Removed code not necessary

src/MATLAB/sandbox2.m

-%% read
-im = tiffReader('DAPI Olig2-514 GFAP-488 Dcx-647 Laminin-Cy3 Bcatenin-568 20x20');
-chan1_8 = uint8(im(:,:,:,1,1));
-
-%% threshold 
-chan1Bin = CudaMex('OtsuThresholdFilter',chan1_8,0.8);
-chan1Close = CudaMex('MorphClosure',chan1Bin,[3,3,2]);
-chan1Open = CudaMex('MorphOpening',chan1Close,[5,5,2]);
-
-%% draw
-figure
-imagesc(chan1_8(:,:,20))
-colormap gray
-figure
-imagesc(chan1Bin(:,:,20))
-colormap gray
-figure
-imagesc(chan1Close(:,:,20))
-colormap gray
-figure
-imagesc(chan1Open(:,:,20))
-colormap gray
\ No newline at end of file

src/MATLAB/tiffReader.m

-function im = tiffReader(datasetName,dirName,nameConvention,cPos,tPos,zPos)
-global DatasetName OrgDir
-
-DatasetName = datasetName;
-im = [];
-
-if (~exist('dirName','var'))
-    fprintf('Select Image Dir...');
-    dirName = uigetdir();
-    disp(dirName);
-end
-
-if (~exist('nameConvention','var'))
-    nameConvention = '_c%d_t%04d_z%04d%s';
-    cPos = 1;
-    tPos = 2;
-    zPos = 3;
-end
-
-OrgDir = dirName;
-
-dList = dir(fullfile(dirName,'*.tif*'));
-
-mxC = 0;
-mxT = 0;
-mxZ = 0;
-
-for i=1:length(dList)
-    vals = textscan(dList(i).name,[datasetName nameConvention]);
-    
-    if (isempty(vals) || isempty(vals{1}) || isempty(vals{2}) || isempty(vals{3}))
-        continue;
-    end
-    
-    c = vals{cPos};
-    t = vals{tPos};
-    z = vals{zPos};
-    im(:,:,z,t,c) = imread(fullfile(dirName,dList(i).name));
-    
-    if (c>mxC)
-        mxC = c;
-    end
-    if (t>mxT)
-        mxT = t;
-    end
-    if (z>mxZ)
-        mxZ = z;
-    end
-end