Re: single slice in stack: make binary / convert to mask

Posted by Stephen Towler on Mar 28, 2008; 3:41pm
URL: http://imagej.273.s1.nabble.com/single-slice-in-stack-make-binary-convert-to-mask-tp3696752p3696754.html

Wayne,

That is *incredibly* helpful.

Thanks so much,
Stephen


On Thu, Mar 27, 2008 at 11:51 AM, Wayne Rasband <[hidden email]> wrote:

> > Hi all. We would like to apply Process -> Binary -> Convert to Mask
>  >  to individual slices in a stack so that manual raters can,
>  > slice-by-slice, threshold slices and create the resulting masks. It
>  > looks like this single-slice option was removed from Make Binary in
>  > v.1.37k, the same revision in which Convert to Mask was introduced.
>  >
>  > Is there some other way to achieve this effect in the current release?
>  > If not with some feature I've overlooked, maybe with an existing
>  > macro or plugin?
>
>  This can be done using a macro. This one that converts the current
>  slice to binary and advances to the next when you press F1.
>
>   macro "Make Slice Binary [F1]" {
>       if (bitDepth!=8)
>           exit("8-bit grayscale image required");
>       run("Select None");
>       setBatchMode(true);
>       id = getImageID;
>       run("Create Mask");
>       run("Copy");
>       close;
>       selectImage(id);
>       run("Paste");
>       setBatchMode(false);
>       n = getSliceNumber;
>       if (n<nSlices)
>          setSlice(n+1);
>    }
>
>  -wayne
>

--
Stephen Towler
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