation of Stitching for large datasets
GNU General Public License v2.0
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Importing H5 from BigStitcher to OMERO? #90

Open cikus3 opened 3 years ago

cikus3 commented 3 years ago

Dears, as great fan of BigStitcher I would like to start using OMERO to share the file generated with colleagues; I noticed that if I save a file as new HDF5 file (after registrations and fusion) I can`t load it on OMERO. Moreover, if I try to open the file with BioFormat Impoerter I got also an error (See both attachment); any solutions to import these H5 file to OMERO?.. Do I have to save them in any special way? Thanks! image image image

StephanPreibisch commented 3 years ago

Hi, I think OMERO might simply not support these high-dimensional datasets. Could you try to export as TIFF and import that instead?

cikus3 commented 3 years ago

Ok, thanks for the feedbcak! So, yes, my currenrt strategy is to save the file also in TIFF and then import them in OMERO; however, ideally I would like to directly import the BigStithcer-HDF5 to Omero. About OMERO: I know that is strictly connected with BioFomat and is possible to load BDV (HDF5) file (but apparently not all them); we are currently working a lot with OMERO and I`ll let you know if we find any good solutions. Cheers