Posted by
George McNamara on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Image-Data-Publication-with-OMERO-tp7584599p7584601.html
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Hi Jason,
With respect to cell biology, how about consolidating all these
resources, and getting BBSRC (as you mentioned), EMBL, Sanger Institute,
NIH, HHMI, and other funders -- Gates Foundation wrt malaria, TB, etc --
, in one place, such as "The Cell: an Image Library" (which I believe
has OMERO under the hood),
http://www.cellimagelibrary.org/(minor detail: that link is not working from home right now),
and eventually a way to move the data hosting to a Teta/Peta/exa
scalable hosts, such as NIH's NCBI and European and Asian equivalents
(or they can pay to have Amazon Web Services, or Google, Microsoft, etc,
equivalents) host it at a lower cost. The
Big Data to Knowledge
http://commonfund.nih.gov/bd2k/indexhttps://commonfund.nih.gov/bd2k/grantshas money - and hopefully current RFA - that might help.
Have you spoken /met with Philip Bourne, NIH's Associate Director for
Data Science,
https://commonfund.nih.gov/bd2k/members(Philip knows big data - was director of the Protein Data Bank (now at
http://www.rcsb.org/pdb/home/home.do ) before joining NIH.
From
http://murphylab.web.cmu.edu/software/searcher/ it looks like
OMERO runs "under the hood" of www.ProteinAtlas.org and that Robert
Murphy has already figured out how to do analysis from both The Cell
library and Human Protein Atlas. Can you 'simply' scale up from Robert's
work?
best wishes,
George
p.s. Listserv members - most light microscopy web sites have boring
1980's style HeLa DAPI/F-actin/microtubules images - can be more
colorful than that I'm a little behind on my reading and only last week
came across "ColorfulCell" a mammalian expression plasmid to express
fluorescent proteins, $65 from addgene,
*MXS-Chaining: A Highly Efficient Cloning Platform for Imaging and Flow
Cytometry Approaches in Mammalian Systems*. Sladitschek HL, Neveu
PA./PLoS One. 2015 Apr 24;10(4):e0124958. doi:
10.1371/journal.pone.0124958. eCollection 2015./PONE-D-15-01385
[pii]PubMed 25909630 <
http://pubmed.org/25909630>
$65 ColorfulCell
https://www.addgene.org/62449/$375 MXS Chaining Kit
https://www.addgene.org/kits/mxs-chaining/ More stuff from Pierre Neveu's lab,
https://www.addgene.org/Pierre_Neveu/It would be useful if all the best FP's from The Michael Davidson
Collection were made into MXS components, and other state of the art
FP's added to addgene and MXS. I've previously suggested additional ways
to improve FP's SNR by localization,
http://works.bepress.com/gmcnamara/75On 1/6/2016 3:51 AM, Jason Swedlow wrote:
> *****
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>
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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
>
--
George McNamara, Ph.D.
Single Cells Analyst, T-Cell Therapy Lab (Cooper Lab)
University of Texas M.D. Anderson Cancer Center
Houston, TX 77054
Tattletales
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