[ome-devel] EM in OMERO

[Will Moore]

Hi Christoph and Ingvar,

  Many thanks for the useful discussions last week. Hope you both had  
a good Christmas.
Here is a bunch of notes I made afterwards. Please correct anything I  
have misunderstood.

I am also sending this to the OME dev team as a basis for our  
discussions...

  Cheers,

    Will.



Goals:

No plans to substantially change the EM-DB itself in the short term.  
Plan is to use OMERO for EM-maps, raw microscope images, and all other  
images in the workflow. EM-DB will remain the location of all  
publication, sample, experiment metadata etc. OMERO will hold limited  
EM imaging metadata equivalent to the LM metadata it currently supports.

E.g. if scientists use OMERO for their EM images in their  
institutions, they should be able to automatically submit the whole  
workflow stack to the EM-DB, adding the necessary publication, sample  
and experimental metadata at the time of submission (not at the  
acquisition or processing stages).


OMERO viewers / API

Want to be able to view a 3D-volume looking at a plane at any angle.  
Not just in the Z-axis. Also to project at any of these orientations.
Needs API changes. Required for maps and for segmentations.
E.g. see qsegment viewer of EMAN.



Web-client is important.

-	Users familiar with web-viewers: CCDB, EMDB etc.
-	Many users on different platforms prefer not to download Java clients
-	UI development on web is much improved with new libraries etc.


Open Astex Viewer

-	Stable code (in active use over 10 years)
-	Runs as web applet (with Javascript controls) or as a Java viewer
-	Needs some changes to make it suitable for EM-maps
-	Burden of maintenance? Shouldn’t be very high.
-	Do we make changes ourselves or ask Mike Hartshorn to implement  
them? openastexviewer at googlemail.com


ROIs / masks

Need 3D masks:
E.g. Highlight regions of an EM-map in different colours.
http://www.ebi.ac.uk/pdbe-srv/emsearch/atlas/5134_visualization.html
Regions shouldn’t be mutually exclusive, since current practices don’t  
ensure this. Combine several masks to produce an image (see link).
Also need this for segmentations. E.g. neurons with parts marked in  
different colours.


File formats

Good place to look is Chimera code:
Chimera.app/Contents/Resources/share/VolumeData/mrc/

-	MRC – OK but pixel size not correct
-	Spider  - no pixel size metadata?
-	Imagic


Ontologies / RDF

Annotate with ontology terms:
-	Flexible (we don’t have to define metadata structures ahead of time)
-	Use for searching etc.
-	Probably won’t use them for reasoning except “is-a” ?
-	Implement in a similar way to Tagging.


Correlative (Maps and PDB coordinates)

-	Chimera allows superimposition, docking etc and the state can be  
saved as a Python script to recreate the session. This script also  
saves the maps and/or PDB coordinates. But this is not a reliable  
means of storing these relationships long-term. Not necessarily a  
stable format etc?
-	Need some other way to define molecule relationships etc.

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