Fiji Channels tool

I have recently downloaded FIJI for Mac (version = 2.0.0-rc-49/1.51d; build = e01a259e5d) onto a computer running Mac OS 10.9.5.

When viewing multicolor composite images, I would like to toggle between successive color channels using the Channel Tools window (Image > Color > Channel Tools… > select Color from dropdown menu). However, this functionality in the version of FIJI that I am running does not seem to work as expected.

(1) First, the channel checkboxes are not mutually exclusive, which I would think they should be and in earlier versions of ImageJ they certainly are. When combinations of checkboxes (or none) are selected, different individual channels are displayed in the image window without rhyme or reason (see attached example images below).

(2) Second, when I toggle between the individual checkboxes, a different channel is displayed in the image window every time. There does not seem to be any correlation between which checkbox is selected and which channel is displayed in the image window (see attached example images below).

I am also running ImageJ (version = 1.50i) on the same computer, and the behavior described above for FIJI does not occur, i.e. toggling between channels in the Channel Tools window works as expected and all checkboxes are mutually exclusive.

Has anyone else experienced this problem with FIJI and is there a fix?


Yes, I can reproduce this problem (on Mac OSX 10.11.4 with Java 8). When switching to Color mode in the Channels Tool, the checkboxes do not update when the channel slider is moved, and checking or unchecking any box will switch the current stack to the corresponding channel, without updating the state of the other checkboxes.

Here’s a macro that illustrates the issue:

run("Fluorescent Cells (400K)");
run("Channels Tool...");

@Wayne this seems to be an ImageJ 1.x regression, as it works for me within Fiji when I downgrade ij.jar to v1.49, but doesn’t work with v1.50 and v1.51d


There is a bug in Java 8 on OS X that causes ImageJ to hang when changing channels with the Channels Tool open. The updateChannels method in works around this bug by not updating the check boxes when running Java 8 on OS X…

Thanks, @Wayne, for this information. Do you know if this bug is likely to be fixed in a future version of Java 8? Or is there something that can be done on the ImageJ side that restores the expected behavior for users?

I wondered why it was working correctly for me (without hanging) with Java 8 (1.8.0_66) when I downgraded to ij.jar v1.49…

It appears that this bug is fixed in Java 1.8.0_66 and later, so the latest ImageJ daily build (1.51e16) removes the work around in Channels.updateChannels().


Thank you everyone for responding to my original post. I have upgraded to the latest ImageJ daily build as recommended (1.51e18 on Mac OS 10.9.5 running Java 1.8.0_91) and the Channel Tools feature works as expected.