Re: Image Data Publication with OMERO

Posted by Tim Feinstein on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Image-Data-Publication-with-OMERO-tp7584599p7584603.html

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Hi Jason,

Very cool project.  I think those resources will be most useful if they
include descriptive metadata.  At a quick glance it appears the images
have extensive experimental metadata (siRNA target etc.) but they lack
technical details like microns per pixel, wavelength, camera, objective
etc.  I would not feel comfortable performing a quantitative analysis on
this dataset or comparing it with my own experimental data as it is.  In
my experience OMERO should have no problem gathering at least some of that
from raw image files.  Possibly you can find this info in the methods
section of the original reports, although those rarely include as much as
OMERO could glean.

 If it is not too much of a burden, possibly you could suggest
experimenters fill out at least the basics when processed images are
uploaded lacking their original metadata. These high-throughput studies
often use the same settings across the board so it may not be that hard to
update them all at once.

All the best,


Tim


Timothy Feinstein, Ph.D.
Research Scientist
University of Pittsburgh Department of Developmental Biology





On 1/6/16, 4:51 AM, "Confocal Microscopy List on behalf of Jason Swedlow"
<[hidden email] on behalf of [hidden email]> wrote:

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>
>Dear All-
>
>We¹ve 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?FundingRef
>erence=BB/M018423/1.]
>
>
>These are obviously quite ambitious goals, but we are making some
>progress.  We¹d 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 ³vanilla² OMERO web interface.  There
>is
>no question that this interface isn¹t built for this type of use case, and
>the datasets ³stretch² and in some cases break the design of this UI.
>We¹ll 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-dat
>a-strategy
>).
>
>Thanks again for your support and comments.
>
>Cheers,
>
>Jason
>
>--
>**************************
>Centre for Gene Regulation & Expression
>School of Life Sciences
>University of Dundee
>Dundee  DD1 5EH
>United Kingdom
>
>phone [phone]
>Intl phone:  [phone]
>FAX   [phone]
>email: [hidden email]
>
>Lab Page: http://www.lifesci.dundee.ac.uk/people/jason-swedlow
>Open Microscopy Environment: http://openmicroscopy.org
>**************************