[ome-devel] New Light Source Model Structure

[Andrew Patterson]

Hello,

We are in the process of updating the light source structure in the OME model on the develop branch. We would appreciate feedback on this before Monday the 9th of September.

Feel free to ask any questions or launch a discussion on the list.

http://downloads.openmicroscopy.org/presentations/2013/August-LightSource/Multi-Lightpath-Proposed.pdf
This PDF shows the current (C) and proposed (P) arrangement of these objects. The linking is shown with green arrows in the second version of each diagram.

Why is this change needed?

The idea of this change is to clearly separate the storage of information about the general setup of the instrument and the setup that was active when a particular image plane was recorded. It is also designed to allow us to support more complex arrangements, for example simultaneous collection of planes using multiple detectors and/or multiple light sources.  Examples include multi-channel imaging, multi-modal imaging, stimulated emission depletion microscopy, and various implementations of localization microscopy and light sheet fluorescence microscopy.


Where in the schema will the data be stored?

In the schema and model, data concerning the setup of an instrument will be stored in a new Configuration object. Each instrument can contain several of these Configuration objects. Each Configuration object holds the adjustable settings for the Objectives, LightSources, LightPaths and Detectors of the instrument. The fixed settings for these are stored separately below Instrument in the individual Objective, LightSource, LightPath or Detector. 

How will the data be linked to images?

The Configuration can be linked to the image at two levels. The usual linking is from Channel, so all the planes of a single channel will share the same settings. The alternative approach is to link from Plane instead. This allows every plane within each channel to use an individual configuration. For a given Image we plan to support Channel linking or Plane linking but not both.

What objects are disappearing?

FilterSet will be removed. Its function will be replaced in the new arrangement by LightPath.
* Remove FilterSet
* Remove FilterSetRef

Where does data change?

In Channel:
        Replace LightSourceSettings, DetectorSettings, LightPathRef and FilterSetRef with ConfigurationSettings
In Instrument:
        Replace FilterSet with Configuration and LightPath
In LightPath:
        An ID is added to support LightPathRef

What objects are added?

Added Configuration:
        This holds collections of ObjectSettings, LightSourceSettings, LightPathRef and Detector Settings.
Added ConfigurationSettings:
        This points at a configuration and optionally identifies one of each LightPath, LightSource, and Detector as being active.
Added LightPathRef, LightSourceRef, and DetectorRef

We would be keen to hear any comments on these new structures.

Thanks,

Andrew Patterson
ajpatterson at lifesci.dundee.ac.uk
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee