3D Maxima Finder parameters

Hi everyone,

I want to use the 3D Maxima Finder that is in the 3D ImageJSuite. However I am not sure about how to set the parameters. It asks me for

  1. Minimmum threshold
  2. RadiusXY
  3. RadiusZ
  4. noise
    Can someone explain what exactly these parameters mean? I tried a lot of combinations on a very simple image to find out, but all combinations result in the same output peaks file.

Thank you!

@MonaF

@ThomasBoudier is the best person to help you with this particular toolkit. I haven’t used it myself…

Hi @MonaF,

There is a basic explanation here . I will try to resume :

  1. Only local maxima above minimum threshold are considered
  2. Local maxima are computed within a ellipsoid of radii (RadiusXY, RadiusXY, RadiusZ)
  3. If noise is set to 0, all local maxima are detected. Else a flooding is performed around local maxima to exclude other local maxima with a difference less than noise.

Basically there are one spatial filter to exclude close local maxima and an intensity filter to remove local maxima with close values.

Hope this helps

Best,

Thomas

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Hi Thomas,

thanks for your explanation! It helped a lot!!

Best,

Mona

Hi Thomas,

maybe one more short question. How far is the flooding performed? Until a certain threshold, or until another flooding region is reached, or something else?

Thanks! Mona

Hi @MonaF,

Some details about the algorithm :

  1. Local maxima are computed within radii
  2. Get the local maximum with highest value and perform flooding within value of this peak - noise
  3. Repeat until no more peaks to process

The flooding process may take some time, especially with high noise values.

Best,

Thomas

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