We are having problems displaying channels properly using ImageJ 1.50f31 and 1.50d Java 1.6.0_20 (64 bit) Windows7 when opening CZI files.
When in Composite mode changing channel using the slider on the bottom of the window changes the image. With one of the three channels turned off, the wrong colors display. This happens when setting each channel manually.
I found this when opening CZI files that had three channels and running this macro. After running the macro, sliding to channel 1 looks correct, sliding to channel 2 shows only the green, and sliding to channel 3 shows the green and gray combined. I tried moving Stack.setDisplayMode("composite"); and Stack.setActiveChannels("1100000"); after the loop, butno improvement.
However, if we first save the CZI file as TIF, then this macro does work.
Regards,
Michael
macro "display proper colors [F4]" {
colors = newArray("Red", "Green", "Grays");
mins = newArray(400, 3000, 2000);
maxes = newArray(16383, 16383, 6500);
Stack.setDisplayMode("composite");
Stack.setActiveChannels("1100000");
for (c=0; c<3; c++) {
Stack.setChannel(c+1);
run(colors[c]);
setMinAndMax(mins[c], maxes[c]);
}
run("Channels Tool...");
}
=========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 ** Office: Skirball 2nd Floor main office, back right **
http://ocs.med.nyu.edu/microscopy &
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