Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #3673 (closed)

Opened 8 years ago

Closed 4 years ago

LightSource evolution

Reported by: jburel Owned by: ajpatterson
Priority: minor Milestone: 5.x
Component: Specification Version: n.a.
Keywords: schema Cc: ajpatterson, rleigh
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/111

Investigate possible new sources of light
and identify impact on existing model

Also, need to allow multiple light-sources.
E.g. Leica 'simultaneous scan' files specify that 2 or more lasers are used for a scan (multiple channels). Currently when we import these, we take a guess at which laser to link to each channel. Really need to link multiple lasers to each channel. Question: if we have multiple light-sources and multiple excitation-filters in the new light-path model, do we want to link the light-source to it's excitation filter? Answer: Not really!

From Forum

Ar/diode laser variable power - these units have a power rating, 
e.g. 40mW, but then have a power control (%) dial.
So a 30mW Ar gas laser can be at 20% current and an AOTF of 10% 
transmission. Is it possible to put 30mW and 20% current into LightSourceRef-Power?

See also Light-Source-Attenuation: #73

Attachments (1)

Multi-Lightpath-v-E.pdf (143.8 KB) - added by ajpatterson 6 years ago.
Version E of the new structure

Download all attachments as: .zip

Change History (13)

comment:1 Changed 8 years ago by ajpatterson

  • Cc jburel added

comment:2 Changed 8 years ago by ajpatterson

  • Cc ajpatterson added; jburel removed

comment:3 Changed 8 years ago by ajpatterson

  • Keywords schema added

comment:4 Changed 7 years ago by jburel

Do we want to consider that one for 4.4? probably next release so we need to keep it in the pipeline.

comment:6 Changed 7 years ago by rleigh

Zeiss LSM

The Zeiss LSM format allows for more than one laser per channel. (I've used 3-4 lasers per channel myself; 2 more commonly). This is supported by at least the Zeiss LSM and Zen software.

When using the system for confocal laser scanning, one may define a number of separate "tracks". Each track is a separate scan over the sample with a certain combination of lasers/detectors/filters/etc, and may also incorporate point/line/frame averaging.

Example: Sample using DAPI, Alexa Fluor 488, Alexa Fluor 594 and Atto 647. We're going to excite with 405, 488, 594 and 633 lasers, respectively. We could use these strategies:

Excite individually using 4 tracks

  1. 405 with 405 dichroic
  2. 488 with 488 dichroic
  3. 594 with 594 dichroic
  4. 647 with 647 dichroic

Each can use the same detector since each channel is on a separate track. The model currently represents this correctly.

Excite in pairs as a speed/bleedthrough tradeoff

  1. 405 and 594 with 405/594 dichroic
  2. 488 and 633 with 488/633 dichroic

Four channels on two tracks of two channels each, using the same two detectors on both tracks, but with different dichroic and bandpass filters. Not representable in current model.

All together

  1. 405, 488, 594 and 633 with a 405/488/594/633 dichroic [note: can't recall if I ever used such a thing; we certainly had dichroics which reflected at least 3 of these wavelengths simultaneously]

4 channels with 4 detectors; A Zeiss 710/780 can do this using 2 PMTs for the 405 and 647 emission, with the 488 and 594 emission being captured using ChS, the "META" head split into two groups of PMTs who's signal is integrated. Not representable in current model.

Model

In terms of the model, there are these points to consider:

  • "Channels" are not tied to a single excitation source; there may be multiple exitation sources and multiple detectors. The light falling into a single detector is a combination of all exitation sources exciting all flourochromes in the sample based on their excitation and emission profiles.
  • When imaging, there is a logical grouping of channels called a "track"; these are the channels collected simultaneously during excitation with a specific set of lasers. In the current model, there is a 1:1 correspondence between track and channel. Ideally, the microscope settings including lasers and filter setup are attached to the track, with individual channels then being associated with a particular track. The channel itself does not need to have any of that information--it only needs to know the wavelength range it is collecting. For images which only use a single laser, they would just have a 1:1 track:channel association, so this is really a generalisation of what we currently store.

Roger

comment:7 Changed 7 years ago by jburel

  • Cc rleigh added

comment:8 Changed 6 years ago by ajpatterson

  • Component changed from Model to Specification
  • Owner set to ajpatterson

comment:9 Changed 6 years ago by ajpatterson

Referencing ticket #10284 has changed sprint.

comment:10 Changed 6 years ago by ajpatterson

  • Milestone changed from Unscheduled to OMERO-5

Changed 6 years ago by ajpatterson

Version E of the new structure

comment:11 Changed 6 years ago by ajpatterson

Version E receives an initial implementation in the xsd files on branch:

https://github.com/qidane/bioformats/compare/lightsource

comment:12 Changed 4 years ago by ajpatterson

  • Resolution set to wontfix
  • Status changed from new to closed

Closed until ready for future work. Listed on trello card: https://trello.com/c/HmCOzJ8c/153-schema-changes-trac-tickets

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.92075 sec.)

We're Hiring!