Image Data Publication with OMERO

Posted by Jason Swedlow-2 on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Image-Data-Publication-with-OMERO-tp7584599.html

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Dear All-

We’ve previously discussed data publication and release on these lists.  To
follow up on this, we wanted to mentioned work OME has been doing on a
BBSRC-funded project, a public Image Data Repository.

The aim is to develop next proof-of-concepts for large-scale data
publication.  There are already several existing public resources using
OMERO to publish image data at scale (e.g., JCB DataViewer
<http://jcb-dataviewer.rupress.org/>, LINCS Database
<http://lincs.hms.harvard.edu/>, Stowers ODR
<http://www.stowers.org/research/publications/odr>, EMDataBank
<http://www.emdatabank.org/>, SSBD <http://ssbd.qbic.riken.jp/>, MovinCell
<http://movincell.org/>, IMPC <http://www.mousephenotype.org/>).  In the
current project, we want to demonstrate the value of aggregating several
large imaging studies into one resource and drawing as many links as
possible between them— at the level of perturbations, ontological
annotations and quantitative features.  Finally, we want to test the
feasibility of making these data available in a virtual resource that users
can use to test their own algorithms and datasets.

[A fuller description of the project is at
http://www.bbsrc.ac.uk/research/grants/grants/AwardDetails.aspx?FundingReference=BB/M018423/1.]


These are obviously quite ambitious goals, but we are making some
progress.  We’d like to show you all where we are, ask for comments or
ideas,  and maybe stimulate your own ideas how you can contribute the
project or use these resources— both data and software-- for your own work.

The IDR resources are now up and available at:

http://idr-demo.openmicroscopy.org
Data from 12 genetic, siRNA, chemical or geographic studies, across 16
screens from a series of published papers.  This link includes several
screens, and pointers to:
http://idr-demo.openmicroscopy.org/mito Data (images and metadata) from the
Mitocheck screen (http://mitosys.org)
http://idr-demo.openmicroscopy.org/tara Data (images and metadata) from the
Tara Oceans study (http://oceans.taraexpeditions.org/en/)
http://idr-demo.openmicroscopy.org/pgpc  Data from recent paper from
Breinig et al (http://msb.embopress.org/content/11/12/846)

These studies are available from different URLs as this helped us during
the data loading phase.

In total, there are:
* 12 studies, 16 screens
* 2500 plates
* 29M frames
* 37TB of image data

We are continuing to add more datasets to this resource.

All of these are available via the “vanilla” OMERO web interface.  There is
no question that this interface isn’t built for this type of use case, and
the datasets “stretch” and in some cases break the design of this UI.
We’ll be doing work on the UI in due course.  Our goal was to get the data
integration done and have a foundation for designing, testing and building
a virtual analysis resource (which is the next phase of our work).

Again, any thoughts or comments welcome. Obviously if you know of datasets
that would be candidates for this resource, please do let us know. The
principles for datasets we want to include are written up in the
Euro-BioImaging/Elixir Data Strategy (
http://www.eurobioimaging.eu/content-news/euro-bioimaging-elixir-image-data-strategy
).

Thanks again for your support and comments.

Cheers,

Jason

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Centre for Gene Regulation & Expression
School of Life Sciences
University of Dundee
Dundee  DD1 5EH
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Open Microscopy Environment: http://openmicroscopy.org
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