Posted by
Michael Schmid on
Jun 03, 2009; 12:49pm
URL: http://imagej.273.s1.nabble.com/Particle-counting-macro-tp3692303p3692304.html
Hi Stoyan,
your code looks fine. There is one point where I don't see whether
you have done it:
It might help to switch off all types of measurements in Analyze>Set
Measurements.
An alternative that might be faster if you have a very large number
of rois:
- Run the particle analyzer once, create a mask with the particles of
correct size.
- Run 'Find Maxima' on the mask, with output type 'single points'.
- In the loop, for each roi, getRawStatistics(nPixels, mean). The
number of particles will be nPixels*mean/255.
This will give you a slightly different result - a particle may be
partly inside a roi, but the point created by 'find maxima' can be
outside.
Michael
________________________________________________________________
On 3 Jun 2009, at 12:09, Stoyan Pavlov wrote:
> Dear ImageJ users,
> I have stacks of binarized images and set of RoIs associated with
> certain
> slides. I need a macro which counts particles of specific sizes
> within each
> RoI and produces a table with the Label of the RoI, and the number of
> particles found inside. I am quite inexperienced with the macro
> language. I
> could devise something, which is both awfully clumsy and time
> consuming:
>
>
> n = roiManager("count");
> for (i=0; i<n; i++) {
> roiManager("select", i);
> run("Analyze Particles...", "size=2-20 circularity=0.00-1.00
> show=Nothing display exclude clear ");
> m=nResults;
> print (i," ",":"," ", m) ;
>
>
>
>
> Can anyone help me?
>
> Thanks in advance!
> --
> Dr. Stoyan P. Pavlov, MD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
> Bulgaria
> Tel: +359 (0) 52 - 650 - 061 #295
> Fax: +359 (0) 52 - 650 - 019
> e-mail:
[hidden email]