Posted by
Rasband, Wayne (NIH/NIMH) [E] on
URL: http://imagej.273.s1.nabble.com/Using-Enlarge-function-with-very-large-ROI-sets-tp5009786p5009789.html
On Sep 26, 2014, at 1:39 PM, Jia-Ren_Lin wrote:
> Dear experts,
>
> I'm trying to quantify timelapse images with nuclear fluorescent marker for
> segmentation and also take cytoplasmic measurements by enlarging ROIs.
> However, because of* very large ROI sets (>50,000)*, my macro ran very slow.
>
> /*counts=roiManager("count");
> for(i=0; i<counts; i++) {
> roiManager(&quot;Select&quot;, i);
> run(&quot;Measure&quot;);
> run(&quot;Enlarge...&quot;, &quot;enlarge=4&quot;);
> run(&quot;Measure&quot;);
> }</b>/
>
> I've already setBatchMode("true"). It helps a little (save about half
> time), but I was wondering if there is a way to speed up my macro.
I get 280ms/ROI when I run your macro on the blobs sample image. If the macro switches to batch mode after running the particle analyzer (the image and ROI Manager are displayed), it takes 22ms/ROI, 13 times faster. If the macro switches to batch mode before running the particle analyzer (the image and ROI Manager are not displayed), the macro takes 5ms/ROI, 46 times faster. At 5ms/ROI, the macro would take about 4 minutes to process 50,000 ROIs. The following is what the fastest version of the test macro I used looks like.
-wayne
setBatchMode(true);
run("Blobs (25K)");
setAutoThreshold("Default");
run("Analyze Particles...", "display exclude add");
t0 = getTime;
counts=roiManager("count");
for(i=0; i<counts; i++) {
roiManager("Select", i);
run("Measure");
run("Enlarge...", "enlarge=4");
run("Measure");
}
print((getTime-t0)/counts);
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