[ome-users] Files duplicated in .lif DropBox import

[Josh Moore]

Harri,

along with the answers to Will's questions it'd also be helpful if you could send us the log output from either the command-line importer or OMERO.importer. The former is printed to stderr:

  bin/omero import your.lsm 2>&1 | tee lsm.log

and the GUI's log can be opened by using the Help menu. DropBox uses bin/omero import itself, so it should be an accurate depiction of what's going on.

Cheers,
~Josh.

On Jan 14, 2011, at 3:10 PM, Will Moore wrote:

> Hi Harri,
> 
> Colin (the drop-box guy) is away this week, but in the meantime...
> 
> This sounds like it might be related to the way that BioFormats tries to understand multi-image file formats.
> For example, if you use the importer to choose a single image from a multi-image format (E.g. a single LSM file from a .mdb collection) then BioFormats works out that this image is part of a larger set and attempts to import all the images. If you choose E.g. 2 LSMs that are part of the same collection, then all the images in the collection would get imported twice.
> We have a ticket to address this issue:
> http://trac.openmicroscopy.org.uk/omero/ticket/3701
> 
> However, that shouldn't be a problem with LIF files, since everything is in one file, right?
> It could be something else that is causing duplicate imports.
> 
> One thing you could try:
> If you have a lif file that has more than 2 images, do you get a corresponding multiplication of the imports?
> E.g. Does a lif file with 3 images result in each image being imported 3 times??
> 
> This would help us narrow the problem down a bit, at least until Colin is back,
> 
> Thanks,
> 
> 	Will.
> 
> 
> On 14 Jan 2011, at 12:01, Harri Jäälinoja wrote:
> 
>> 
>> Hello all,
>> 
>> I noticed that when I imported a big .lif file that contained a stack and a single image, both of these were duplicated in the OMERO server. I see both of them twice in the OMERO.insight and in /OMERO/Pixels.
>> 
>> The duplication did not happen when I imported a .lif that contained only one stack. These two are the only imports I have done so far, so I don't know if the file content is the key.
>> 
>> Where should I look to figure out why the data was saved twice in the first case?
>> 
>> Best regards,
>> Harri