EzColocalization plugin freezes after recent Fiji update

Usage & Issues
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#1

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!

Fiji Update August 2020
#2

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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#3

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!

#4

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");
#5

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

EVM

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#6

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!

Best,
Weston

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