Re: Counting Barnacles on a panel

Posted by Emiliano Pinori on Nov 02, 2009; 10:52am
URL: http://imagej.273.s1.nabble.com/Counting-Barnacles-on-a-panel-tp3690575p3690579.html

Tank you very much Michael,
I'm testing youre ideas, and it looks much better, the resoults are more easily validable and comparable to those obtained by manual counting. This will be inserted in my next pubblication, and many people will be happy to have some help by imageJ analisys on theirs panels. I would like to cite you in my paper, if you are agree e-mail me your name and position.

PS: Of course when i shooted those photos i was'n thinking ImageJ but manual analysis. I was on the swedish coast with no much experties in photo shooting, or knwoledge of the facilities of the marine station that was guesting me. Next year I will shoot everything in a better illumination, to get less or better none overexposed areas.

Thank again for the quick answer / Emiliano Pinori

Michael Schmid-3 wrote

Hi Emiliano,

your image looks pretty difficult to process (one might even call it
hopeless). If you want to have any chance, make sure that there are no
overexposed features (in your test images, some of the brighter ones are
overexposed)

Some random thoughts:

- First of all, better illumination, avoiding reflections from the
background. (The number one rule in image processing!)

- Removing 'salt' noise (reflections from small water drops?) by
Process>Noise>Remove outliers (radius=1 seems to be a good compromise that
does not eliminate your small barnacles)

- Playing with Fourier custom filter to get rid of the vertical lines (the
filter should be very smooth, use Gaussian Blur on the filter).

- Convert to 32 bit and subtract an image created by "edge detection" from
the original.

- Do all the adult ones have a dark spot in the center? Then you could use
"Find Maxma" with bright background to search for these minima. If you
select "Maxima within tolerance" for the output, you could use Analyze
particles to get rid of unwanted ones (size, circularity); also you can
combine it with the thresholded original to get only minima above a
certain brightness.

Hope this helps a bit,

Michael
_______________________________________________________________________

On Thu, October 29, 2009 15:24, Emiliano Pinori wrote:
> Hi,
> I'm working on antifouling marine paints and had lots of panels to
> analyze.
> I found ImageJ a very helpfull tool. Anyway when it cames to the more
> adult
> and close togheter barnacles individuals on my panels i had experienced
> some
> difficoults in using my very simple macro to count for Barnacle at the ROI
> area.
> I use a subtcract background, followed by set scale, rectangular selection
> find maxima within tollerance, and finally analyze Particles.
>
> Now the problem is that I will lose a lot of adult barnacles in my results
> becouse they will never become not even 0.5 circular after find maxima due
> to the close presence of ather smaller barnacle. Or becouse the edge do
> not
> are at the same brightness all over the preimeter. How can i improve the
> accurancy without having too much false positives?
>
> I don´think I asked my question in a understandable way, so i put a photo
> of
> wath i have to analyze and hope someone understand me anyway.
>
> I need counts and area to have a % difference between Prov and Control
> side
> (just a 9 square cm ROI of each side)
>
> http://s943.photobucket.com/albums/ad273/zapatainsvezia/Barnacles%20Exemp/
>
> thank you Emiliano Pinori
> Ph.D. student
> Gothemburg University (Sweden)
>