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image_registration.m

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+%% Image Registration
+% Sources:
+% National Eye Institute
+% National Institute on Aging
+%% Geometric Transformations
+% Load the data
+early    = imread('earlyAMD.jpg');
+advanced = imread('advancedAMD.jpg');
+
+% Display them
+figure(1)
+imshowpair(advanced,early,'montage')
+title('Original Images')
+
+% Rotate advanced AMD (Age-related macular degeneration)
+rotatedAdv = imrotate(advanced,90);
+
+% Resize rotated advanced AMD to 10% larger
+resizedAdv = imresize(rotatedAdv,1.1);
+
+% Translate resized advanced AMD
+shiftedAdv = imtranslate(resizedAdv,[5 10]);
+
+% Display the last version with early AMD
+figure(2)
+imshowpair(shiftedAdv,early)
+title('Geometrically Transformed Images')
+
+%% Automating Registration
+% Estimate the similarity transformation, advanced as moving, eary as fixed image
+transAMD = imregcorr(advanced,early);
+
+% Extract the transformation matrix
+Tmat = transAMD.T;
+
+% Apply the transformation
+advTrans = imwarp(advanced,transAMD);
+
+% Display auto-transformed advanced AMD
+figure(3)
+imshowpair(advTrans,early)
+title('Auto-Transformed Advanced AMD')
+
+%% Translation with Spatial Reference
+% Extract size of images (moving and fixed)
+movSize = size(advTrans);
+fixSize = size(early);
+
+% Create a spatial referencing object
+spFixed = imref2d(fixSize);
+
+% Transformation with spatial reference
+advtransp = imwarp(advanced,transAMD,'OutputView',spFixed);
+
+% Display spatially transformed advanced AMD
+figure(4)
+imshowpair(advtransp,early)
+title('Spatially Transformed Advanced AMD')
+
+%% What about more complex tranformations ?
+%% Register Brain Scans with Control Points
+% Load images
+normal    = imread('normalBrain.png');
+alzheimer = imread('alzheimerBrain.png');
+
+% Display them
+figure(5)
+imshowpair(alzheimer,normal,'montage')
+title('Alzheimer vs Normal Brain Scans')
+
+% Define control points
+normalP    = [173.375 377.375; 223.125 375.375; 81.875 126.125; 311.625 87.375];
+alzheimerP = [155.375 357.375; 207.625 360.875; 71.375 134.625; 293.925 121.575];
+
+% Adjust control points for the moving image
+alzheimerP = cpcorr(alzheimerP,normalP,alzheimer,normal);
+
+% Create a geometric transformation
+Tform = fitgeotrans(alzheimerP,normalP,'affine');
+
+% Create a spatial reference
+spFixed = imref2d(size(normal));
+
+% Apply transformation
+alzheimerTrans = imwarp(alzheimer,Tform,'OutputView',spFixed);
+
+% Visualize transformation
+figure(6)
+imshowpair(normal,alzheimerTrans)
+title('Purple Areas are brighter in Alzheimer')
+
+%% end