clear all %% Plot the example images SourceFileCell = {... './ExtractedStacks/Cond_1/Image_80.mat',... './ExtractedStacks/Cond_2/Image_6.mat',... './ExtractedStacks/Cond_4/Image_40.mat' }; SourceFileCell{1} = './ExtractedStacks/Cond_1/Image_58.mat'; SourceFileCell{1} = './ExtractedStacks/Cond_1/Image_53.mat'; SourceFileCell{1} = './ExtractedStacks/Cond_1/Image_52.mat'; SourceFileCell{3} = './ExtractedStacks/Cond_4/Image_3.mat'; TitlesCell = {... 'Control','Flavopiridol','JQ-1'}; DNA_blurRange = 0.06; % micrometers K27ac_blurRange = 0.01; % micrometers Ser2P_blurRange = 0.0001; % micrometers Ser5P_blurRange = 0.01; % micrometers imgRanges = {... [18,36,16,34],... [21,41,14,34],... [6,24,24,42]}; imgRanges{1} = [31.5,31.5,24,24]+[-1,+1,-1,+1].*8.5; imgRanges{2} = [31,31,23.5,23.5]+[-1,+1,-1,+1].*8.5; imgRanges{3} = [18.5,18.5,11.5,11.5]+[-1,+1,-1,+1].*8.5; zCoordinate = [14,23,23]; rotate_flag = [false,false,false]; scaleBar = 5.0; % in microns zoomLocations = {... [5.1,5.4],... [6.5,8.5],... [12.8,7.0]}; zoomRange = 4.0; % in microns numPlots = numel(imgRanges); figure(1) clf for pp = 1:numPlots pp thisFilePath = SourceFileCell{pp}; loadStruct = load(thisFilePath,... 'imgStack','imgSize','pixelSize','zStepSize'); imgStack = loadStruct.imgStack; imgSize = loadStruct.imgSize; pixelSize = loadStruct.pixelSize; zStepSize = loadStruct.zStepSize; thisImg = imgStack; thisPixelSize = pixelSize; % --- Removal of DNA background DNA_img = double(thisImg{1}(:,:,zCoordinate(pp))); K27ac_img = double(thisImg{2}(:,:,zCoordinate(pp))); Ser5P_img = double(thisImg{3}(:,:,zCoordinate(pp))); Ser2P_img = double(thisImg{4}(:,:,zCoordinate(pp))); if rotate_flag(pp) DNA_img = DNA_img'; K27ac_img = K27ac_img'; Ser2P_img = Ser2P_img'; Ser5P_img = Ser5P_img'; end DNA_img = imgaussfilt(DNA_img,... DNA_blurRange./thisPixelSize); K27ac_img = imgaussfilt(K27ac_img,... K27ac_blurRange./thisPixelSize); Ser5P_img = imgaussfilt(Ser5P_img,... Ser5P_blurRange./thisPixelSize); Ser2P_img = imgaussfilt(Ser2P_img,... Ser2P_blurRange./thisPixelSize); thisImgRange = round(imgRanges{pp}./thisPixelSize)+1; DNA_img = DNA_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); K27ac_img = K27ac_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); Ser2P_img = Ser2P_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); Ser5P_img = Ser5P_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); thisSize = size(Ser5P_img); thisSize DNA_img = DNA_img./median(DNA_img(:)); DNA_lims = prctile(DNA_img(:),[30,100]); K27ac_img = K27ac_img-prctile(K27ac_img(:),0.01); K27ac_lims = [500,12000]; Ser5P_img = Ser5P_img-0.*prctile(Ser5P_img(:),0.01); Ser5P_lims = [600,4500]; Ser2P_img = Ser2P_img-prctile(Ser2P_img(:),0.01); Ser2P_lims = [0,2000]; subplot(4,numPlots.*2,numPlots.*0+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... DNA_img,DNA_lims) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') hold on plot(0.5+[0,scaleBar],thisSize(1).*thisPixelSize-[0.5,0.5],... 'w-','LineWidth',3) % Plot scale bar textObject = ... text(0.5+0.5.*scaleBar,thisSize(2).*thisPixelSize-2.0,... sprintf('%d \\mum',scaleBar)); set(textObject,'Color',[1,1,1],'HorizontalAlignment','center',... 'FontSize',12,'FontName','Helvetica Neue') if pp==1 ylabel('DNA') end title(TitlesCell{pp},'FontWeight','normal') subplot(4,numPlots.*2,numPlots.*2.*1+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... K27ac_img,K27ac_lims) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') hold on if pp==1 ylabel('H3K27ac') end subplot(4,numPlots.*2,numPlots.*2.*2+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser5P_img,Ser5P_lims) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') hold on if pp==1 ylabel('Pol II Ser5P') end subplot(4,numPlots.*2,numPlots.*2.*3+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser2P_img,Ser2P_lims) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') hold on if pp==1 ylabel('Pol II Ser2P') end % Prepare the color channels for RGB plotting thisZoomLoc = zoomLocations{pp}; thisImgRange = ... [thisZoomLoc(2)+zoomRange.*[-0.5,+0.5],... thisZoomLoc(1)+zoomRange.*[-0.5,+0.5]]; for kk = 1:4 subplot(4,numPlots.*2,numPlots.*2.*(kk-1)+pp) plot(thisImgRange([3,4,4,3,3]),... thisImgRange([1,1,2,2,1]),... 'w-','LineWidth',1.5) end thisImgRange = round(thisImgRange./thisPixelSize)+1; DNA_img = DNA_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); K27ac_img = K27ac_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); Ser2P_img = Ser2P_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); Ser5P_img = Ser5P_img(... thisImgRange(1):thisImgRange(2),... thisImgRange(3):thisImgRange(4)); thisSize = size(Ser5P_img); subplot(4,numPlots.*2,numPlots.*2.*0+numPlots+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... DNA_img) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') title(TitlesCell{pp},'FontWeight','normal') subplot(4,numPlots.*2,numPlots.*2.*1+numPlots+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... K27ac_img) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') subplot(4,numPlots.*2,numPlots.*2.*2+numPlots+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser5P_img) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') subplot(4,numPlots.*2,numPlots.*2.*3+numPlots+pp) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser2P_img) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') end colormap(inferno)