Use roipoly or poly2mask to calculate intensity

Hi,

I used the function mmROI to draw three ROIs on multiple images (n=10). Now I have corrected the original images and I want to calculate the mean value within the ROI again. I tried two things with both the roipoly and poly2mask from the mmROI function. However, I cannot get the mean value from the predefined ROI in the new images.

if true
  I = Fluo_Corrected_ExpTime(:,:,:,1);
J = imadjust(I);
BW = roipoly(X1, Y1,J,720,1080);
imshow(J)
hold on
plot(X1, Y1, 'r.-', 'MarkerSize',15);
end

and

if true
  I = Fluo_Corrected_ExpTime(:,:,:,2);
J = imadjust(I);
imagesc(I)
ROI1 = poly2mask (X1, Y1,720,1080); %mxn is size image
Bimg = imagesc(ROI1)  end

Hope you can help me again

Answer 1

[Image Analyst]

You need to call poly2mask() for each ROI that the user draws and then OR them together:

ROI1 = poly2mask(x1, y1, rows, columns);
ROI2 = poly2mask(x2, y2, rows, columns);
ROI3 = poly2mask(x3, y3, rows, columns);
ROI = ROI1 | ROI2 | ROI3;

You can get the x,y from imfreehand(), roipoly(), or roipolyold().

[Ihiertje]

Thank you for your reaction. I managed to get coordinates from the ROIs. However, I have problems to apply these ROI to another image and measure the mean intensity value within that ROI. Can you maybe help me with that as well?

[Image Analyst]

Sure. What's the problem? You used regionprops() didn't you? That should do it. See my Image Segmentation Tutorial for a full well commented demo. http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862