Measuring color spots area from a ultrasound image

HI, I am trying to measure the area of colored spots ( many) from and ultrasound image , My idea is to measure the area of the structure I am interest and substract from that the area of the colored spots inside the structure.
However , when I transform the image to 8 bite and use the threshold to fill the spots it does not get to fill them in their totallity therefore my measurement is not precise. Does someone have any idea of how can I do this in a better way ?
I attached a image with the structure selected in red and the colored spots inside of it , so it can be more understandable.

I don’t know the origin of the file, but it looks like, at some point, the red and blue objects were probably separate channels. If you have the original files where the signal is still separate, this will be much easier with just FIJI and thresholding (grey and white can make it much more difficult to find other colors). The other option would be to look into a pixel classifier like Weka or Ilastik, both of which have numerous posts on the forum that you might find useful.

thanks for the answer , the image is originally like that ultrasounds image are displayed in a scale from black to white depending in the density of the structures.

Right, the ultrasound part should be gray-scale. The question about the separate channels had to do with the red and blue.

so I tried to split the channels and I obtained blue and red separate however when start setting the threshold I have the same problem I can not get to full fill the spots in their totality.

Not sure what is happening without some examples, but there are many ways to set thresholds. At some point you should be able to set thresholds that entire encompass the red or blue spots within their own channels, but I don’t know what kind of background noise you might also pick up. Always a tradeoff between collecting too much and too little, if the signal to noise ratio is not good.

so this is what I do , I select the are of my structure once I obtained it I clear outside so only my structure is displayed then I split the channels ( green , blue, red) So I would think that if I get to measure every spot from each channel and then sum them I will have the total area of the spots. I attached the pictures of the procedure.

In the image number Is where I find the problem with the threshold. I just move the bars ultil I get the red spots full fill but I cant ( the same with the blue) beause some spots in the structure that I am not interested start to full fill too.


Yeah, that looks like the problem I expected without splitting the original channel data.

I would expect the sonogram to be grayscale, but by dropping the red and blue into that picture and saving it as an RGB image, you have severely hampered your ability to detect the red and blue with simple thresholding methods. You may want to try Thershold “Color” rather than Threshold if you cannot get the original data channels. Splitting the RGB channels afterwards doesn’t separate out your data, as you have shown. It needs to be done before. You might also have some luck if you look into Weka Segmentation, but I am not sure how well that will interact with your manually drawn areas. If you can use Weka, you shouldn’t need to split the channels, though the white “shine” on the red and blue could be problematic.