[ome-users] Round trip issues with omero - loci-imageJ

Chris Allan callan at lifesci.dundee.ac.uk
Fri Aug 6 14:05:02 BST 2010

On 5 Aug 2010, at 14:51, Scott Grieshaber wrote:

> Hello,

Hi Scott,

> I have been using the combination of Omero for data storage and ImageJ for image analysis.  In the past this has been very successful.  I am having trouble using omero 4.2 and loci 4.2 together.  I can export an ome.tif file from Omero and open it in ImageJ with LOCI and this works.  I then do some things to the images and export the data set as an ome.tif with LOCI.  This works well.  I can then import the file into Omero 4.2 successfully and the image Looks fine in insight.  However, If i re-export this data set as an ome.tif file and import into imageJ using LOCI the images are out of order the channels and Zs are mixed up.  Using the Omero ImageJ plugin i can download the data set successfully into imageJ with out the rearrangement of the C and Z channels.  I tried this a second time with another data set and just opened it with LOCI in ImageJ and resaved the data as ome.tif and imported into Omero.  On this data set the Z was transposed to T but is not mangled.  It appears to be a problem with Export from LOCI.

Without the intermediate files it's very difficult to find out exactly what has gone wrong. Would it be possible for you to go through your workflow, save the intermediate OME-TIFF files and get them to us?

> Thanks for your help,
> All the Best,
> Scott

Thanks for the feedback!


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