OTSU for fibrosis quantification

wall area (ROI) is highlighted.

Answer 1

[Image Analyst]

I don't know what you want. If you want Otsu threshold, use graythresh

help graythresh

 GRAYTHRESH Global image threshold using Otsu's method.
    LEVEL = GRAYTHRESH(I) computes a global threshold (LEVEL) that can be
    used to convert an intensity image to a binary image with IMBINARIZE.
    LEVEL is a normalized intensity value that lies in the range [0, 1].
    GRAYTHRESH uses Otsu's method, which chooses the threshold to minimize
    the intraclass variance of the thresholded black and white pixels.
 
    [LEVEL, EM] = GRAYTHRESH(I) returns effectiveness metric, EM, as the
    second output argument. It indicates the effectiveness of thresholding
    of the input image and it is in the range [0, 1]. The lower bound is
    attainable only by images having a single gray level, and the upper
    bound is attainable only by two-valued images.
 
    Class Support
    -------------
    The input image I can be uint8, uint16, int16, single, or double, and it
    must be nonsparse.  LEVEL and EM are double scalars. 
 
    Example
    -------
        I = imread('coins.png');
        level = graythresh(I);
        BW = imbinarize(I,level);
        figure, imshow(BW)
 
    See also OTSUTHRESH, IMBINARIZE, IMQUANTIZE, MULTITHRESH, RGB2IND.

    Documentation for graythresh
       doc graythresh

See my Image Segmentation Tutorial in my File Exchange:

Image Analyst's File Exchange

It's a generic, general purpose demo of how to threshold an image to find blobs, and then measure things about the blobs, and extract certain blobs based on their areas or diameters.

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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