NOTICE! This is a static HTML version of a legacy LOCI Software ticket.

LOCI projects are now located on GitHub. The Bio-Formats project can be found here.

Ticket #241 (closed defect: fixed)

Opened 2008-02-19T08:50:50-06:00

Last modified 2008-09-02T15:33:28-05:00

More robust channel assignment

Reported by: melissa Owned by: melissa
Priority: major Milestone:
Component: bio-formats Severity: minor
Keywords: Cc: wsr@…
Blocked By: Blocking:


We naively assign channel 0 to red, channel 1 to green, channel 2 to blue, etc. For many microscopy formats, however, this is incorrect - we should look at the relevant metadata to determine which channel number corresponds to which color. Leica LEI and Leica LIF are the two most obvious examples of this.

There are a few ways to solve the problem. One way is to pre-define an order that the channels should be in, (e.g. "RGBA"), then re-order the channels within the reader as needed based on the metadata values.

Another approach would be to expand the API to include a "channel order" field. Client applications would then be responsible for checking the channel order field and handling color assignment appropriately.

Change History

comment:1 Changed 2008-04-16T08:46:23-05:00 by melissa

This issue is also present in FV1000 OIB/OIF - see ImageJ thread from 2008-04-16.

comment:2 follow-up: ↓ 3 Changed 2008-04-23T14:41:13-05:00 by melissa

One way to solve this might be to bypass changes to Bio-Formats entirely, and instead add more color options to the ImageJ importer. So, we could have an option "Specify channel colors" that would pop up a box that allows the user to choose a color for each of the channels (probably want a drop-down box, but could be a palette). This would be way easier than trying to mess with each reader individually, and provides more flexibility.

comment:3 in reply to: ↑ 2 Changed 2008-04-23T17:17:32-05:00 by curtis

Replying to melissa:

One way to solve this might be to bypass changes to Bio-Formats entirely, and instead add more color options to the ImageJ importer.

While I agree that more color options in the importer plugin would be useful, there are times when the metadata does specify the color ordering, and it would be a shame not to provide that in some fashion. The simplest way would be as OME-XML metadata, using DisplayOptions's RedChannel, GreenChannel, BlueChannel and GreyChannel elements, which I am currently working on adding to the MetadataStore API.

comment:4 Changed 2008-05-05T13:32:43-05:00 by curtis

  • Cc wsr@… added

comment:5 Changed 2008-07-09T15:51:31-05:00 by melissa

Finished for FV1000 OIB/OIF (r4179).

comment:6 Changed 2008-08-26T11:32:39-05:00 by melissa

Finished for Leica LIF (r4330).

comment:7 Changed 2008-09-02T14:42:15-05:00 by melissa

Finished for Leica LEI (r4351).

comment:8 Changed 2008-09-02T15:33:28-05:00 by melissa

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