Task #3677 (new)
Opened 13 years ago
Last modified 9 years ago
Basic EM metadata support
Reported by: | wmoore | Owned by: | jburel |
---|---|---|---|
Priority: | minor | Milestone: | Unscheduled |
Component: | Specification | Version: | n.a. |
Keywords: | EM, schema | Cc: | ajpatterson, jburel, ilagerstedt-x, wmoore |
Resources: | n.a. | Referenced By: | n.a. |
References: | n.a. | Remaining Time: | n.a. |
Sprint: | n.a. |
Description (last modified by 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).
Change History (17)
comment:1 Changed 13 years ago by ajpatterson
- Cc ajpatterson added
comment:2 Changed 13 years ago by wmoore
- Description modified (diff)
comment:3 Changed 13 years ago by ajpatterson
- Keywords schema added
comment:4 Changed 12 years ago by jburel
- Cc jburel added
comment:5 Changed 12 years ago by jburel
- Cc ilagerstedt-x added
comment:6 Changed 12 years ago by jburel
should be set now
comment:7 Changed 12 years ago by jburel
- Milestone changed from Unscheduled to OMERO-Beta4.4
- Sprint set to 2012-02-28 (9)
To discuss during this week meeting. Adding to sprint (9) so we can find it.
comment:8 Changed 12 years ago by jburel
- Sprint changed from 2012-02-28 (9) to 2012-03-13 (10)
Moved from sprint 2012-02-28 (9)
comment:9 Changed 12 years ago by jburel
- Cc wmoore added
- Sprint 2012-03-13 (10) deleted
Any progress on the model front?
comment:10 Changed 12 years ago by ajpatterson
- Milestone changed from OMERO-Beta4.4 to OMERO-Beta4.4.1
comment:11 Changed 11 years ago by jmoore
Is this still intended for 4.5.0?
comment:12 Changed 11 years ago by wmoore
- Milestone changed from OMERO-4.5 to Unscheduled
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).
comment:13 Changed 11 years ago by ajpatterson
- Component changed from Model to Specification
- Owner set to ajpatterson
comment:14 Changed 11 years ago by 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.
comment:15 Changed 11 years ago by mlinkert
Would also be useful to model the spot size, which is recorded primarily in SEM files. See again #10488.
comment:16 Changed 9 years ago by ajpatterson
- Owner changed from ajpatterson to jburel
- Version set to 5.0.8
comment:17 Changed 9 years ago by ajpatterson
- Version 5.0.8 deleted
Meeting 09/11/11 Dundee.
Model (work in progress) given by Ingvar see https://docs.google.com/leaf?id=0B6K_5MCpRQkmZDdjOGYzNTMtMmFlYS00N2FhLTkyZGYtNzBkODdlZTliZTZl&hl=en_US