[ome-devel] .Flex File integration

[Ghislain Bonamy]

Thanks josh,

For the path: this is what I meant:
[FlexReaderServerMaps]
CIA-1 = \\\\hostname1\\mount;\\\\archivehost1\\mount;... 

>From the description, I was not sure whether the total number of path is limited to 2 or more.

With OMERO.fs in OMERO 4.1, one could simply point to the location of the images, or location of the .mea file, so that the import is done automatically without data duplication. Right?

For the ROI, storage, I think the advantage of the chain code is that it is much more concise (so it would use less storage space). The disadvantage is the computing portion of it. Perhaps something we should keep discussing.

I am not sure I see how the PyTables and OMERO interact. Can you expect to have these PyTables saved as separate (physical) files, to which OMERO points, or is it an actual table in OMERO (in the PLSQL database)?

Best,

Ghislain Bonamy, PhD
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Genomic Institute of the
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-----Original Message-----
From: josh.moore at gmx.de [mailto:josh.moore at gmx.de] 
Sent: Wednesday, October 14, 2009 9:15 AM
To: Ghislain Bonamy
Cc: josh.moore at gmx.de; Curtis Rueden; OME-devel mailing list; Frick, Manfred; Haque, Nuzrul
Subject: Re: [ome-devel] .Flex File integration

Ghislain Bonamy writes:
 > Josh, Curtis,

Hi Ghislain,

 > 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.

Right. Do the semicolon separated values not fulfill this? 

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

That's certainly what the HCS_PREVIEW is intended to be the beginning
of. It's non-trivial, of course, but you can take a look at:

  http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/src/omero/util/populate_roi.py

for what we're doing at the moment.

 > 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.

Unfortunately, I don't think it will be possible to visualize anything
like your chains in the preview, unless you convert them and store
them as bit masks. But it's certainly something we can keep talking
about.

 > 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?

It's currently being stored in HDF via PyTables. For more information,
see:

  http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTables


Cheers,
~Josh