[ome-devel] .Flex File integration

[Ghislain Bonamy]

Josh, Curtis,

I looked at this page:
https://trac.openmicroscopy.org.uk/omero/wiki/FlexSupport
One thing that I wanted to point out is that the Opera supports several archiving paths.

Another thing that I was wondering is whether OMERO will start federating the results from various analysis tools.

Finally I see that the "HCS Preview" provide storage support for ROI. Acapella does not currently provide support generating ROI. Thus, I have developed a library which generates the chain code for simple shape (ie. not composite shapes). Any information how this data can be formatted into something usable by OMERO would be great.

Regarding single cell data, ROI etc. Am I correct to believe that all of this data is stuffed into OMERO? If so is there any plans to provide support for file storage rather storage in the database?

Best,

Ghislain Bonamy, PhD
__________________________________________
Research Investigator

Genomic Institute of the
Novartis Research
Foundation
Department of Informatics, room C117
10675 John Jay Hopkins Drive
San Diego CA 92121
USA

+1 (858) 812-1534 (W & F)
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-----Original Message-----
From: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of josh.moore at gmx.de
Sent: Wednesday, October 14, 2009 6:26 AM
To: Curtis Rueden
Cc: OME-devel mailing list; Frick, Manfred; Haque, Nuzrul
Subject: Re: [ome-devel] .Flex File integration


Hi Stuart,

to follow-up on Curtis' email, yes, in the upcoming 4.1 release you'll
be able to import *.flex files and view them in Insight. If you have
analysis results from Acapella, you will need to do extra
configuration, which we are beginning to outline here:

  https://trac.openmicroscopy.org.uk/omero/wiki/FlexSupport

If you then downloaded the HCS_PREVIEW clients (rather than the standard
downloads), you would be able to see the measurement results attached
to each image.

With the release, we'll have screencasts demonstrating the
functionality, which should make everything clearer.

Thanks for your interest,
~Josh

Curtis Rueden writes:
 > Hi Stuart,
 > 
 > OMERO Beta 4.1, due later this month, will feature support for reading Flex
 > files. As I said before, OMERO provides limited support for high-content
 > screening, in that it can maintain your data's screen-plate-well structure,
 > but we anticipate expanding the HCS features in a future release.
 > 
 > I am forwarding your message to the OME developer mailing list, as the OME
 > developers will be the best ones to elaborate further on Flex support in
 > OMERO.
 > 
 > -Curtis
 > 
 > On Thu, Oct 8, 2009 at 4:38 AM, Smith, Stuart C
 > <Stuart.C.Smith at pfizer.com>wrote:
 > 
 > >  Hi Curtis, firstly I appoligise for the very long delay in replying to
 > > the below email, but the OME evaluation was put on hold, but after doing
 > > further reading on the $,1r|Bio-Formats$,1r} product, if I am reading it correctly
 > > it could add $,1r|.flex$,1r} file support to $,1r|OME Server/Client$,1r}.  Is this correct?
 > > If so, how can it be implemented & are there any limitations on the .flex
 > > file support?  or have I completely miss understood the product?
 > >
 > >
 > >
 > > Thanks in advance,
 > >
 > >
 > >
 > > Stuart
 > >
 > >
 > >
 > > *From:* ctrueden.wisc at gmail.com [mailto:ctrueden.wisc at gmail.com] *On
 > > Behalf Of *Curtis Rueden
 > > *Sent:* 11 June 2009 22:19
 > > *To:* Smith, Stuart C
 > > *Cc:* ome-devel at lists.openmicroscopy.org.uk
 > > *Subject:* Re: [ome-devel] .Flex File integration
 > >
 > >
 > >
 > > 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