Bug 949 – Non-functional color annotation merge

Bug 949 - Non-functional color annotation merge


Summary:	Non-functional color annotation merge

Status:	RESOLVED INVALID

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	Macintosh Mac OS

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2014-10-29 04:46 CDT by claudia.mattissek
Modified:	2016-04-22 16:34 CDT
CC List:	5 users (show)

See Also:

Description claudia.mattissek 2014-10-29 04:46:52 CDT

Image>Color>Merge Channels

If a multichannel image is split and subsequently merged, the channels are not colored according to the user's choice but according to the original channel color no matter what you choose. This has not been working since some versions but worked earlier (>1/2 year ago).

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-462-10M4609
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-462
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20141026020028)
Fiji: http://fiji.sc/update/ (last check:20141023165357)

Files not up-to-date:
  98e84990 (MODIFIED) 20111109183954 Contents/MacOS/fiji-macosx
  65733e10 (MODIFIED) 20111109183954 Contents/MacOS/fiji-tiger
  b2afde18 (LOCAL_ONLY) 20130108125412 plugins/cell_counter.jar
  d3260180 (LOCAL_ONLY) 20110303204101 scripts/Record_Desktop.py
  0ea7f8fc (LOCAL_ONLY) 20110303204101 scripts/Record_Window.py

Comment 1 Johannes Schindelin 2014-10-29 05:18:46 CDT

> If a multichannel image is split and subsequently merged, the channels are not colored according to the user's choice but according to the original channel color no matter what you choose.

Can you reproduce this with a sample image from File>Open Samples? If so, please record a macro that reproduces the problem and post it here.

Also, could you see whether it is related to the SCIFIO option in Edit>Options>ImageJ2...?

> This has not been working since some versions but worked earlier (>1/2 year ago).

Please note that the longer you wait with a bug report, the harder it is for volunteers to fix the bug.

However, it is better to report the bug late than never to report it at all!

Comment 2 Jan Eglinger 2014-10-29 05:43:14 CDT

I believe this is intended behaviour. The following macro shows what I think Claudia is describing:

  run("Fluorescent Cells (400K)");
  run("Split Channels");
  run("Merge Channels...", "c1=C3-FluorescentCells.tif c2=C2-FluorescentCells.tif c3=C1-FluorescentCells.tif create");


Note that in the resulting image, the channel order has changed to [blue-green-red] from [red-green-blue] in the original image ("Fluorescent Cells").

The ImageJ User Guide states this [*1*]:

> When creating composite images, original LUTs and display ranges are preserved unless Ignore source LUTs is checked.


If you want to change the colors in addition to the channel order, you need to activate the "Ignore source LUTs" option. The following macro should produce the result you expect (i.e. swapping the red and blue channels):

  run("Fluorescent Cells (400K)");
  run("Split Channels");
  run("Merge Channels...", "c1=C3-FluorescentCells.tif c2=C2-FluorescentCells.tif c3=C1-FluorescentCells.tif create ignore");

Hope that helps.
Jan


[*1*]: http://imagej.net/docs/guide/146-28.html#sub:Merge-Channels...

Comment 3 Loria Braley 2016-04-22 07:53:45 CDT

Thought-provoking writing . Apropos , others are wanting a a form , We encountered a fillable form here <a href="http://pdf.ac/apLyY3" >http://pdf.ac/apLyY3</a>.

Comment 4 Curtis Rueden 2016-04-22 16:34:52 CDT

Based on Jan's comments, and the lack of responses since (other than the spammer ;-), I am closing this issue.