[ome-users] Bio-Formats and Omero

[Jason Swedlow]

Hi All-

Apologies for the delayed response-- we've been pretty busy.

Ok, it all seems so simple.....if only.

As Paulo and Sriram highlighted, the support for images in Bio- 
Formats is much broader than in OMERO.  There are many reasons for  
this, but ultimately it comes down to metadata and testing-- we only  
turn on support for a specific file format in OMERO if we have a good  
set of test data and if we have a home for as much metadata as  
possible coming from Bio-Formats.  This rather picky approach is very  
laborious, so we have turned on file formats slowly.

HOWEVER, there is another question-- "metadata completeness".  Have  
we found a home for every element of metadata in a proprietary file  
format in Bio-Formats and also OMERO?  This has been our focus  
(really, obsession) for the last few weeks-- see for example:

http://trac.openmicroscopy.org.uk/omero/query? 
status=assigned&status=new&status=reopened&group=status&component=Import 
&milestone=OMERO-Beta4
http://trac.openmicroscopy.org.uk/omero/query? 
status=assigned&status=new&status=reopened&group=status&component=Model& 
order=priority&milestone=OMERO-Beta4

Some of you who use the Leica fie formats know how important this  
work is:

http://trac.openmicroscopy.org.uk/omero/ticket/1124

Having supported some 30+ file formats in OMERO, and 60+ in Bio- 
Formats, we have turned our attention to metadata completion.   This  
is slow, painful work, requiring alot of updates to the OME Data  
Model (http://ome-xml.org/query? 
status=closed&group=resolution&milestone=September+2008+Schema 
+Release), Bio-Formats, and OMERO.  But we are making headway-- that  
is the good news.  The bad news is that we have just a few file  
formats fully supported.  The amount it takes to fully support more  
gets smaller and smaller, but this will still be slow.  "Completion"  
is synonomous with "perfection", and we are quite good at being  
imperfect. Think of this as an asymptotic approach to a Holy Grail.

(Just to toot our horn-- we have a saying on the OME project: "we eat  
our own dog food".  That means we don't just issue specifications, we  
write and release software based on these specifications, so we find  
many of  the mistakes, limitations, etc.  Honestly, we really are  
intimately familiar with our spec, and are working very hard to make  
it better-- more accurate, more usable-- and release software based  
on it.  Not many format and specification projects do this, and it is  
one of the reasons we have been, dare I say it,  marginally successful.)

Sooooooooooooo, uh, no, the release of Beta4 most likely won't  
include a large number of new file formats.  What you will see is a  
big change in the amount of metadata supported and visible in our  
clients, and slowly, the existing file formats more fully supported  
(hopefully completely).  For anyone going to ASCB, we are hoping to  
show examples of this at the OME Booth-- so please come by and tell  
us what metadata you must have.

HOWEVER, please do keep those file format requests coming, and if at  
all possible, write to us and let us have some samples of the files  
you'd like to have supported-- testing helps us be sure we are  
releasing useful software.   We'll start adding more formats soon,  
probably in the next couple of months.

Cheers,

Jason

On 26 Nov 2008, at 16:35, Paulo Almeida wrote:

> Hi,
>
> Regarding a recent question about .svs images, does Omero intend to  
> support
> everything in Bio-Formats? That question arose because one of our  
> users
> wanted to upload a QuickTime movie, which is listed in Bio-Formats  
> but not in
> the Omero ImporterFormats that Sriram pointed to (
> http://trac.openmicroscopy.org.uk/omero/wiki/ImporterFormats ).
>
> Best,
> Paulo
> Instituto Gulbenkian de Ciência
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



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