Aim:
Complete the macro below and run it on the images in the folder 15.
Useful commands:
run("Set Measurements...", options) sets the features and options that will be measuredsetAutoThreshold(..) sets the threshold using an auto-threshold method, use the macro recorder to find the optionsrun("Analyze Particles...", options); runs the particle analyzer with the given options
saveAs("Results", file-path); saves a result table to a tab-separated text fileYour code starts after this line
// set the measurements here
path = getDirectory("Input directory"); // Ask the user for the input directory
print("\\Clear");
print("batch measure nuclei started");
setBatchMode(true);
files = getFileList(path); // get an array containing the names of all files in the directory path
File.mkdir(path + "out"); // create the output directory
for(i=0; i<files.length; i++) { // iterate over all files
image = files[i]; // get the name of the current file
print("\\Update1: processing file " + (i+1) +"/" + files.length);
if (indexOf(image, ".tif") != -1) { // if the current file is a an image...
open(path + image);
// set the threshold here
// run the particle analyzer here
save(path + "out/" + image);
close();
}
}
// Save the results table here
Your code ends before this line
run("Close");
print("batch measure nuclei finished");
The code below is for automatically checking the result. Please ignore it!
ok = (nImages==0);
ok = (ok && File.exists(path+"/out"));
files = getFileList(path+"/out");
ok = (ok && files.length==4);
if (ok)
showMessage("That's right. Great, you did it!");
else
showMessage("Your result is wrong! Please check your macro and try again!");