selectWindow("C2-shctl airy1 15sectlps_Airyscan Processing.czi");
// cleared spurious bright spots and contrast enhanced

run("Measure");
run("Select None");
run("Subtract...", "value=3250 stack");
saveAs("Tiff", "R:\\MicroscopyCore\\mcammer\\Schmidt lab\\Devi Thiagarajan\\20171207_mitochondira_ER\\overlap math\\02 ER shctl airy1 15sectlps_Airyscan Processing.tif");
 
selectWindow("C1-shctl airy1 15sectlps_Airyscan Processing.czi");
run("Enhance Contrast...", "saturated=0 normalize process_all use");
makeRectangle(625, 620, 224, 176);
run("Measure");
selectWindow("Results");
run("Select None");
run("Subtract...", "value=540 stack");
run("Save", "save=[R:\\MicroscopyCore\\mcammer\\Schmidt lab\\Devi Thiagarajan\\20171207_mitochondira_ER\\overlap math\\02 mito -shctl airy1 15sectlps_Airyscan Processing.tif]");
selectWindow("02 ER shctl airy1 15sectlps_Airyscan Processing.tif");
imageCalculator("Difference create stack", "02 mito -shctl airy1 15sectlps_Airyscan Processing.tif","02 ER shctl airy1 15sectlps_Airyscan Processing.tif");
selectWindow("Result of 02 mito -shctl airy1 15sectlps_Airyscan Processing.tif");
run("Image Calculator...");
rename("difference");
imageCalculator("Subtract create stack", "difference","02 mito -shctl airy1 15sectlps_Airyscan Processing.tif");
selectWindow("Result of difference");
rename("diff minus mito");
imageCalculator("Subtract create stack", "difference","02 ER shctl airy1 15sectlps_Airyscan Processing.tif");
selectWindow("Result of difference");
rename("difference minus er");
run("Merge Channels...", "c1=[diff minus mito] c2=[difference minus er] c3=[02 mito -shctl airy1 15sectlps_Airyscan Processing.tif] create keep ignore");
makeArrow(1101, 472, 1018, 464, "filled");
Roi.setStrokeWidth(3);
Roi.setStrokeColor("white");
run("Add Selection...");
//setTool("rectangle");
makeRectangle(89, 114, 1043, 1018);
makeRectangle(149, 114, 983, 1018);
run("Crop");
makeRectangle(37, 28, 943, 990);
run("Crop");
run("In [+]");