directory = getDirectory("Choose a Directory");
// get image IDs of all open images
for (i=0;i<nImages;i++) {
saveAs("tiff", directory+title);
///### When selecting images manually
directory = getDirectory("Choose a Directory");//
// Get image directory and list image numbers
list = getFileList(directory);
// Create directory for processed images
File.makeDirectory(directory+"processed");
processed_Dir = directory+"processed";
// Start looping through the save tiff files applying the 'operation' function
for(i=0; i < list.length; i = i+1){//list.length ; i = i++){
if (endsWith(list[i], ".tif")){
filename = directory + list[i];
//*directory = getInfo("image.directory");
File.makeDirectory(directory+"processed");
processed_Dir = directory+"processed";
makeRectangle(205, 225, 100, 100);
selectWindow("crop_raw01");
run("Z Project...", "start=8 stop=9 projection=[Max Intensity]");
run("Brightness/Contrast...");
run("Enhance Contrast", "saturated=0.35");
run("Duplicate...", "title=MIP_selstack_ch01_dup duplicate channels=1");
selectWindow("MIP_selstack");
run("Duplicate...", "title=MIP_selstack_ch01 duplicate channels=1");
selectWindow("MIP_selstack");
run("Duplicate...", "title=MIP_selstack_ch02 duplicate channels=2");
selectWindow("MIP_selstack_ch01");
run("Duplicate...", "title=02");
run("Morphological Filters", "operation=Laplacian element=Square radius=1");
imageCalculator("Subtract create", "01","02-Laplacian");
rename("MIP_selstack_ch01");
rename("MIP_selstack_ch01");
run("Gaussian Blur...", "sigma=1");
selectWindow("MIP_selstack_ch01");
setAutoThreshold("Yen dark stack");
run("Shape Filter", "area=0.5-Infinity area_convex_hull=0-Infinity perimeter=0-Infinity perimeter_convex_hull=0-Infinity feret_diameter=0-Infinity min._feret_diam eter=0-Infinity max._inscr._circle_diameter=0-Infinity area_eq._circle_diameter=0-Infinity long_side_min._bounding_rect.=0-Infinity short_side_min._bounding_rect.=0-Infinity aspect_ratio=1.6-Infinity area_to_perimeter_ratio=0.1-Infinity circularity=0-62 elongation=0.69-1 convexity=0-1 solidity=0-1 num._of_holes=0-Infinity thinnes_ratio=0.2-1 contour_temperatur=0-1 orientation=0-180 fractal_box_dimension=0-2 option->box-sizes=2,3,4,6,8,12,16,32,64 draw_holes black_background exclude_on_edges");
run("Analyze Particles...", "size=50-Infinity pixel circularity=0.00-0.90 show=Masks exclude include add");
selectWindow("MIP_selstack_ch02");
nROIs = roiManager("count");
selectWindow("MIP_selstack_ch01_dup");
saveAs("tif", processed_Dir + "/" + title + "_MIP_selstack_ch01_dup.tif");
selectWindow("MIP_selstack_ch02");
saveAs("tif", processed_Dir + "/" + title + "_MIP_selstack_ch02.tif");
selectWindow("MIP_selstack_ch01");
saveAs("tif", processed_Dir + "/" + title + "_Mask_of_MIP_selstack_ch01-1.tif");
nROIs = roiManager("count");
sel_array = newArray(nROIs);
for (i = 0; i < nROIs; i++) {
roiManager("Select", sel_array);
roiManager("Save",processed_Dir + "/" + title + "_cilia_masks.zip");
saveAs("Results", processed_Dir + "/" + "Results.csv");