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

[Kai Schleicher]

Hi Roger,

thanks for your reply and the easy fix :)

Renaming the images works fine for me!

Thanks & cheers,
Kai


On 10/31/2017 05:37 PM, Roger Leigh wrote:
> 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
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