how can i calculate morphological features such as nucleus area and perimeter, number of the separated parts of nucleus, mean and variance of the nucleus boundaries and roundness criterion of nucleus are extracted from the segmented area ? any code?

example segmented image.

Answer 1

[Image Analyst]

You can get most of that from regionprops(). See my Image Segmentation Tutorial: https://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862&sort=downloads_desc

props = regionprops(binaryImage, grayImage, 'Area', 'Perimeter', 'EulerNumber');
allAreas = [props.Area];
allPerimeters = [props.Perimeter];
allRoundnesses = 4 * pi * allAreas ./ allPerimeters .^ 2; % Or whatever formula you use.

To get the mean and variance of the boundaries, you have to define what the mean of the boundary is. One way might be to smooth it out until it's really smooth using the function sgolayfilt() in the Signal Processing Toolbox. See attached demo. Then you can use min() to find the closest original point and get the distance between them with sqrt(). Then take the standard deviation of all those distances with std().

[sumu nowshin]

Thank you.

[sumu nowshin]

how can be the boundary values are counted? I want to measure the boundary values

[Image Analyst]

I don't even know what that means. What "values" are you talking about? To get the number of boundaries, which included internal boundaries, you can use length

numBoundaries = length(boundaries)

[sumu nowshin]

I want to calculate the pixel values of a boundary. thank u so much for replying.

[Image Analyst]

You can do

perimImage = bwperim(binaryImage); % Get perimeter
boundaryValues = grayImage(perimImage); % Get list of gray level values at location of perimeters.  For whole image, not per blob.

[sumu nowshin]

Thanks

[Nancy]

how can i identify Nuclei and stoma of a RGB image may i know the argument please

[Image Analyst]

@Nancy If you have any more questions, then attach your data and code to read it in with the paperclip icon after you read this:

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