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: |
Description
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
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:8 Changed 2008-09-02T15:33:28-05:00 by melissa
- Status changed from new to closed
- Resolution set to fixed
This issue is also present in FV1000 OIB/OIF - see ImageJ thread from 2008-04-16.