27 June, 2013

ImageJ Notes

ImageJ is pretty powerful, but oh the documentation is horrible. It's like it was only meant for programmers. This is what I've figured out.

Installing macros into the menu

When they say "Macros in the file ImageJ/macros/StartupMacros.txt are automatically installed when ImageJ starts up.", they mean copy the entire macro text into the file, meaning all startup macros are contained in that file. In plain English, copy everything from macro "macroname" { to the final } into StartupMacros.txt and save it. (hmm, I thought Blogger had code tags. It doesn't, so I'm using colour to depict code.) This seems to make your StartupMacros.txt big, confusing, and prone to errors, so I'm not sure why they don't just use links in StartupMacros.txt instead. It's like saving all your Word templates into one file.

File -- Import -- Image Sequence

This really opens the entire folder, but they still want you to open the folder and select one file.

Stack profile Plot macro

Ok this seems rather useful, but there's a glaring mistake:
n = nSlices;
for (i=1; i < n; i++) {

(Hmm, Blogger can't display < n without a space) Is it me, or does this code mean you'll only get n-1 graphs for n slices? I changed it to i<=n and it seems to work.

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