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+====== MATLAB-Stuff ======
+  * [[code:matlab:main.m|my rudimentary file skeleton]]
+===== Code and other snippets =====
+==== Write a multipage TIFF ====
+<code MATLAB>
+for i=1:100
+    a(:,:,i)=rand(256);
+    imwrite(a(:,:,i),'file.tif', 'writemode', 'append')
+end
+size(a)
+</code>
+Adapted from [[http://www.mathworks.com/support/solutions/en/data/1-6EWKKN/index.html?product=ML&solution=1-6EWKKN|this MATLAB support question]]. Generates a random 256x256 pixel large image, saves it in the i<sup>th</sup> slice of a while looping through i. In the same loop MATLAB writes the slice to a tif-File with the 'append' write mode, resulting in a random tif-File with a size of 256x256x100 pixels.
+==== start matlab headless with some file ====
+  cd filepath
+  matlab -r file (WITHOUT .m extension!)
+==== turn off warning about big images ====
+<code MATLAB>warning off Images:initSize:adjustingMag</code>
+==== Overlay Image over another one ====
+<code MATLAB>
+Img = imnoise(phantom(64));   % Load 64 pixel wide Phantom and make it noisy
+Threshold = graythresh(Img);  % calculate Otsu-Threshold
+BW = im2bw(Img,Threshold );   % binarize with above Threshold
+Color = [155 188 221] % define overlay colour RGB (this is the unibe-presentation color)
+Img = im2uint8(mat2gray(Img)); % separate image into 3 channels
+red = Img;
+green = Img;
+blue = Img;
+red(BW) = Color(1);    % populate channels with thresholded image
+green(BW) = Color(2);
+blue(BW) = Color(3);
+Overlay = cat(3, red, green, blue); % make RGB-image
+figure % display everything
+    subplot(131)
+        imshow(Img,[])
+        title('Original')
+    subplot(132)
+        imshow(BW,[])
+        title(['Thresholded with: ' num2str(intmax(class(Img))*Threshold) ]); % see http://www.ana.unibe.ch/~haberthuer/matlab#threshold_image
+    subplot(133)
+        imshow(Overlay,[])
+        title('Overlay')
+</code>
+adapted from [[http://www.mathworks.com/matlabcentral/fileexchange/15818-upslope-area-functions|upslope area functions]]
+==== Threshold Image ====
+And return Human-readable Threshold
+<code MATLAB>
+Img = imread('rice.png');       % read Image
+Threshold = graythresh(Img);    % calculate Otsu Threshold of Image
+BW = im2bw(Img,Threshold);      % Threshold Image
+Bitdepth = intmax(class(Img));  % Get Bitdepth of Image
+disp(['Image has been thresholded with ' num2str(Threshold) ' (grayvalue: ' num2str(Bitdepth*Threshold) ')' ]);
+figure
+    subplot(121)
+        imshow(Img)
+        title('Original')
+    subplot(122)
+        imshow(BW)
+        title(['Thresholded with: ' num2str(Bitdepth*Threshold) ])
+</code>
+==== Select Components in a (thresholded) Image ====
+<code MATLAB>
+BW = imread('rice.png');        % Load Image
+BW = im2bw(BW,graythresh(BW));  % Threshold Image with Otsu
+% inform user
+wait=helpdlg('Select rice corns in the picture. Stop with right mouse button','Corn Selection');
+uiwait(wait)
+% open figure (bwselect outputs figure to screen, so we put it in a subplot
+% to start with. when right mouse button is pressed, right figure is updated
+figure;
+    subplot(121)
+        BW2 = bwselect(BW);
+    subplot(122)
+        imshow(BW2)
+</code>