Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
- Timestamp:
-
06/28/11 12:48:04 (13 years ago)
- Author:
-
wmoore
- Comment:
-
Legend:
- Unmodified
- Added
- Removed
- Modified
-
- Property Cc ajpatterson added
-
|
initial
|
v2
|
|
| 3 | 3 | Current proposal: |
| 4 | 4 | |
| 5 | | Most EM metadata/attributes can go at the 'Image' level, in a single 'EM-settings' element, instead of attached to Channel, Plane etc. In this proposal, the EM data model does not attempt to mimic the current LM model, E.g. by attaching LightSource / to Channel. |
| 6 | | It would also not add anything under Instrument. |
| 7 | | |
| 8 | | The goal here is simplicity, and follows the approach of current EM data models where there is no attempt to model Instrument, Objectives etc. See |
| | 5 | 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. |
| | 6 | This is in contrast to EM data models which don't attempt to model Instrument, Objectives etc. See |
| 9 | 7 | * http://blake.bcm.edu/emanwiki/Eman2Metadata |
| 10 | 8 | * http://www.wadsworth.org/spider_doc/spider/docs/image_doc.html |
| 11 | 9 | * http://www.imagescience.de/formats/formats.htm |
| 12 | 10 | |
| 13 | | 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). NB. This should also allow for future support of Images with one or more LM channels and one EM channel, even though all the EM data would be at the Image level. |
| 14 | | |
| 15 | 11 | The essential EM image metadata is voltage, magnification, defocus, electron dose, energy filter. Possibly Cs (used by EMAN2). |
| 16 | | In the EM-DB schema, the units are |
| | 12 | Units below are from the EM-DB schema. |
| 17 | 13 | |
| 18 | 14 | * acceleratingVoltage (kv) |
| | 15 | This should be an attribute of "Lightsource Settings". |
| | 16 | * electronDose (e/A**2) |
| | 17 | Also as an attribute of "Lightsource Settings". Scope is per-channel |
| 19 | 18 | * defocus (nm) |
| 20 | | * electronDose (e/A**2) |
| | 19 | Should become an attribute of "Objective" - since it's not something you adjust, scope is per-image |
| 21 | 20 | * energyFilter (String) |
| | 21 | Can be modeled as "Filter" with the string as 'Model' attribute. |
| 22 | 22 | * coefficient of Spherical Abberation "naminalCs" (mm) |
| 23 | | |
| | 23 | Attribute of Objective-Settings. |
| 24 | 24 | and could be put into a single EM-settings element, on Image. |
| 25 | 25 | * Magnification - simply put this in a 'dummy' Objective, OR in an EM-settings element. |
| … |
… |
|
| 34 | 34 | |
| 35 | 35 | * Pixel sizes might be in Angstroms or Nanometers in EM files. Need to convert these to microns or add support for units: #114. |
| | 36 | |
| | 37 | 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). |
1.3.13-PRO © 2008-2011
Agilo Software all
rights reserved
(this page was served in: 0.14927 sec.)
