Re: Touching particle accurate counting

Posted by ctrueden on Jan 14, 2015; 7:38pm
URL: http://imagej.273.s1.nabble.com/Touching-particle-accurate-counting-tp5011214p5011219.html

Hi Al,

> The problem is that they are sometimes overlapping, making
> them hard to separate, even by using the watersheding tool.

The "Find Maxima" command is sometimes useful in situations like these.

Here is a workflow which counts 643 diamonds on your dense image:

run("8-bit");
run("Invert");
run("Subtract Background...", "rolling=50");
run("Gaussian Blur...", "sigma=2");
run("Find Maxima...", "noise=10 output=[Point Selection] exclude");
run("Measure");

Not perfect, but not terrible.

You could also try the Trainable Weka Segmentation plugin [1] and see how
that treats you.

Regards,
Curtis

[1] http://fiji.sc/Trainable_Weka_Segmentation


On Wed, Jan 14, 2015 at 11:02 AM, Al Menia <[hidden email]>
wrote:

> Hi,
>
> I am desperately trying to find an automatic way to count diamonds (approx
> 100 um size) on a metallic substrate on SEM imaging. The problem is that
> they are sometimes overlapping, making them hard to separate, even by using
> the watersheding tool. (you'll see very big parts not affected by this
> tool)
> The method I use is not very accurate:
> - gaussian blur or substrack background (sometimes it works better)
> - tresholding
> - watersheding
> - analyse particle (area 200-infinite, circularity 0.35-1.00)
>
> There are around 620 diamonds in the dense onem and 240 in the less dense
> one. I can only manage to reach a 10% accuracy in the counting, but I would
> like to reach 1%.
>
> Does anybody knows a better way to do this, or knows a good plugin for this
> kind of work?
> A good thing would be to be able to force the watersheding above a given
> area, so that I don't have big agglomerates, but I don't know if this
> already exists...
>
> Thanks,
>
>
> <http://imagej.1557.x6.nabble.com/file/n5011214/dense.png>
> <http://imagej.1557.x6.nabble.com/file/n5011214/low_density.png>
>
>
>
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