Also my EzColoc freezes when using thresholds inside of the program.
For me, a workaround was to set the threshold before starting EzColoc, store the selection in the ROI-manager and use the ROI-manager as “Cell identification input”.
See this example using the MinError Auto-Threshold
setAutoThreshold("MinError dark");
run("Create Selection");
roiManager("Add");
If you would want to use EzColocalization in a macro you could continue similar to this:
title = getTitle();
dir = getDirectory("image");
run("Split Channels");
C1 = "C1-" + title;
C2 = "C2-" + title;
C3 = "C3-" + title;
// EzColoc for Channel 1 vs. Channel 3
// This includes some arbitrary settings. To get your preferred settings, test your preferred settings in the EzColocalization plugin and record the call with the Macro Recorder.
run("EzColocalization ", "reporter_1_(ch.1)=" + C1 +
" reporter_2_(ch.2)=" + C3 +
" cell_identification_input=[ROI Manager] " + // cell selection from ROI-manager
"alignthold4=default "+ // no additional alignment of channels
"area=100-Infinity " + // exclude small particles
"tos metricthold1=ft allft-c1-1=10 allft-c2-1=20 " + // TOS from top 10% Channel 1 and top 20% Channel 3
"pcc metricthold2=all allft-c1-2=10 allft-c2-2=10 " + // PCC from top 10% of both channels
"srcc metricthold3=all allft-c1-3=10 allft-c2-3=10 " + // SRCC from top 10% of both channels
"average_signal"); // measures for mean intensity
saveAs("Results", dir + title + "_1-3.csv");