clear all %% Plot the example images SourceFileCell = {... './ExtractedStacks/Cond_25/Image_2.mat',... './ExtractedStacks/Cond_19/Image_2.mat',... './ExtractedStacks/Cond_15/Image_1.mat',... './ExtractedStacks/Cond_17/Image_1.mat',... './ExtractedStacks/Cond_21/Image_6.mat',... }; Ser2P_blurRange = 0.0001; % micrometers Ser5P_blurRange = 0.0001; % micrometers SourceFileCell = {... './ExtractedStacks/Cond_25/Image_2.mat',... './ExtractedStacks/Cond_19/Image_2.mat',... './ExtractedStacks/Cond_23/Image_5.mat',... './ExtractedStacks/Cond_15/Image_12.mat',... './ExtractedStacks/Cond_17/Image_5.mat',... './ExtractedStacks/Cond_21/Image_6.mat',... }; zoomLocations = {... [23.2,18],... [9.8,7.63],... [6.2,13.4],... [12.5,5.8],... [16.5,12.1],... [14.6,3.6]}; zoomRange = 3.0; % in microns Ser2P_blurRange = 0.0001; % micrometers Ser5P_blurRange = 0.0001; % micrometers % imgInds = {[1,7],[2,8]}; %[1,3] imgRanges = {... [22,22+32,35,35+32],... [8.5,8.5+32,42,42+32],... [21,21+32,37,37+32],... [13,13+32,18,18+32],... [20,20+32,49,49+32],... [26,26+32,19,19+32]}; zCoordinate = [19,5,10,18,10,9]; rotate_flag = [false,false,false,false,false,false]; plotTitles = {'Control','3 h RHB','6 h RHB','12 h RHB','24 h RHB','48 h RHB'}; scaleBar = 10.0; % in microns scaleBar_zoom = 1.0; % in microns Ser5P_lims = [0,550]; Ser2P_lims = [50,1300]; 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 Ser2P_img = double(thisImg{2}(:,:,zCoordinate(pp))); Ser5P_img = double(thisImg{1}(:,:,zCoordinate(pp))); if rotate_flag(pp) Ser2P_img = Ser2P_img'; Ser5P_img = Ser5P_img'; end Ser5P_img = imgaussfilt(Ser5P_img,... Ser5P_blurRange./thisPixelSize); Ser2P_img = imgaussfilt(Ser2P_img,... Ser2P_blurRange./thisPixelSize); thisImgRange = round(imgRanges{pp}./thisPixelSize)+1; 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(5,numPlots,numPlots.*0+1+(pp-1).*1) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser5P_img,Ser5P_lims) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') if pp == 1 ylabel('Pol II S5P') end colormap(inferno) hold on thisZoomLoc = zoomLocations{pp}; plot(thisZoomLoc(1)+zoomRange.*[-0.5,+0.5,+0.5,-0.5,-0.5],... thisZoomLoc(2)+zoomRange.*[-0.5,-0.5,+0.5,+0.5,-0.5],... 'w-','LineWidth',1) plot([0.5,0.5+scaleBar],thisSize(1).*thisPixelSize-[1,1],... 'w-','LineWidth',3) % Plot scale bar textObject = ... text(0.5+0.5.*scaleBar,thisSize(2).*thisPixelSize-2.5,... sprintf('%d \\mum',scaleBar)); set(textObject,'Color',[1,1,1],'HorizontalAlignment','center',... 'FontSize',12) title(plotTitles{pp},'FontWeight','normal') subplot(5,numPlots,numPlots.*2+1+(pp-1).*1) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser2P_img,Ser2P_lims) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') if pp == 1 ylabel('Pol II S2P') end colormap(inferno) hold on thisZoomLoc = zoomLocations{pp}; plot(thisZoomLoc(1)+zoomRange.*[-0.5,+0.5,+0.5,-0.5,-0.5],... thisZoomLoc(2)+zoomRange.*[-0.5,-0.5,+0.5,+0.5,-0.5],... 'w-','LineWidth',1) % --- Zoomed images of selected foci thisZoomLoc = zoomLocations{pp}; thisImgRange = ... [thisZoomLoc(2)+zoomRange.*[-0.5,+0.5],... thisZoomLoc(1)+zoomRange.*[-0.5,+0.5]]; thisImgRange = round(thisImgRange./thisPixelSize)+1; 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); % Zoom plots Ser5P_lims_zoom = prctile(Ser5P_img(:),[0.1,99.9]); Ser2P_lims_zoom = prctile(Ser2P_img(:),[0.1,99.9]); Ser5P_zoom_img = ... (Ser5P_img-Ser5P_lims_zoom(1))./(diff(Ser5P_lims_zoom)); Ser2P_zoom_img = ... (Ser2P_img-Ser2P_lims_zoom(1))./(diff(Ser2P_lims_zoom)); subplot(5,numPlots,numPlots.*1+1+(pp-1).*1) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser5P_zoom_img,[0,1]) hold on plot(0.5.*zoomRange,0.5.*zoomRange,'k+','MarkerSize',8) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') subplot(5,numPlots,numPlots.*3+1+(pp-1).*1) imagesc([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... Ser2P_zoom_img,[0,1]) hold on plot(0.5.*zoomRange,0.5.*zoomRange,'w+','MarkerSize',8) axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') hold on plot(0.5.*zoomRange,0.5.*zoomRange,'w+','MarkerSize',8) subplot(5,numPlots,numPlots.*4+1+(pp-1).*1) redChannel = Ser5P_zoom_img; blueChannel = Ser5P_zoom_img; greenChannel = Ser2P_zoom_img; rgb_img = zeros(thisSize(1),thisSize(2),3); rgb_img(:,:,1) = redChannel; rgb_img(:,:,2) = greenChannel; rgb_img(:,:,3) = blueChannel; image([0,thisSize(2)].*thisPixelSize,... [0,thisSize(1)].*thisPixelSize,... rgb_img) set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') if pp == 1 title('Detail merge','FontWeight','normal') end axis equal tight axis equal tight set(gca,'XTick',[],'YTick',[]) set(gca,'YDir','normal') hold on plot(0.5.*zoomRange,0.5.*zoomRange,'k+','MarkerSize',8) plot([0.1,0.1+scaleBar_zoom],thisSize(1).*thisPixelSize-[0.1,0.1],... 'w-','LineWidth',3) % Plot scale bar textObject = ... text(0.1+0.5.*scaleBar_zoom,thisSize(2).*thisPixelSize-0.4,... sprintf('%d \\mum',scaleBar_zoom)); set(textObject,'Color',[1,1,1],'HorizontalAlignment','center',... 'FontSize',12) end