Commit 5d1fb96b authored by rhaase's avatar rhaase

added solution using imagej

parent 188069e9
// blob segmentation of images in folders
//
// This script analyses folders full of image with blobs and measures their average size
//
// Author: Robert Haase, rhaase@mpi-cbg.de
// May 2019
//
///////////////////////////////////
folder = "C:/structure/mpicloud/Projects/201909_Teaching_BioImageAnalysis_Praque/prague/05_examples/example_images/";
function main() {
run("Clear Results");
processFolder(folder + "condition_A/");
saveAs("Results", folder + "ResultsA.xls");
run("Clear Results");
processFolder(folder + "condition_B/");
saveAs("Results", folder + "ResultsB.xls");
run("Clear Results");
}
function processFolder(foldername) {
filelist = getFileList(foldername);
number_of_files_in_folder = lengthOf(filelist);
// go through all images, segment them and collect results in a table
for (i = 0; i < number_of_files_in_folder; i++) {
open(foldername + filelist[i]);
processImage();
close();
}
}
function processImage() {
// remoive noise
run("Gaussian Blur...", "sigma=5");
// segment
setAutoThreshold("Otsu dark");
setOption("BlackBackground", true);
run("Convert to Mask");
// analyze
run("Set Measurements...", "area redirect=None decimal=3");
run("Analyze Particles...", "display");
}
main();
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