[ome-devel] SPIM and OMERO

[Will Moore]

  Hi Stephan,

  --  I'm replying to the ome-devel list (since this is of general  
interest) so I've put the various cc e-mails to Bcc. If you're happy  
for those e-mail addresses to be public then we can just cc??

Our current efforts to model SPIM in OME can be found here: http://www.ome-xml.org/wiki/SPIM/InitialSupport

This shows in principle how we would support the 'Angle' and Tiles: by  
using a separate "Image" in OME for each angle.
Various other pieces of metadata can either be represented in our  
model, or added as annotations on the images.
The images themselves are linked by a "spim" annotation that is  
preserved on import to OMERO.

As a proof-of-principle, I made an attempt to display images in this  
format in a web viewer grid layout that lets you choose the dimension  
to use on each axis.
Choice of: Time, Z, Channel or Angle.
NB: This viewer does not support Tiling at the moment. Tiles are  
interleaved with Angle. Also just noticed that splitting channels has  
a bug.

You can try this out: If you grab the example ome file from the page  
above and import it into the latest OMERO, then (using the ID from any  
one of the imported images) you go to the OMERO.web
<your-server>/webtest/image_dimensions/<image-id>

Screen-shot below.

Most of the code for getting the info from the annotations in OMERO  
can be seen http://git.openmicroscopy.org/?p=ome.git;a=blob;f=components/tools/OmeroWeb/omeroweb/webtest/webtest_utils.py;hb=HEAD

So, our main questions going forward:

  - Does this model support all the types of metadata you need to  
store for SPIM data?
  - How do you need to access the data from OMERO?
      - For viewing (we talked about a time-lapse view, which is kinda  
supported by the webtest viewer)
      - For analysis
  - Can we get some sample data and metadata, try to get it in to  
OMERO and see if we can get the data out as you need it?

   Cheers,

    Will.



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William Moore
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

Phone 01382 386364
http://openmicroscopy.org