[ome-users] [ome-devel] Problem with metadata

[Jason Swedlow]

Hi Sebastian-

Ok, again; a few problems.

Many people have noted the limited exposure of metadata in  
OMERO.insight.  The good news is that this is a subset of what is in  
the database-- so much of what you want is in the DB.  But it is not  
all there-- some metadata is not supported by Bio-formats, some  
doesn't have a home in OMERO.

This is why we are (as I type) are in the middle of a "metadata  
completeness" iteration-- from Bio-Formats through to OMERO.insight  
and OMERO.editor, we are working hard to address a complete metadata  
workflow. This is a massive undertaking, and much of the team is  
focussed on it. As an example, it means going through each file  
format and ensuring we have a home for all metadata somewhere in  
OMERO.  Given the huge disparity in metadata support across different  
vendor file formats, this takes some work.  It also means finding  
ways to define what people want to see and how, and raises the  
question of what metadata is editable.  We've had long discussions  
about this for many years, and we also have survey data coming from  
our partners at Usable Image.  We'll provide updates on release of  
these facilities over the next few days.

It's good to hear the 510 and 710 file formats are behaving  
similarly-- this is helpful.

I'll ask Brian to follow-up on your question about Bio-Rad .PIC.

Cheers,

Jason

Sebastian Cachero wrote:

> Hi Jason,
>
> We are having the same problem with both types of files.
>
> If I open a 710 or 510 file in imageJ using bio-formats importer  
> and the ask for the file info I get a whole bunch of metadata but  
> after importing them into OMERO I can only see a basic set of data.
>
> A second problem seems to be that the LSM software from Zeiss gives  
> a different voxel size than the metadata retrieved by bio-formats  
> importer/OMERO (the LSM toolbox gives the same voxel size as the  
> LSM soft, I guess that bio-formats might be calculating voxel size  
> differently) .
>
> Lastly, is there anything special about importing the biorad PIC  
> files? I usually have a folder with two pic files (one for each  
> channel) and one data.raw, lse.xml and one experiment.lse files.
>
> Best,
>
> Sebastian
>
>
> On 30 Oct 2008, at 12:23, Jason Swedlow wrote:
>
>> Hi Sebastian-
>>
>> These are problems we are dealing with right now (you have a  
>> number of issues, from complete metadata support to number of  
>> channels) -- the bad news is the vendors are doing various things  
>> in their file formats that we have to deal with.  They tailor  
>> their software to handle the problem for their file format-- we  
>> get to do it for all of them!
>>
>> A more detailed response will follow, but can you confirm whether  
>> the problem you are having with Zeiss is a 510 or 710 file?
>>
>> We are having a meeting to discuss all these problems tomorrow and  
>> will report back to the community over the weekend.
>>
>> Thanks!
>>
>> Cheers,
>>
>> Jason
>>
>> On 30 Oct 2008, at 12:03, Sebastian Cachero wrote:
>>
>>> Hi,
>>>
>>> We have just installed omero in the lab and are having a couple  
>>> of problems while trying to import some confocal stacks from a  
>>> number of different microscopes (leica sp5, zeiss 510-710, biorad).
>>>
>>> 1. For some reason importing of leica .lif files fails (although  
>>> bioformats-importer has no trouble importing them to imageJ).
>>>
>>> 2. Zeiss files are imported correctly but we get only a limited  
>>> amount of the metadata from the original file.
>>>
>>> 3. Biorad .pic files get imported but have little metadata (same  
>>> as zeiss files) and the channel information is incorrect (a two  
>>> channel file gets imported as 6 channels, each one looking as  
>>> being one slice offset the others)
>>>
>>> Any help with this will be greatly appreciated!
>>>
>>> Thanks!
>>>
>>> Sebastian
>>>
>>> MRC Laboratory of Molecular Biology,
>>> Hills Road,
>>> Cambridge,
>>> CB2 2QH.
>>> United Kingdom.
>>>
>>> Office: +44 (0)1223 252944
>>> Lab	+44 (0)1223 252943
>>> Fax: +44 (0)1223 402310
>>> E-mail: scachero at mrc-lmb.cam.ac.uk
>>>
>>>
>>>
>>> _______________________________________________
>>> ome-devel mailing list
>>> ome-devel at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>>
>>
>>
>> **************************
>> Wellcome Trust Centre for Gene Regulation & Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> phone (01382) 385819
>> Intl phone:  44 1382 385819
>> FAX   (01382) 388072
>> email: jason at lifesci.dundee.ac.uk
>>
>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
>> Open Microscopy Environment: http://openmicroscopy.org
>> **************************
>>
>> The University of Dundee is a Scottish Registered Charity, No.  
>> SC015096.
>>
>>
>>
>
> MRC Laboratory of Molecular Biology,
> Hills Road,
> Cambridge,
> CB2 2QH.
> United Kingdom.
>
> Office: +44 (0)1223 252944
> Lab	+44 (0)1223 252943
> Fax: +44 (0)1223 402310
> E-mail: scachero at mrc-lmb.cam.ac.uk
>
>
>



**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.



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