-
Notifications
You must be signed in to change notification settings - Fork 0
/
benchmark_median.ijm
37 lines (32 loc) · 1.13 KB
/
benchmark_median.ijm
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
/* Macro by Félix de Carpentier, 2020, CNRS / Sorbonne University / Paris-Saclay University, France
Inspired by Guzmán, Camilo, Manish Bagga, Amanpreet Kaur, Jukka Westermarck, and Daniel Abankwa.
« ColonyArea: An ImageJ Plugin to Automatically Quantify Colony Formation in Clonogenic Assays ».
PLOS ONE 9, no 3: e92444. https://doi.org/10.1371/journal.pone.0092444. */
//Allows the user to choose the folder containing the images and the folder for the results
inputFolder=getDirectory("Choose input folder");
med = "med";
run("CLIJ2 Macro Extensions", "cl_device=");
Ext.CLIJ2_clear();
setBatchMode(true);
list=getFileList(inputFolder);
for(i=0; i<list.length; i++) {
loc=inputFolder+list[i];
open(loc);
run("32-bit"); //Convert to black and white
t1 = getTime();
run("Mean 3D...", "x=3 y=3 z=3");
t2 = getTime();
close();
print("ImageJ;"+ list[i] + ";" + (t2-t1));
open(loc);
run("32-bit"); //Convert to black and white
bw = getTitle();
t3 = getTime();
Ext.CLIJ2_push(bw);
Ext.CLIJ_mean3DBox(bw, med, 3, 3, 3);
Ext.CLIJ2_pull(med);
t4 = getTime();
close();
print("CLIJ2;"+ list[i] + ";" + (t4-t3));
}
setBatchMode(false);