[ome-devel] Housekeeping..

[Jason Swedlow]

Claude-

OME does not support import of JPG's as "data", because they aren't, as 
far as we can tell, a real data format.  Generating JPEG'S is fine, but 
they are not anything you would want to analyse in any quantitative 
way, at least as far as we know.  We are working hard on trying to get 
more data file formats supported.  Obviously, OME UI's do generate 
JPEG's and TIFFs.

One issue with TIFFs-- OME "understands" TIFF, but somehow must 
incorporate as much metadata around a specific TIFF.  This is 
especially a problem for those commercial file formats that store 
binary data as individual TIFFS but encode accessory metadata in the 
file name-- like the UIC screening format-- or in an accessory filew.  
At the moment, we are not providing UI tools for filling this data in-- 
again, this is coming.  The VisBio project does have an alpha release 
of an importer tool capable of solving this problem.

Hope this helps.

Cheers,

Jason


On 20 Jul 2004, at 11:13, Claude Bonnard wrote:

> Thanks for your reply, Ilya.
>
> The "zealous spam filter" has been submitted to the  IT people , and I 
> want to
> present my appologies for this possible problem which made some of 
> Chris'reply
>  lost who knows where. I now carefully watch in
> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/
>
> and .. let's try all to do our best :-)
>
>
> As far as import, I have tested again with a jpg, although my tiff 
> were very
> standard single image tiff.
>
> I have the same "Successfully imported 0 images" as result, but I 
> found a line
> in the error log... Is this a clue for you?
>
> ....
>
> *DEBUG* PARAM[import_queue]: /DATA_OME/cbonnard/zoom.jpg
> *DEBUG* PARAM[Path]: /DATA_OME/cbonnard
> *DEBUG* PARAM[action]: import
> *DEBUG* PARAM[new_or_existing]: existing
> *DEBUG* PARAM[existing_dataset]: new_dataset
> *DEBUG* PARAM[name]:
> *DEBUG* PARAM[description]: Une image jpg (nom de l'image= zoom, 
> taille 171KB)
> *DEBUG* PARAM[q_selected]: /DATA_OME/cbonnard/zoom.jpg
> [Tue Jul 20 09:47:39 2004] -e: Use of uninitialized value in -d at
> /usr/lib/perl5/site_perl/5.8.0/OME/Web/ImportFiles.pm line 94.
> ....
>
> Thanks for your help!
>
> Claude
>
>
> On Jul 19,  6:26pm, Ilya Goldberg wrote:
>> Subject: Re: [ome-devel] Housekeeping..
>>
>> On Jul 16, 2004, at 6:15 AM, Claude Bonnard wrote:
>>
>>> When images import terminates without the "two active imports" 
>>> message
>>> above,
>>> the success message is: "Successfully imported 0 images". The images
>>> are tif.
>>
>> Ahh.  But what kind of tiff?  The release unfortunately has this
>> 'hanging' bug which is fixed in the release we're currently packing 
>> up.
>> You can release all the hung database handles by restarting apache
>> (sudo apachectl restart).
>> Sorry about this, but we'll have a release candidate up in a few days
>> (not to be used in production environments).
>>
>> Also, it appears that email sent to you from ome-devel is rejected at
>> your end.  Probably an over-zealous spam filter.
>> -Ilya
>> -- End of excerpt from Ilya Goldberg
>
>
>
> -- 
> Claude Bonnard Ph.D.
> ISREC (Swiss Institute for Experimental Cancer Research)
> Microscopy, Imaging and Morphology Core Facility [MIM]
> Lab F216
> Ch des Boveresses 155
> CH-1066 Epalinges
> Switzerland
> phone: [41-21]-692-5891
>   fax: [41-21]-652-6933
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>

NOTE NEW EMAIL ADDRESS: jason at lifesci.dundee.ac.uk
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