--- a
+++ b/functions/functions_preProc/deConvStain.m
@@ -0,0 +1,78 @@
+function [H, E, Bg] = deConvStain(im, filename, dirResults, plotta, savefile)
+
+%Alsubaie N, Trahearn N, Raza SEA, Snead D, Rajpoot NM (2017)
+%Stain Deconvolution Using Statistical Analysis of Multi-Resolution Stain Colour Representation.
+%PLOS ONE 12(1): e0169875.
+
+[~, ~, H, E, Bg] = SCD_MA(im, plotta);
+
+offsetHist = 50;
+
+% figure, imshow(H)
+% figure, imshow(E)
+% figure, imshow(Bg)
+
+
+%find E
+
+%the one with greatest red channel
+[cH, xH] = imhist(H(:,:,1));
+[cE, xE] = imhist(E(:,:,1));
+[cBg, xBg] = imhist(Bg(:,:,1));
+sumH = sum(cH(end-offsetHist : end));
+sumE = sum(cE(end-offsetHist : end));
+sumBg = sum(cBg(end-offsetHist : end));
+[maxSum, indM] = max([sumH, sumE, sumBg]);
+
+%cell
+stainCell{1} = H;
+stainCell{2} = E;
+stainCell{3} = Bg;
+
+%switch
+appoggio = stainCell{2};
+stainCell{2} = stainCell{indM};
+stainCell{indM} = appoggio;
+
+%revert
+if 1
+    H = stainCell{1};
+    E = stainCell{2};
+    Bg = stainCell{3};
+end %if 0
+
+
+
+if plotta
+    fh = fsfigure;
+    
+    subplot(1, 4, 1);
+    imshow(im);
+    title('Source');
+    
+    subplot(1, 4, 2),
+    imshow(H);
+    title('H');
+    
+    subplot(1, 4, 3),
+    imshow(E);
+    title('E');
+    
+    subplot(1, 4, 4),
+    imshow(Bg);
+    title('Bg');
+
+    str = [filename '; Stain deconvolution'];
+    
+    mtit(fh, str, 'Interpreter', 'none', 'fontsize', 14, 'color', [1 0 0], 'xoff', .0, 'yoff', .0);
+    
+    %save
+    if savefile
+        export_fig(gcf, [dirResults str '.jpg']);
+    end %if save
+    
+end %if plotta
+
+
+
+