Basic EM metadata support

[wmoore]

Moved from ​http://www.ome-xml.org/ticket/107

Current proposal:

The 'proper' places for EM metadata should be used where possible to preserve extensibility of the model, E.g. correlative EM when combining LM and EM in a single Image.
This is in contrast to EM data models which don't attempt to model Instrument, Objectives etc. See

• ​http://blake.bcm.edu/emanwiki/Eman2Metadata
• ​http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html
• ​http://www.imagescience.de/formats/formats.htm

The essential EM image metadata is voltage, magnification, defocus, electron dose, energy filter. Possibly Cs (used by EMAN2).
Units below are from the EM-DB schema.

• acceleratingVoltage (kv)

This should be an attribute of "Lightsource Settings".

• electronDose (e/A2)

Also as an attribute of "Lightsource Settings". Scope is per-channel

• defocus (nm)

Should become an attribute of "Objective" - since it's not something you adjust, scope is per-image

• energyFilter (String)

Can be modeled as "Filter" with the string as 'Model' attribute.

• coefficient of Spherical Abberation "naminalCs" (mm)

Attribute of Objective-Settings.

and could be put into a single EM-settings element, on Image.

• Magnification - simply put this in a 'dummy' Objective, OR in an EM-settings element.

Defocus could be at the Image level, since people only take a single defocus per image. But sometimes take 2 images at different defocus values. So maybe this could be another dimension, at the Plane level?!
Also, defocus is assigned to particles, and some Spider images are a stack of Particles, each with (potentially) a different defocus? Maybe in practice they are all the same?
(see e-mail 13th Jan 2010).

• Tilt angle (degrees)

This should go on plane, and is really another dimension. Needs to wait for N-dimension to be implemented. Increment is not always consistent (Store as PlaneInfo?).

• Pixel sizes might be in Angstroms or Nanometers in EM files. Need to convert these to microns or add support for units: #114.

The only limitation is support of formats (E.g. spider) where it is common to bundle many different particle images into a single stack for convenience, making it 'possible' that each plane has different value for a particular attribute (see below).

[jburel]

Meeting 09/11/11 Dundee.
Model (work in progress) given by Ingvar see ​https://docs.google.com/leaf?id=0B6K_5MCpRQkmZDdjOGYzNTMtMmFlYS00N2FhLTkyZGYtNzBkODdlZTliZTZl&hl=en_US

[jburel]

should be set now

[jburel]

To discuss during this week meeting. Adding to sprint (9) so we can find it.

[jburel]

Moved from sprint 2012-02-28 (9)

[jburel]

Any progress on the model front?

[jmoore]

Is this still intended for 4.5.0?

[wmoore]

Unfortunately we haven't got enough feedback from OMERO EM users to go ahead with this yet. And it's not such a high priority yet as the OMERO / EM project has focussed elsewhere (and largely complete now).

[mlinkert]

One other thing to consider adding here would be the "Pressure" setting, which while not present in Spider/EMAN2 is present in other EM formats (e.g. Gatan DM3, see #10488). Not sure where that belongs or what the correct units would be.

[mlinkert]

Would also be useful to model the spot size, which is recorded primarily in SEM files. See again #10488.