EzColocalization plugin freezes after recent Fiji update

Hi there,

I have problems using the EzColocalization plugin after the update. When I click “Show Threshold(s)”, no thresholds are applied to the images and the plugin will freeze. It worked perfectly fine before I updated ImageJ, so I’m wondering if the problem I’m experiencing is related to this major update. Thank you!

Hi @kara.hyx and welcome to the forum!

It’s hard to say what causes your issue. But as far as I can see from the EzColocalization repository, the plugin uses only ImageJ1 functionality.

Could you try if downgrading your ij.jar via Help > Update ImageJ… and selecting a version such as 1.52 or 1.51 helps in your case?

For what it’s worth, I invited Dr. Han Lim, the corresponding author of the EzColocalization paper, to this discussion.

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I have the same problem using the EzColocalization plugin as Kara described on August 6. It’s still there and the suggested downgrading the plugin .jar doesn’t work. Any other suggestions? Thanks!

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");

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");

Setting the threshold before starting EzColoc worked well. Thanks!!!


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Hi all,

We have posted a new version of EzColocalization on GitHub and the update site that fixes the issues with the new version of Fiji. Thanks for using the plugin!