Applying Save XY Coordinates to every image in stack

[Francis Burton]

Hi,

I'm wanting to do some stats on pixel values from the same ROI in different
images, using another program. I use ImageJ to export the values to an ASCII
data file which I then imported into the stats program.

My images happen to be stacked. For many commands, a "Process all n slices?"
dialog allows a choice of operating on one or all (or zero) images in the
stack. I use "Edit/Clear Outside" on all images. However, when I ask for
"Analyze/Tools/Save XY Coordinates...", I am not given the option to have
this done on all slices, and only the current image is processed. That means
I have to repeat this command manually for each stack slice.

It would be very useful to have "Save XY Coordinates..." apply to all images.

There are probably two ways to do this sensibly. One is to output two columns
for X and Y coordinates, and a separate column for each slice. This would be
my ideal choice, though it could get unwieldy if there were very many slices.
(I don't know how efficiently one can switch from accessing one image's pixel
data to the next.)

Alternatively, an additional column could be output so that you had columns
e.g. X Y Z V. This would be easier to implement for a (possibly large) sequence
of slices.

At present "Save XY Coordinates..." puts up a simple comfirmatory dialog which
allows the user to proceed or cancel the operation. The dialog could be changed
to one like that of the "Scale..." command. It could include a "Process whole
stack" checkbox (if appropriate). It could also offer a choice between the two
formats above. It could allow selection of a background pixel value other than
the current default upper left corner. It might also afford the means to export
the =entire= image in X Y [Z] V format.

Is something like this "enhancement" in the pipeline? Would it be considered?
If not, is it fairly common for users like me (ImageJ newbie with some Java
programming experience) to modify plug-in code?

Thanks in advance!

Francis

--
Dr Francis L Burton,          |  [hidden email]
West Medical Building,        |
University of Glasgow,        |  Tel [phone]
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