Doppler Image - calculate colored area

Hello everyone!

I’m working on an assignment where we try to calculate the doppler flow inside the thyroid. Since this is eventually going to be a part of a research project, we try to do this as thorough as possible. We have a Matlab application that was intended for another purpose so it’s not really ideal.

Here’s what we try to do: we make a ROI which contains a transverse slice of the thyroid. Then we would like calculate how much of that ROI is having colored pixels.

The images are JPEG 24-bit. Does anyone know of a plugin that could solve this? I’m not afraid of a little bit of programming if it’s needed.

Thank you everyone in advance!

Hi @Ianpeters,
first of all welcome to the ImageJ forums!

Regarding to your question:

Do you want to do this in an automated fashion based on some metric? Or do you want to select the ROI in each image by hand?

This can be easily accomplished with ImageJ (might require a little bit of scripting).

Hi, thank you for your quick reply!

Regarding ROI, since the thyroid can have a varying morphology, I think it’s sufficient to do the ROI “by-hand”.

Yes, calculating is the important part. The answer we want is someting like, the ROI-area is covered by x% colored pixels, no matter if red, blue, yellow, just the total. The black/white/grey is parenchyme and is not to be calculated.

The clinical implication is that we can compare a patients Doppler flow on the following visits and see if the situation is improving e.g. the Doppler flow has decreased so and so when comparing the ROIs.

Hi @Ianpeters,
Adding to what @gab1one is saying, I would actually walk back the analysis.
You are trying the analyze jpeg colored images which are rendering of the real, raw data. Is there any chance that you can directly access the raw dopler info from the machine? This is particularly important, especially if you are going to build on this project.

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I believe that I can recieve DICOM-data from the machine but I’m not sure. Any other raw data, doubtful. It could mean that I have to make some changes in the machine and I’m not the only one using it. Would raw data make it easier?

Because it directly contains what you want.
On the jpeg image, you have to go an extra step to extract only the colored pixel. Plus, hoping that the way they are colored do not change too much from image to image.

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Would a DICOM-image be sufficient or does it have to be raw data?

Normally the DICOM is the raw data. It contains the raw pixels. But I am not sure it contains the Dopler data.
Here I would contact the support engineer, the company, or read the manual.
Sorry I cannot help your further; I deal with microscopes in my everyday life.


Any tips on how to move further with this issue?

It wasn’t clear that this was still an issue. Do you have the DICOM raw data now and can post them somewhere?

No sadly enough, I wasn’t able to get them and we have no engineer service that can help us.

Have you tried SIOX to extract the color areas?

I just played a bit with your image and it looks doable:

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