MATLAB: Segmenting bitmap micro CT images using MATLAB’s image processing capabilities.

Question

Hello, I am interested in getting some input about using MATLAB's image processing app. I want to obtain a binary image of my area of interest so I can perform some basic analysis (calculate area, path length, etc.).

I want to know if what I describe below is possible in MATLAB or not. I will show the process that I have gone through so far and any input would be greatly appreciated.

Progress Thus Far:

% This will be used for image segmentation of cranial sutures.
% Reading raw images
Raw = imread('3351_Coronal_CRotated0964.bmp');
figure
imshow(Raw)
title('Raw Image')

% Adjusting raw images so they can be turned into binary
Raw_Adjusted = imadjust(Raw);
figure
imshow(Raw_Adjusted)
title('Adjusted Image')

% Converting to black and white images
BW_Original = imbinarize(Raw_Adjusted,'adaptive','Sensitivity',0.6);
figure
imshow(BW_Original)
title('Binary Image')

% Inverting the black and white image
BW_Inverse = imcomplement(BW_Original);
figure
imshow(BW_Inverse)
title('Inverted Binary Image')

% Cropping the image
BW_Cropped = imcrop(BW_Inverse,[900,1000,825,500]);
figure
imshow(BW_Cropped)
title('Cropped Image')

% Segmenting
Segmented = bwpropfilt(BW_Cropped,'Area',1);
figure
imshow(Segmented)
title('Semi-Isolated Cropped Image')

Next Steps/Moving Forward

I want the final product to include only the squiggly line running horizontal, outlines below in red, and get rid of the sections that are outline in blue. (i.e. turn them black)

Any guidance would be greatly appreciated, thank you for reading my question.

Answer 1

If Segmented is your binary image, obtain the largest blob, which will be the one you outlined in red, using bwareafilt():

largestBlob = bwareafilt(Segmented, 1);