12/16 bit composite: setMinAndMax(), macro, keep values

[Guenter Giese]

Dear list members,

I am using ImageJ (FIJI distribution, ImageJA v. 1.45b) on two PCs with 8
and 24 GB RAM, respectively (Windows 7 64 bit, Service Pack 1). I try to
keep FIJI / ImageJ versions identical (up to date) between the PCs.

I am dealing with huge (GB) image stacks recorded with a CCD (2 to 4
channels recorded sequentially, 12 bit data, saved as TIFF 16 bit). These
image data are then processed and stored using macros.


My questions / issues:


1. Although I can use the setMinAndMax() function in a macro to set the B&C
values, these values act globally on all composite channels. Is there a way
to set these values individually for each channel by a macro function?


2. The following behaviour I observe is somehow inconsistent: When I store
and reopen the composite image stacks, sometimes the min and max of the
first channel are set to some values different from the one at saving. They
now seems to be set to a value calculated from the B&C values of the top
first composite channel image displayed. The min and max values of the
second and third channel, respectively, now sometimes equal the values
initially stored for the first and second channel, respectively. But the
latter values may take another value (e.g. new min, but keeping the max set
at storage).


3. Are the min and max values of the 16 bit composite channels stored with
the images? If yes, how can I read these values interactively or with a
macro (individual values for each channel)?



Best,

Guenter


---------------------------------------------------------------------
Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung Jahnstr. 29
D-69120 Heidelberg, Germany
Phone [phone] (Fax: -325)
e-mail: [hidden email]

[Frank Sprenger]

Dear Guenther,

for adjusting the individual channels use Hyperstacks and Channel tools, in macro language this would be
Stack.setChannel(1);
for example:


run("Stack to Hyperstack...", "order=xyczt(default) channels=3 slices=1 frames=30 display=Color");
Stack.setChannel(1);
run("Enhance Contrast", "saturated=0.35");
Stack.setChannel(2);
run("Enhance Contrast", "saturated=0.35");
Stack.setChannel(3);
run("Enhance Contrast", "saturated=0.35");