// Measures the cellular mitochondrial content in each cell and mitochondrial morphology. Fire up the program with [F9]" macro "Measure mitochondrial Morphology and Mitochondrial Content open image [F9]" { open(); setTool(2); // Measure the area of the cell on the green channel only run("Restore Selection"); print ("select the region or cell of interest to analyze then press function 10 key"); print ("press F10= process image"); print ("press F11= measures image"); print ("press F12= measures colocalized points"); print ("press F4= closes all unused windows"); setColor(0, 0, 0); x=50; y=20; //Welcome window pops open newImage("Welcome Frame", "RGB white", 550, 100, 1); setFont("SansSerif" , 16, "bold"); y += 30; setColor(0, 0, 255); drawString("Welcome to the ImageJ Mitophagy Marcro by Ruben K. Dagda" x, y); } wait(1000) macro "Process RGB Image [F10]" { run("Clear Results"); // Select the outline of the cell containing mitos on the appropriate channel only setTool(2); // Measure the area of the cell on the green channel only run("Copy"); run("Duplicate...","\n"); run("Paste"); run("RGB Split"); close(); close(); run("Invert"); run("Sharpen"); setAutoThreshold(); //run("Threshold..."); run("Restore Selection"); beep(); } macro "Measure image [F11] { run("Set Measurements...", "area perimeter circularity redirect=None decimal=2" ); setTool(2); run("Analyze Particles...", "minimum=30 maximum=100000 bins=100 show=Outlines display summarize"); for (i=0; i0) { selectImage(nImages); close(); } //Closes all windows except your results which you can transfer to Excel beep(); } macro "Colocalization of pixels [F12] { run("Clear Results"); setTool(2); // Measure the area of the cell on the green channel only run("Copy"); run("Internal Clipboard"); run("Invert"); run("RGB Split"); close(); run("Colocalization ", "channel_1=[Clipboard (red)] channel_2=[Clipboard (green)] ratio=80 threshold_channel_1=0 threshold_channel_2=0 display=255 colocalizated"); selectWindow("Clipboard (red)"); run("Make Binary"); run("Invert"); run("Analyze Particles...", "size=10-50000 circularity=0.00-1.00 show=Outlines display exclude summarize"); selectWindow("Clipboard (green)"); run("Make Binary"); run("Invert"); run("Analyze Particles...", "size=10-50000 pixel circularity=0.00-1.00 show=Outlines display exclude summarize"); selectWindow("Colocalizated points (8-bit) "); run("Make Binary"); run("Invert"); run("Analyze Particles...", "size=10-50000 pixel circularity=0.00-1.00 show=Outlines display exclude summarize"); } }