Task #3681 (closed)
Opened 13 years ago
Closed 13 years ago
Intermediate Support for SPIM
| Reported by: | ajpatterson | Owned by: | |
|---|---|---|---|
| Priority: | minor | Milestone: | Unscheduled |
| Component: | Specification | Version: | n.a. |
| Keywords: | schema | Cc: | jamoore, jburel |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
Moved from http://www.ome-xml.org/ticket/127
This will provide an initial solution for storing SPIM data in OME-XML and OME-TIFF files.
SPIM = Single (or Selective) Plane Illumination Microscopy
It is different in that the sample is illuminated by a sheet of light projected from the side using a second objective. This second objective uses a cylindrical lens to create the thin strip of light. The regular objective, illumination objective & cylindrical lens are moved in step to keep the focal point in the sample at the same depth as the sheet of light.
This causes a problem as the sample is only being illuminated from one side. To get round this the light is rotated relative to the sample, or the sample relative to the light, and a sequence of images from different angles are collected. These images can then be combined to create the final image.
Extra data needing stored
This falls into the following groups:
Information about the extra optical elements: Illumination Objective & Cylindrical Lens - This would map to the light source or objective area of our model.
Information about the physical location of the extra optical elements: Illumination Objective position & Cylindrical Lens position - This could map to either the Settings (the light source settings or objective setting) area of our model or the StageLabel contained with Image that defines physical points on the stage of the instrument.
Information for the extra dimension: Angle. As the sample (or light) is rotated the pixels are generated defined by X, Y, Z, Time, Channel and Angle. We can store the first 5 in our existing model but the extra would need to wait for N-Dim support (Ticket #112). As this solution has to pre-date that work an XmlAnnotation will be used to tie together several images in the OME-XML each taken from a unique angle. This approach will work as there is a small number of discreet angles. e.g. 0, 45, 90, 135,...
There is also information specific to the collection system that the software may want to store. This should not go into the general OME Data Model so is best places in an XmlAnnotation within the file.
Initial sample data courtesy of Guenter Giese @ mpimf-heidelberg.
The samples attached have been derived from the data supplied by Guenter but have been restructured to work in the OME-XML 2010-06 Schema.
restructure-2010-06.xml - this is a simple enclosing of the supplied data in XmlAnnotations
Attachments (1)
Change History (8)
comment:1 Changed 13 years ago by ajpatterson
- Cc jmoore jburel added
comment:2 Changed 13 years ago by wmoore
comment:3 Changed 13 years ago by ajpatterson
- Component changed from Model to Specification
comment:4 Changed 13 years ago by ajpatterson
Referencing ticket #2730 has changed sprint.
comment:5 Changed 13 years ago by ajpatterson
- Keywords schema added
comment:6 Changed 13 years ago by jburel
Referencing ticket #2730 has changed sprint.
comment:7 Changed 13 years ago by ajpatterson
- Resolution set to fixed
- Status changed from new to closed
Covered by 8D Modulo Soulution
(In [8909/omero]) Prototype web viewer for SPIM data in the http://www.ome-xml.org/wiki/SPIM/InitialSupport format. See #3681