Commit f5425cdf authored by rhaase's avatar rhaase

upload exercise solutions

parent ffe9eefb
// This ImageJ macro analyses a folder of 2D MRI
// images showing a banana slice by slice. It measures
// the position of the banana and writes it in a CSV file.
//
// Usage: run it in Fiji (http://fiji.sc)
//
// Robert Haase, MPI CBG, rhaase@mpi-cbg.de
// April 2019
//
folder = "C:/structure/teaching/lecture_applied_bioimage_analysis_2020/03_Feature_extraction_and_ImageJ_Macro/example_images/banana/"
// access the folder
filelist = getFileList(folder);
for (i = 0; i < lengthOf(filelist); i++) {
// get the nth entry from the filelist array
file = filelist[i];
if (endsWith(file, ".tif")) {
// open the image
open(folder + file);
// segment the object in the image
setAutoThreshold("Default dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
// measure the position of this one single object
run("Set Measurements...", "centroid redirect=None decimal=3");
run("Create Selection");
run("Measure");
// close the image
close();
}
}
// save the positions as CSV to disc
result_filename = "Position.csv"
saveAs("Results", folder + result_filename);
// configuration
folder = "C:/structure/teaching/lecture_applied_bioimage_analysis_2020/03_Feature_extraction_and_ImageJ_Macro/example_images/rounding_assay/";
image_file = "rounding_assay0035.tif";
result_csv_file = "summary.csv";
// configure measurement
run("Set Measurements...", "fit shape redirect=None decimal=3");
// process image
open(folder + image_file);
// duplicate to show ROIs later on
//run("Duplicate...", " ");
setAutoThreshold("MaxEntropy dark");
setOption("BlackBackground", true);
run("Convert to Mask");
// get rid of single pixels
run("Erode");
run("Dilate");
// measure properties
run("Analyze Particles...", "summarize");
// show outline on original image
//run("Create Selection");
//close();
//run("Restore Selection");
// save the result table
IJ.renameResults("Summary", "Results");
saveAs("Results", folder + result_csv_file);
// 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";
// configure measurement
run("Set Measurements...", "fit shape redirect=None decimal=3");
// retrieve all files in the folder in an array
filelist = getFileList(folder);
for (i = 0; i < lengthOf(filelist); i++) {
image_file = filelist[i];
if ( endsWith(image_file, ".tif")) {
// process imagge
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("Analyze Particles...", "summarize");
close();
}
}
// save the result table
IJ.renameResults("Summary", "Results");
saveAs("Results", folder + result_csv_file);
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