[ome-users] error opening stitched *.lsm using Bio-formats

[Roger Leigh]

On 30/10/17 16:29, Kai Schleicher wrote:
> Dear OME team,
>
> I have come across a couple of user images
> <https://filesender.switch.ch/filesender/?vid=04329d13-fe8b-93c9-b234-000076047e49>
> which don't import properly into OMERO as they are not read by the
> Bio-formats, see quoted error message below:
[...]
> The individual channel images open fine with the normal file -> open
> from FIJI.
>
> When opening the image in FIJI and checking the info (ctrl-i) I did
> actually find the "unmatched"
> urn:uuid:faa8d48e-8cd2-414a-a041-1a9bc24e8cec in the ome-xml metadata block.
>
> Is there maybe something else missing, i.e is the set of images not
> complete?

Dear Kai,

The metadata is unfortunately incorrect I think as a result of the files
being renamed.  The UUID in the OME-XML metadata for each files is this:

   FILE="wt_16k_spn488_brp568_C0.Tile Scan.Tile_1.lsm_stitched.ome.tif"
   UUID="urn:uuid:faa8d48e-8cd2-414a-a041-1a9bc24e8cec"

   FILE="wt_16k_spn488_brp568_C1.Tile Scan.Tile_1.lsm_stitched.ome.tif"
   UUID="urn:uuid:b1ad7666-d049-47df-bbf1-c0fc7e7f6175"

However, if you look at the TiffData elements:

   <UUID FileName="Experiment_C0.Tile
Scan.Tile_1.lsm_stitched.ome.tif">urn:uuid:faa8d48e-8cd2-414a-a041-1a9bc24e8cec</UUID>
   <UUID FileName="Experiment_C1.Tile
Scan.Tile_1.lsm_stitched.ome.tif">urn:uuid:b1ad7666-d049-47df-bbf1-c0fc7e7f6175</UUID>

You can see that the same UUIDs are used, but the filenames differ and
the UUID<->filename mapping is broken as a result.  It's looking for
files with an "Experiment_" prefix while the files are actually named
"wt_16k_spn488_brp568_".  As a result, it can't determine where to read
the pixel data from.

I don't know if this renaming occurred manually, or if it was introduced
in a processing step.  It can be fixed by updating the FileName
attribute on the TiffData UUID elements (you can use the tiffcomment
tool to do this if you want to manually edit the XML), or by using the
name you want it to be called when you originally create it.


Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096