Commit 4bfe7d0b authored by rhaase's avatar rhaase

added script for plotting circularity over time

parent c451b03e
// configuration
folder = "C:/structure/teaching/lecture_applied_bioimage_analysis_2020/03_Feature_extraction_and_ImageJ_Macro/example_images/rounding_assay/";
result_csv_file = "summary.csv";
frame_delay_in_minutes = 0.2;
// configure measurement
run("Set Measurements...", "fit shape redirect=None decimal=3");
// retrieve all files in the folder in an array
filelist = getFileList(folder);
number_of_files = lengthOf(filelist);
// create two arrays to put measurements in later
time_array = newArray(number_of_files);
circularity_array = newArray(number_of_files);
for (i = 0; i < number_of_files; i++) {
image_file = filelist[i];
if ( endsWith(image_file, ".tif")) {
// process image
open(folder + image_file);
setAutoThreshold("MaxEntropy dark");
setOption("BlackBackground", true);
run("Convert to Mask");
// get rid of single pixels
run("Erode");
run("Dilate");
// measure properties
run("Clear Results");
run("Analyze Particles...", "display");
run("Summarize");
// read out value from table
circularity = getResult("Circ.", nResults() - 4);
// put value and time in array
time_array[i] = i * frame_delay_in_minutes;
circularity_array[i] = circularity;
// close the current image
close();
}
}
Plot.create("Circularity", "Time / min", "Circularity", time_array, circularity_array);
Plot.setColor("green");
Plot.show();
// save the result table
//IJ.renameResults("Summary", "Results");
saveAs("Results", folder + result_csv_file);
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment