Bug in "Re-order Hyperstack..."

fiji
Tags: #<Tag:0x00007fb87cc1e710>

#1

Hello,

I am reordering Z and T in a hyperstack which has following channel LUTs:

channel 1: blue
channel 2: gray
channel 3: green, and
channel 4: red

After I run Re-order Hyperstack… command, my Z and T are reordered correctly, but the channel colors are all messed up. New channel colors become (Red, Green, Blue, Gray). Can this be fixed so that reordering preserves the channel colors?

Thank you!
Ved

PS: Here are a few specs: Windows 10, ImageJ 1.52b, Java 1.6.0_24


Ved Sharma, PhD
Department of Anatomy and Structural Biology
Albert Einstein College of Medicine, New York


#2

I’m unable to reproduce this with an up-to-date Fiji on Java 8.

The following macro works as expected without changing channel LUTs:

newImage("HyperStack", "8-bit composite-mode label", 400, 300, 4, 20, 3);
Stack.setChannel(1);
run("Blue");
Stack.setChannel(2);
run("Grays");
Stack.setChannel(3);
run("Green");
Stack.setChannel(4);
run("Red");
waitForUser("Please check the hyperstack, press ok to re-order")
run("Re-order Hyperstack ...", "channels=[Channels (c)] slices=[Frames (t)] frames=[Slices (z)]");

Unless you have reasons to require Java 6, I’d recommend you download a fresh Fiji bundled with Java 8.


#3

Hi Jan,

I think that Java 6 was the problem. I did a fresh Fiji install (with Java 8) and the problem disappeared.

Thank you so much!


Ved Sharma, PhD
Department of Anatomy and Structural Biology
Albert Einstein College of Medicine, New York