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FILOMAP_Fiji.ijm
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FILOMAP_Fiji.ijm
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requires("1.51a"); // To maintain general compatibility requirements (i.e. presence of CLAHE)
current_version_script = "v2"; // The version number is saved in the log of the expriment
number_of_tif = 0; // Initialization of file counter
file_name_index = 0; // Initialization of index for storage
// Directory structure
source_directory = getDirectory("Choose the directory to analyze"); // Source data loading
results_directory = getDirectory("Choose the result directory "); // Path for the results and various outputs
LineProf_results_directory = results_directory+"Line Profiles"+File.separator; // Assemble string for temporary folder
File.makeDirectory(LineProf_results_directory);
// Create temporary directory within the results location
Contrast_adjusted = results_directory+"Projection to analyse contrast adjusted"+File.separator;
File.makeDirectory(Contrast_adjusted);
// File listing and counting the number of compatible files available
Dialog.create("FiloMap: Settings"); // GUI: create dialog box
Dialog.addMessage("FiloMap: Settings"); // GUI comment
Dialog.addNumber("Number of Channels:", 2);
Dialog.addString("File extension:", ".dv");
Dialog.show();
channels = Dialog.getNumber();
file_extension = Dialog.getString();
LineProf_results_directory_C1 = LineProf_results_directory+"C1"+File.separator; // Assemble string for temporary folder
File.makeDirectory(LineProf_results_directory_C1);
if (channels>=2) {
LineProf_results_directory_C2 = LineProf_results_directory+"C2"+File.separator; // Assemble string for temporary folder
File.makeDirectory(LineProf_results_directory_C2);}
if (channels>=3) {
LineProf_results_directory_C3 = LineProf_results_directory+"C3"+File.separator; // Assemble string for temporary folder
File.makeDirectory(LineProf_results_directory_C3);}
if (channels>=4) {
LineProf_results_directory_C4 = LineProf_results_directory+"C4"+File.separator; // Assemble string for temporary folder
File.makeDirectory(LineProf_results_directory_C4);}
// File listing and counting the number of compatible files available
all_files_list = getFileList(source_directory); // Create an array with the name of all the elements in the folder
number_files = lengthOf(all_files_list); // Count the total number of elements in the source folder
for (i=0; i<number_files; i++) { // |
if (endsWith(all_files_list[i], file_extension) || endsWith(all_files_list[i], ".tif")) { // |
number_of_tif = number_of_tif + 1; // |— Count the number of TIFF/TIF files
} // |
} // |
if (number_of_tif == 0) { // ||
exit("Duh! This folder doesn't contain any compatible files!"); // ||— Clean exit if no compatible file present in the location
} // ||
// Creating array for full and extensionless filenames
length_file_extension = lengthOf(file_extension);
file_shortname=newArray(number_of_tif); // Array allocation
file_fullname=newArray(number_of_tif); // Array allocation
for (i=0; i<number_files; i++) { //
length_name=lengthOf(all_files_list[i]); //
if (endsWith(all_files_list[i], file_extension)) { // |
file_fullname[file_name_index]=all_files_list[i]; // |
file_shortname[file_name_index]=substring(all_files_list[i],0,length_name-length_file_extension); // |— Storage of filename for TIFF file
file_name_index = file_name_index + 1; // |
} // |
if (endsWith(all_files_list[i], ".tif")) { // ||
file_fullname[file_name_index]=all_files_list[i]; // ||
file_shortname[file_name_index]=substring(all_files_list[i],0,length_name-4); // ||— Storage of filename for TIF file
file_name_index = file_name_index + 1; // ||
} // ||
} //
// Main analysis loop, 1 iteration per file
for (p=0; p<number_of_tif; p++) { // Beginning of main analysis loop
showProgress(p+1, number_of_tif); // Update progress bar within ImageJ status bar
open(source_directory + file_fullname[p]); // Load the image rank p
resetMinAndMax(); // Reset the intensity scale (to make predicatable results in case autoscale is default)
run("Grays");
rename("image");
// Split and rename the Channels
run("Split Channels");
selectWindow("C1-image"); rename("image-0001");
if (channels>=2) {
selectWindow("C2-image"); rename("image-0002");}
if (channels>=3) {
selectWindow("C3-image"); rename("image-0003");}
if (channels>=4) {
selectWindow("C4-image"); rename("image-0004");}
// adjust the contrast
setTool("rectangular");
run("Brightness/Contrast...");
waitForUser("Adjust contrast in each image.\n Then click Ok"); // Dialog box for user to choose the cell to analyse
selectWindow("image-0001"); run("16-bit");
if (channels>=2) {
selectWindow("image-0002"); run("16-bit");}
if (channels>=3) {
selectWindow("image-0003"); run("16-bit");}
if (channels>=4) {
selectWindow("image-0004"); run("16-bit");}
// Create a Merged image and save it
if (channels==2) {
run("Merge Channels...", "c1=image-0001 c2=image-0002 keep");}
if (channels==3) {
run("Merge Channels...", "c1=image-0001 c2=image-0003 c6=image-0002 keep");}
if (channels==4) {
run("Merge Channels...", "c1=image-0001 c2=image-0003 c3=image-0002 c6=image-0004 keep");}
selectWindow("RGB"); saveAs("Tiff",Contrast_adjusted+file_shortname[p]+" - RGB.tif");rename("RGB2");
selectWindow("RGB2");
setTool("polyline");
run("ROI Manager...");
roiManager("Show All");
waitForUser("Draw each Filopodium and add them to ROI manager.\n Then click Ok");
roiManager("Save", Contrast_adjusted+file_shortname[p]+" - ROI.zip");
array1 = newArray("0");;
for (i=1;i<roiManager("count");i++){
array1 = Array.concat(array1,i);
Array.print(array1);
}
// Save the line profiles
selectWindow("image-0001");
roiManager("select", array1);
roiManager("Multi Plot");
Plot.showValues();
saveAs("Results", LineProf_results_directory_C1+file_shortname[p]+" - 001.csv");
selectWindow("Profiles"); close();
run("Clear Results");
selectWindow("image-0001"); saveAs("Tiff",Contrast_adjusted+file_shortname[p]+" - 0001.tif");
if (channels>=2) {
selectWindow("image-0002");
roiManager("select", array1);
roiManager("Multi Plot");
Plot.showValues();
saveAs("Results", LineProf_results_directory_C2+file_shortname[p]+" - 002.csv");
selectWindow("Profiles"); close();
run("Clear Results");
selectWindow("image-0002"); saveAs("Tiff",Contrast_adjusted+file_shortname[p]+" - 0002.tif");
}
if (channels>=3) {
selectWindow("image-0003");
roiManager("select", array1);
roiManager("Multi Plot");
Plot.showValues();
saveAs("Results", LineProf_results_directory_C3+file_shortname[p]+" - 003.csv");
selectWindow("Profiles"); close();
run("Clear Results");
selectWindow("image-0003"); saveAs("Tiff",Contrast_adjusted+file_shortname[p]+" - 0003.tif");
}
if (channels>=4) {
selectWindow("image-0004");
roiManager("select", array1);
roiManager("Multi Plot");
Plot.showValues();
saveAs("Results", LineProf_results_directory_C4+file_shortname[p]+" - 004.csv");
selectWindow("Profiles"); close();
run("Clear Results");
selectWindow("image-0004"); saveAs("Tiff",Contrast_adjusted+file_shortname[p]+" - 0004.tif");
}
run("Close All");
roiManager("Deselect");
roiManager("Delete");
}