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

Scott Grieshaber sgriesha at mac.com
Thu Aug 5 14:51:00 BST 2010


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.

Thanks for your help,
All the Best,

Scott Grieshaber Ph.D.
Assistant Professor
University of Florida
Department of Oral Biology
School of Dentistry
PO BOX 100424 Room D5-33D
1600 SW Archer Road
Gainesville FL 32610
(352) 273-8856
sgriesha at ufl.edu
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