[ome-devel] Update on OMERO and HCS

[Harri Jäälinoja]

Dear Jason,

this looks very interesting. Would it be possible to display also image 
analysis results attached to the original images? It would be great to 
have an easy access to segmentation and/or object recognition results, 
to have the possibility to check how the analysis has worked.

Actually I have never seen how the HCS support in OMERO is currently, 
because OMERO doesn't have readers for our HCS systems. In our unit we 
have a Cellomics CellInsight and a Leica HCS-A. How is the situation, 
are there any plans to add support for these? Both image formats are 
supported, so that's not a problem. Just the plate level reading is 
missing. I will have look at the code for the existing HCS readers, but 
I don't know if I have enough time or skills to implement something.

Best regards,
Harri


On 02/10/11 10:57, Jason Swedlow wrote:
> Dear All-
>
> Just an update on our activities with OMERO and HCS data.
>
> At the beginning of September, the Journal of Cell Biology published
> four HCS screens on the JCB DataViewer (a custom version of OMERO, built
> and maintained by Glencoe Software), totalling about 300 GB of data. The
> first was a genome wide screen of the S. cerevisiae non-essential
> collection, looking for modifiers of the DNA repair pathway. This was
> essentially a "re-publishing" of a previously published paper. The new
> paper is at:
>
> http://jcb.rupress.org/content/194/5/665
>
> and the data is at:
>
> http://jcb-dataviewer.rupress.org/jcb/browse/4608/S1/
>
> Maybe most useful to click on the "Chart" button.
>
> A second paper, which looked for modifiers of actin structure in cells,
> used one screen in Drosophila cells and two targetted screens in human
> cells: The paper is at:
>
> http://jcb.rupress.org/content/194/5/789
>
> and the data is at:
>
> http://jcb-dataviewer.rupress.org/jcb/browse/4609/
>
> The presentation of the data there can be debated-- there are advantages
> and disadvantages to what was done, and the decisions were made by many
> people. For example, we think we can do a better job at visualising the
> plates and their content. However, as a scientist, I do like the
> browser-based view of the screen results, that shows what the authors
> scored as hits, and allows me to browse their interpretation of the results.
>
> Data download is enabled at the level of wells (and thus individual
> genes) at the moment. Plate-based data download is coming.
>
> This custom UI was built by Glencoe Software, under contract to
> Rockefeller University Press. As always, this code is being rolled into
> the GPL-released version of OMERO. We have some versioning issues to
> reconcile, but getting these facilities into the open source codebase is
> a major priority. We'll send updates on this list as the code becomes
> available.
>
> Let us know if you have any questions about this resource, the code or
> our steps going forward.
>
> Cheers,
>
> Jason
>
>
>
> **************************
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>
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> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
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>
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-- 
__________________________________________________
Harri Jäälinoja
Light Microscopy Unit
Institute of Biotechnology, University of Helsinki
http://www.biocenter.helsinki.fi/bi/lmu/
+358 9 191 59370 fax +358 9 191 59366