calculate sbr in vascular image stacks in matlab

To calculate SBR (Signal-to-Background Ratio) in vascular image stacks in MATLAB, you can follow the steps below:

1. Load the image stack using the 'imread' function.

main.m
im = imread('image_stack.tif');
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2. Preprocess the image stack to enhance the blood vessels using any suitable image enhancement technique of your choice.

main.m
im_enhanced = imadjust(im);
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3. Segment the blood vessels from the background using a suitable thresholding or segmentation algorithm such as Otsu's method, adaptive thresholding, or active contours.

main.m
bw = imbinarize(im_enhanced);
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4. Extract the region of interest (ROI) that contains the blood vessels, for example, by cropping or masking the image.

main.m
roi = bw .* im_enhanced; % Applying binary mask to enhanced image to keep only blood vessels
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5. Calculate the mean intensity value of the blood vessels (signal) and the background (either the ROI outside of the vessels or a separate ROI in a nearby region without vessels) using the 'mean' function.

main.m
vessel_mean = mean(roi(:));
background_mean = mean(background_roi(:));
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6. Calculate the SBR by dividing the vessel mean by the background mean.

main.m
sbr = vessel_mean / background_mean;
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You can also apply these steps in a loop to calculate the SBR for multiple image stacks or for different regions of interest within the same stack.