Measuring area of particles which are in the same color as background

[karthikp]

Hello,

I am working on measuring the area covered by the particles in the image using ImageJ. However, particles I am measuring are transparent and have a surface color similar to the background of the image, making the analysis challenging. I will have to use drawing tools measure the area of the particles individually which is taking me a long time. Can anyone help with the method to process the image to identify the area of the particles in the image. Thank you.

[Joel Sheffield]

can you post an example of an image?



Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  *http://tinyurl.com/khbouft <http://tinyurl.com/khbouft>*

On Sat, Dec 3, 2016 at 9:16 PM, karthikp <
[hidden email]> wrote:

> Hello,
>
> I am working on measuring the area covered by the particles in the image
> using ImageJ. However, particles I am measuring are transparent and have a
> surface color similar to the background of the image, making the analysis
> challenging. I will have to use drawing tools measure the area of the
> particles individually which is taking me a long time. Can anyone help with
> the method to process the image to identify the area of the particles in
> the
> image. Thank you.
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/Measuring-area-of-particles-which-are-in-the-same-color-as-background-
> tp5017681.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[karthikp]

Here is the image attached of transparent particles. I wanted to calculate total area covered by the particles and area of the black layer separately. Thank you.

[Joost Willemse]

Based on this image I think going with a edge detection is the only feasible manner.

So make the image 8-bit,
then find the edges
blur these a bit again
threshhold the image and voila there are your particles

Hope this works for you, i tested on your image and it seems to do fine.


Here is the macro code i used
run("8-bit");
run("Find Edges");
run("Gaussian Blur...", "sigma=4");
setAutoThreshold("Li dark");
//run("Threshold...");
//setThreshold(17, 255);
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
run("Analyze Particles...", "add");

Joost Willemse

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Jeremy Adler-2]

Intensity thresholding obviously does not work and neither does edge detection - because the edges are caused
by a refractive index mismatch between your particles and the medium, so edges of particles that are thin in the illumination direction produce little contrast. In addition the illumination is uneven, there are some vertical lines at the lower edge that are not related to your particles and some of the particles are out of focus.

Get better images: using a medium with a different refractive index from the particles - then edge detection will work.
Depending on the interaction of white light with the material making up the particles one of the red, green and blue images contained in your RGB picture will have greater contrast. If you have the  option try DIC imaging or dark field imaging. You could also try mounting the particles in a solution of a dye - the particles will pass more light.

It will help to capture a blank image (without particles) and calculate the difference between this and the image with particles.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of karthikp
Sent: den 6 december 2016 16:41
To: [hidden email]
Subject: Re: Measuring area of particles which are in the same color as background

<http://imagej.1557.x6.nabble.com/file/n5017696/0.png>

Here is the image attached of transparent particles. I wanted to calculate total area covered by the particles and area of the black layer separately.
Thank you.



--
View this message in context: http://imagej.1557.x6.nabble.com/Measuring-area-of-particles-which-are-in-the-same-color-as-background-tp5017681p5017696.html
Sent from the ImageJ mailing list archive at Nabble.com.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html