Demo EM workflow in OMERO

[wmoore]

As a result of discussion during Christoph and Ingvar's visit to Dundee - May 2010:

We have decided to develop and link various pieces of EM functionality in order to demonstrate the utility of OMERO as an agnostic data storage solution and algorithm framework for EM. These include:

• Spider
• EMAN2
• Open Astex Viewer
• Chimera
• Segger ​http://sourceforge.net/projects/segger/

Outline of potential workflows:

Import EMAN2 project

• Import a complete EMAN2 project (setting up Image-Image links)

Use Spider to pick particles, EMAN2 for rest

• Data imported into OMERO
• Filter data (E.g. EMAN2 or Spider)
• Use Spider to auto-pick particles - Save ROIs
• Generate Images from ROIs
• EMAN2 ctf correction on Server
• EMAN2 classification - store results in Pytables / Tags
• Export to do EMAN2 reconstruction locally

Maps, Masks, PDB

• Open the map in Chimera - segment with segger
• Save segments as masks, linked to map
• Browse map, masks and pdb in Open Astex Viewer.

Features of OMERO that will be used:

• Annotations: Projects/Datasets?, Descriptions, Tags, Comments, File Annotations
• Image-Image links will initially be implemented using text annotations, pending a 'proper' solution
• Scripting service
• API (Java and Python)
• Measurement tool (viewing particle ROIs)

Single Particle Reconstruction Project

Need to represent this in a consistent way in OMERO:

• One Project per SPR
• Dataset for raw images
• Dataset for particles. Particles named/tagged and linked to Parent image
• Dataset for phase-flipped particles
• Dataset for wiener particles
• Dataset for selected particles (selected from wiener particles)
• Dataset for Model-free class averages. Each image should link to the members of that class: Selected particles should 'link' to the class they were assigned (PyTables)
• Dataset for Reference class averages. (links as above) This dataset reflects the final iteration. Additional Datasets may preserve other points in the reconstruction.
• Dataset for Map!

[wmoore]

Many of these features have been worked on - ticketed elsewhere.
Now we will look at the possibility of a VM package of our current functionality.