Installing JACoP

Hello,

When I save the JACoP plugin as an executable jar file to my plugins folder in FIJI, JACoP does not show up in my list of plugins once I start FIJI. I download JACoP from here:
https://imagejdocu.list.lu/media/plugin/analysis/jacop_2.0/just_another_colocalization_plugin/jacop.jar

Also, when I search within FIJI using the search commands feature, JACoP does not show up in the command list.
Has anyone else encountered this problem? How did you resolve it? Thank you.

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Hey @GopherConfocal,

the website is down unfortunately. Can you share the jar file?

Thanks!

Cheers,
Robert

Hi,

I have attached the jar file. Thank you so much!
jacop_.jar (36.5 KB)

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Ok, I have the suspicion your jar file is corrupted.

If you try putting the JACoP_.class from this website to your Fijis Plugin folder, it should work:
https://imagej.nih.gov/ij/plugins/track/jacop2.html

Can you confirm?

Cheers,
Robert

Robert,

Thank you for your help! I believe the class file is from the original JaCoP plugin and I had hoped to get version 2.1.1 from the JACoP website: https://imagej.net/JaCoP#JACoP
But I will give this version a whirl! Thank you for your prompt responses!

Mary

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Ok, let’s ask @Fabrice_Cordelieres for the current up-to-date Jacop_.jar. I’m sure he has it :wink:

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Hello Thank you very much for your help and for clarifying the issues related to that plugins, I’m also looking for a recent version of “JACOP” and “colocalization finder” plugins, for use in FIJI, so please when you have it or if another one has it, it will be very helpful to share it for downloading, many thanks for all.

Hi,

Sorry for the late reply: I’ve finally added it to GitHub (at last !!!): https://github.com/fabricecordelieres/IJ-Plugin_JACoP/releases/download/2.1.1/_JACoP.jar
Please use the 2.1.1 version, as I’m currently trying to track a potential bug (only on the macro/graphical user interface, not on the calculation part) in 2.1.2 :wink:

Cheers,

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Hi, I wonder if you could help with a problem. I am trying to install JACoP, however it seems to be freezing. When I run the analysis a blank window titled Log opens, however FIJI just freezes. I made sure it was updated, and I uninstalled JACoP and installed the version 2.1.1 that @Fabrice_Cordelieres posed but still the same result. I also tried running it on ImageJ rather than FIJI and the same again. Any help would be greatly appreciated

Hi,

What kind of analysis are you trying to perform ?
Could you try to crop your images to get smaller ones and see if the problem persists ? If so, it might be that the memory required to perform the analysis is larger than the available memory.

Hi @Fabrice_Cordelieres,

Would it be possible to have the .jar file for JACoP v2.1.3?
It appears to be absent from the releases.

Thanks a lot!

Hi,
Thanks for pointing it out. It seemed GitHub came across an issue when I’ve first tried to upload it.
Cheers,

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HI @Fabrice_Cordelieres,
I’m getting this exception when trying JACoP v2.1.3:

java.lang.NullPointerException
	at GUI.updateImgList(GUI.java:1250)
	at GUI.<init>(GUI.java:813)
	at JACoP_.run(JACoP_.java:35)
	at ij.IJ.runUserPlugIn(IJ.java:241)
	at ij.IJ.runPlugIn(IJ.java:204)
	at ij.Executer.runCommand(Executer.java:151)
	at ij.Executer.run(Executer.java:69)
	at java.lang.Thread.run(Thread.java:748)

Not sure why?

Hi,
Sounds weird: I’ve uploaded the version I’m currently working with and didn’t had that behavior.
Could you have a look at Fiji/plugins folder and make sure you have only one version of JACoP in it ?

Thanks,

Hey,

I’ve been digging a bit into the issue you’ve mentioned… and finally found a way to reproduce the issue. It was linked to the generation of the image list at startup of the plugin. When no images were opened, everything was fine. When at least an image was opened before JACoP, you got the message.
I’ve corrected the bug and released v2.1.4 available from my GitHub.

Thanks for pointing this out !

Cheers,

F.

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