Automate Embryoid Body Measurements

Hi everyone :wave: ,
So getting back into ImageJ after not using it for a while, I’m trying to find an automated way (like a macros program maybe?) to measure parameters like area, diameter, circularity, perimeter of single images of EBs. I’ve got a few examples of my images here. Doing it one at a time is very tedious and time consuming. Willing to try anything new as well.

Thanks in advance :+1:
E7D7 Basal 10x_3.tif (2.9 MB) E7D7 L-Pro SB 10x_2.tif (2.9 MB) E7D7 50% MEDII 10x_1.tif (2.9 MB) E7D7 50% MEDII 10x_4.tif (2.9 MB)

if your images is in the same size, you can import sequence at one time. then process them in bat.

1 Like

@SalSciences
Can it be okay?

dir1 = "Choose Source Directory ";
//dir1= "F:/Embryoid body/"; // is my "Source Directory" 
list = getFileList( dir1 );
for ( i=0; i<list.length; i++ ) {
    open( dir1 + list[i] );
run("Set Measurements...", "area perimeter bounding add redirect=None decimal=0");
run("Set Scale...", "distance=0 known=0 pixel=1 unit=pixel");
run("32-bit");
setAutoThreshold("RenyiEntropy");
//run("Threshold...");
run("Convert to Mask");
run("Analyze Particles...", "size=10000-Infinity display exclude add");
roiManager("reset");
}
run("Close All");

Thanks for the reply. Um so do I copy and paste this into a batch processing window (So Process>Batch>Macro), change the source directory to the folder of my interest and run the macro, making sure my images are converted into 32-bit?

Thanks for the reply. Um so do I copy and paste this into a batch processing window (So Process>Batch>Macro), change the source directory to the folder of my interest and run the macro, making sure my images are converted into 32-bit?

Hi
@SalSciences
This is a macro that must be copied and pasted into:
plugin-> news-> macro