Metadata "lost" when uploaded to OMERO and opened back in Fiji

Hi all and especially @OMETeam !

I have noticed something this morning. I have a ND2 file which if opened in Fiji through Bio-Formats shows quite a lot of metadata as you can see here :

If uploaded to OMERO, some metadata is parsed and shown as Microscope metadata while most is kept as “General Metadata” as you can see here :

The main issue is that if I open the file in Fiji through the OMERO-Fiji plugin, then almost all metadata is lost as you can see here :

Am I missing something ? Is there anyway to attach back all the metadata from the original file ?

Thanks !

2 Likes

Hi @lguerard
Nothing is lost, when you are using the plugin, planes are read from OMERO, i.e. the original file is not downloaded from the OMERO server to your local machine. This explains the difference in the metadata you can see.
If you want to also view the metadata in Fiji, you could request via a script or we will need to add an option to the plugin(s).

Cheers

Jmarie

Hi @j.burel,

Thanks for the answer ! :slight_smile:

Would you have any example scripts to do so ? At the moment we’re using this function to get the image back from OMERO, and it seems to be the one mentioned quite a lot on the forum but I’d be curious to know if there’s a better/another way to do so.

def openImagePlus(HOST, USERNAME, PASSWORD, groupId, imageId):
    """Open an ImagePlus from an OMERO server

    Parameters
    ----------
    HOST : str
        Adress of your OMERO server
    USERNAME : str
        Username to use in OMERO
    PASSWORD : str
        Password
    groupId : double
        OMERO group ID
    imageId : int
        ID of the image to open
    """
    stackview = "viewhyperstack=false stackorder=XYCZT "
    datasetorg = "groupfiles=false swapdimensions=false openallseries=false concatenate=false stitchtiles=false"
    coloropt = "colormode=Default autoscale=true"
    metadataview = "showmetadata=false showomexml=true showrois=true setroismode=roimanager"
    memorymanage = "virtual=false specifyranges=false setcrop=false"
    split = " splitchannels=false splitfocalplanes=false splittimepoints=false"
    other = "windowless=true"
    options = ("location=[OMERO] open=[omero:server=%s\nuser=%s\npass=%s\ngroupID=%s\niid=%s] %s %s %s %s %s %s %s " %
               (HOST, USERNAME, PASSWORD, groupId, imageId, stackview, datasetorg, coloropt, metadataview, memorymanage, split, other))
    IJ.runPlugIn("loci.plugins.LociImporter", options)