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Ticket #289 (closed task: fixed)

Opened 2008-04-29T15:51:15-05:00

Last modified 2010-07-13T17:03:04-05:00

Review and adjust ImageJ color-related options

Reported by: curtis Owned by: curtis
Priority: critical Milestone: bio-formats-4.2
Component: plugins Severity: major
Keywords: Cc: simon.andrews@…, wsr@…, acardona@…
Blocked By: Blocking:


The options available in the Bio-Formats Importer plugin for handling color channels are in need of update.

1) ImageJ now provides a CompositeImage class for working with multichannel data in a variety of configurations (including >8 bits per channel). We probably do not make optimal use of this class in all cases.

2) We may not always be handling 8-bit and 16-bit indexed color in the best way. In particular, application of 16-bit indexed color tables is currently disabled, which we should readd somehow. At worst, we can have an "expand indexed color images" checkbox.

3) Certain combinations of color options may make no sense. We should test each combination to verify that they either work as expected, or are disallowed when invalid.

4) Certain options may be obsolete or misleading. For example, instead of a "Merge channels to RGB" checkbox, we could have a combo box labeled "Channels" with options like "Default," "Always merge" and "Always separate."

If we end up with more color-related options, we may want to consider subdividing the available options in the dialog box according to category, to make them easier to read and understand.

Change History

comment:1 Changed 2008-05-05T13:33:43-05:00 by curtis

  • Cc simon.andrews@…, wsr@… added

comment:2 Changed 2008-07-09T13:08:28-05:00 by curtis

  • Status changed from new to assigned

comment:3 Changed 2009-03-11T16:53:26-05:00 by curtis

  • Milestone changed from bio-formats-m2 to bio-formats-4.1.0

comment:4 Changed 2009-10-21T07:28:16-05:00 by melissa

  • Milestone bio-formats-4.1 deleted

comment:5 Changed 2010-01-05T19:58:13-06:00 by curtis

  • Cc acardona@… added
  • Milestone set to bio-formats-4.2

The work in this ticket naturally feeds in to ticket #310.

comment:6 Changed 2010-06-03T18:09:45-05:00 by curtis

As part of the Importer refactoring (see #310), the color options have been consolidated. There is now a single color combo box called "Color mode" with options: Default, Composite, Colorize, Grayscale, and Custom Colorize. These choices mostly correspond to the various color modes of ImageJ's CompositeImage.

There are still some kinks with the color modes in various cases though, as well as the need for backward compatibility with macros using the old color options, so I am waiting to close this ticket until they are solved.

comment:7 Changed 2010-06-03T19:43:22-05:00 by curtis

With r6476, the obsolete color options should work again. This includes the macro keys merge_channels, rgb_colorize, and custom_colorize.

However, note that the merge_channels option will always create a CompositeImage in Composite mode now, rather than an ImagePlus of type "RGB Color" as before. If an RGB Color image is required, it can be converted with "Image > Type > RGB Color."

comment:8 follow-up: ↓ 9 Changed 2010-06-09T00:28:40-05:00 by curtis

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

As explained above, the color options have been reworked as per this ticket. There are still some edge cases, which will be resolved in time, including: #506, #507,  imagej:#58,  imagej:#65.

comment:9 in reply to: ↑ 8 Changed 2010-06-28T16:54:17-05:00 by curtis

Replying to curtis:

#506, #507,  imagej:#58,  imagej:#65.

These tickets are all fixed now.

comment:10 Changed 2010-07-09T12:55:02-05:00 by melissa

  • Milestone bio-formats-4.2 deleted

Milestone bio-formats-4.2 deleted

comment:11 Changed 2010-07-13T17:03:04-05:00 by melissa

  • Milestone set to bio-formats-4.2