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Task #7709 (new)

Opened 12 years ago

Last modified 10 years ago

Re-evaluate strategy for assigning channel colors

Reported by: mlinkert Owned by:
Priority: major Milestone: Unscheduled
Component: General Version: 5.0.0
Keywords: n.a. Cc: jburel, wmoore, rleigh, cblackburn, dsudar@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by jamoore)

From https://trac.openmicroscopy.org.uk/ome/ticket/3651#comment:7:

Also need to review the color selection based on wavelength:

E.g. lei/joel/sequental scan 2/

  • Currently cut-off red->green is 560.
  • We have two channels with emission filters: 553-618 and 665-800
  • We pick wavelength as cut-in + 15 (ignore emission).
  • Both these channels are therefore colored Red.

Although the above example could be fixed by adjusting the "+15" > increment to cut-in or by moving the green->red boundary, this could > easily "break" another format / example.

Color selection algorithm could be improved to order channels by > wavelength - Preferentially color Blue -> Green -> Red, instead of > color 2 channels same color.

If it's not being done already, it would also be a good idea to do something with the Channel.Color attribute, as this is now populated for a handful of formats (see #3651).

See also:

Change History (3)

comment:1 Changed 10 years ago by jamoore

  • Cc rleigh cblackburn added; cxallan removed
  • Description modified (diff)
  • Priority changed from minor to major
  • Version set to 5.0.0

comment:2 Changed 10 years ago by mtbcarroll

In http://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7431 is commented,

When importing multi-color channel image data (in my case Olympus ScanR screen-type data) which does not encode the "appropriate" display color of each of the channels, OMERO's rendering engine defaults to the order Red, Green, Blue. Unfortunately my data was acquired in the order DAPI, A488, A568 so the order Blue, Green, Red would be more appropriate as a default. Is there a way during import to set a different default color channel order?

comment:3 Changed 10 years ago by mtbcarroll

  • Cc dsudar@… added
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