[ome-devel] .Flex File integration

Thu Jun 11 23:50:20 BST 2009

Hi Stuart-

Thanks for your comments.  I may have been the ultimate source, so  
I'll just clarify what I am pretty sure I said.  But this is all a  
little complicated, and I may not have made myself clear.

First, as Curtis pointed out. .flex IS supported in Bio-Formats.  When  
we say this, we mean that using Bio-Formats, you can read the .flex  
format file.  However, we don't explicitly guarantee the extent of  
metadata support.  It is almost always at least some of the included  
metadata, but achieving what we call "metadata completion" (which  
means we've found a home for every piece of metadata in the file we  
can identify is a big task.  It is one we are working through for a  
number of files (see the Beta4.0 release announcement on 27 Mar 09),  
but is certainly a work in progress.

Second, as you have heard and seen, we are working to support usage of  
OMERO in HCS.  This is a stepwise, progressive effort, where we first  
deal with the data model (http://www.ome-xml.org/wiki/ 
ScreenPlateWell), put this into the OMERO backend (ScreenPlateWell was  
included in our Beta3 release, released 30 June 08, but we didn't tell  
anyone), then begin importing data (in the the code for Beta4.0, just  
not turned on), and then finally deliver full support in all the  
clients.  We want to deliver a working, useful solution for HCS-- that  
enables real work with the data, and so that takes time.

So, because of all this, support for files within OMERO is necessarily  
a subset of files supported in Bio-Formats.  As Curtis mentioned,  
following feedback at our recent OME User's Meeting, we are working on  
a number of pieces of tech to make it MUCH  easier to bring in new  
file types into OMERO.  But, no, full HCS support is not yet available.

Following the logic above, .flex is supported within Bio-Formats, but  
we want to ensure that we properly support the various metadata  
associated with the files.  That will still take some time, but if you  
want to see what's going on, go to the OMERO clients Trac for the  
current milestone:

http://trac.openmicroscopy.org.uk/shoola/milestone/OMERO-Beta4.1

and search on 'SPW'  (that's OME-ese for ScreenPlateWell, or in  
English, HCS).  You'll see we are laying the groundwork for what you  
are asking about.

So, you'll want to know when you will have full HCS support.  We had  
planned to release an HCS viewer within OMERO.insight this summer, but  
our priorities were shifted by the response from the attendees at our  
User's meeting (we MUST deliver what the community asks for and the  
meeting is a great way for the community to express its opinions and  
priorities).  The roadmaps show these changed priorities.  We are  
HOPING to release HCS support in Beta-4.1 (targetted 30 Sept 09  
release), but we won't be sure we can make that til we get done with  
the work we are doing now, building infrastructure for moving data in  
and out of OMERO and also to deal with the data duplication problem.   
We'll update this list as we get through the next few weeks.

We're sorry we don't have a full solution for the data you need.  We  
have a limited amount of work we can achieve, and are doing as well as  
we can with what we have.  Note that OME is completely grant-funded.   
If you want to help drive the development, you can commission Glencoe  
Software to do work you need, and this work will be contributed to the  
open source code base.  Alternatively, if you have people who can work  
with our code base on your team, then implementing this facility won't  
be that hard (if you follow the list, you'll see that a number of  
people have already done this).  If you go through the emails to this  
list, you'll find comments from people who have found HCS support  
within OMERO.insight and want to turn it on.  You are welcome to do  
this-- that is the point of open source work-- but it is not supported.

That's a long answer, and I'd be happy to discuss in more detail--  
just contact me directly.

As always, thanks for your support.

Cheers,

Jason

On 11 Jun 2009, at 22:19, Curtis Rueden wrote:

> Hi Stuart,
>
> Sorry for the confusion. The Bio-Formats library supports the Flex  
> format, so it is only a matter of time before that support is  
> integrated into the OMERO system. For reference, the Bio-Formats web  
> site (http://www.loci.wisc.edu/ome/formats.html#formats) lists all  
> supported formats, with blue-highlighted entries also supported by  
> the OMERO server.
>
> It is my understanding that an upcoming release of the  
> OMERO.importer client will allow users to toggle which formats are  
> enabled. This would allow you to "turn on" support for Flex within  
> OMERO, with the caveat that any such manually enabled formats have  
> NOT been well tested with the OMERO system, and you may experience  
> quirks or problems.
>
> Regarding more thoroughly tested Flex support, I believe it will  
> come at the same time as many of the planned high-content screening  
> improvements to the OMERO system. We recently reprioritized some  
> features due to feedback at this year's OME European Users meeting,  
> and so I am not certain of the timeline for the HCS improvements,  
> but they are definitely still planned.
>
> -Curtis
>
> On Thu, Jun 11, 2009 at 11:15 AM, Smith, Stuart C <Stuart.C.Smith at pfizer.com 
> > wrote:
> Afternoon,  we were hoping to evaluate OME within our organisation  
> to see if it aided our Scientists, but after setting up the server  
> (windows) and installing clients on several peoples PC, we were  
> surprised to find that .flex files were not supported, despite being  
> advised otherwise in the form of a conversation between someone  
> within my organisation and someone associated with OME.  Are they  
> any plans to support .flex? or is this a restriction imposed by  
> Perkin Elmer? If so, is there scope for us to  implement .flex file  
> support internally within our own organisation? or if we made  
> contributed in some way to the development of OME, would that clear  
> the path for .flex file support within our OME setup?
>
>
> If you feel this conversation is best carried on outside of this  
> forum, please feel free to email me directly.
>
>
> Thanks in advance,
>
>
> Stuart
>
>
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