Login  Register

Re: Counting empty circles

Posted by JaapK on Jan 05, 2011; 12:55pm
URL: http://imagej.273.s1.nabble.com/Counting-empty-circles-tp3686043p3686044.html

Dear Scott,

You have a very interesting image processing challenge here. What you
are suggesting to do, is to segment the image by a form of pattern
recognition: recognizing particles with a certain size of hole. Not
the easiest of image processing tasks in general, but because you
particles are more or less circular (and hence rotation invariant),
you might just have one of those cases where it is not totally
impossible.

I tried calculating the crosscorrelation between the image you refer
to and another image that contained a white 'dougnut' with the
approximate size of a trichome. If all is well, this should give an
image where the highest pixel values correspond to the best template
matches. By using "process>find maxima..." you can select them and
count them.

Bad new though, it didn't work, I'm sorry to say. Most matches did not
correspond to trichomes and I didn't have time to do a proper analysis
about why this was. I'm confident though, that with some additional
tweaking it still might work, but I can guarantee that you that there
will always be a larger error margin on the eventual count of
trichomes.

Unfortunately, template matching is something that we humans just do
much,much better than any computer can even dream of...

Good luck,
Kind regards,

Jaap Kokorian



2011/1/4 schamber789 <[hidden email]>:

> Hello,
>
> I have images (see below) that have many glandular trichomes (the round
> shiny objects) which I would like to quantify. I simply want to know how
> many of them there are.  It seems like I should be able to ask ImageJ to
> count the number of these glandular trichomes, but I don't know how to do
> this. I have tried many things already, but have hit a wall. The smaller
> circles within each gland seem to be very consistent in size. I wonder if
> this consistency in size can be used somehow. Thanks so much!
>
> Sincerely,
>
> Scott Chamberlain
> Rice University, EEB Dept.
>
>
> http://imagej.588099.n2.nabble.com/file/n5889708/2309-1.jpg
> --
> View this message in context: http://imagej.588099.n2.nabble.com/Counting-empty-circles-tp5889708p5889708.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>