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JaCoP Tools

Olivier Burri
Hi all,

Just a quick announcement that we placed a new little macro collection onto our PTBIOP Update Site called "JaCoP Tools"

This simplifies and batch processes multichannel images for coloc analysis by calling JaCoP and formatting the output to a table, and providing a simple report of the channels.

Hopefully someone will find it useful. If you have any questions, please do not hesitate to ask.

Best

Oli

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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R: JaCoP Tools

Casalini Patrizia
Hi Oli,

I'm interested to update "Jacop Tools" plugin, but I didn't find it.
Could you please send me the updated plugin?

Thanks a lot,

Patrizia

-----Messaggio originale-----
Da: ImageJ Interest Group [mailto:[hidden email]] Per conto di Burri Olivier
Inviato: giovedì 9 luglio 2015 16:06
A: [hidden email]
Oggetto: JaCoP Tools

Hi all,

Just a quick announcement that we placed a new little macro collection onto our PTBIOP Update Site called "JaCoP Tools"

This simplifies and batch processes multichannel images for coloc analysis by calling JaCoP and formatting the output to a table, and providing a simple report of the channels.

Hopefully someone will find it useful. If you have any questions, please do not hesitate to ask.

Best

Oli

--
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This communication, which may contain confidential and/or legally privileged information, is intended solely for the use of the intended addressees. All information or advice contained in this communication is subject to the terms and conditions provided by the agreement governing each particular client engagement. If you have received this communication in error, please notify us immediately by responding to this email; then please delete it from your system. Any use, disclosure, copying or distribution of the contents of this communication by a not-intended recipient or in violation of the purposes of this communication is strictly prohibited and may be unlawful. The transmission technology used to send this mail can grant neither the sender identity nor the data integrity

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Re: JaCoP Tools

Olivier Burri
Hi Patrizia, hi all,

So as a quick step by step

0. Use Fiji to have access to the update sites

1. Install JaCoP
http://rsb.info.nih.gov/ij/plugins/track/jacop.html

2. Install ActionBar
http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start

3. Subscribe to the PTBIOP Update site by going to the following menu
Help - Update - Manage Update Sites
Check the box next to PTBIOP

After restarting ImageJ, the Plugins Menu should have a BIOP Folder where you will find, among others JaCoP Tools

I made a quick documentation to help you get started
https://drive.switch.ch/public.php?service=files&t=7c814b8369803ddbf07279596a5186ed


Best Regards,

Oli

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R: JaCoP Tools

Casalini Patrizia
Thank you very much,
Patrizia

Inviato da smartphone Sony Xperia™


---- Burri Olivier ha scritto ----

Hi Patrizia, hi all,

So as a quick step by step

0. Use Fiji to have access to the update sites

1. Install JaCoP
http://rsb.info.nih.gov/ij/plugins/track/jacop.html

2. Install ActionBar
http://imagejdocu.tudor.lu/doku.php?id=plugin:utilities:action_bar:start

3. Subscribe to the PTBIOP Update site by going to the following menu
Help - Update - Manage Update Sites
Check the box next to PTBIOP

After restarting ImageJ, the Plugins Menu should have a BIOP Folder where you will find, among others JaCoP Tools

I made a quick documentation to help you get started
https://drive.switch.ch/public.php?service=files&t=7c814b8369803ddbf07279596a5186ed


Best Regards,

Oli

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[cid:image97b7e7.png@590f6050.96e74caa]
La presente comunicazione, che potrebbe contenere informazioni riservate e/o protette da segreto professionale, è indirizzata esclusivamente ai destinatari della medesima qui indicati. Ogni informazione qui contenuta, che non sia relativa alla nostra attività caratteristica, deve essere considerata come non inviata. Nel caso in cui abbiate ricevuto per errore la presente comunicazione, vogliate cortesemente darcene immediata notizia, rispondendo a questo stesso indirizzo di e-mail, e poi procedere alla cancellazione di questo messaggio dal Vostro sistema. E' strettamente proibito e potrebbe essere fonte di violazione di legge qualsiasi uso, comunicazione, copia o diffusione dei contenuti di questa comunicazione da parte di chi la abbia ricevuta per errore o in violazione degli scopi della presente. Ricordiamo che la tecnologia di trasmissione utilizzata non consente di garantire l’autenticità del mittente né l’integrità dei dati

This communication, which may contain confidential and/or legally privileged information, is intended solely for the use of the intended addressees. All information or advice contained in this communication is subject to the terms and conditions provided by the agreement governing each particular client engagement. If you have received this communication in error, please notify us immediately by responding to this email; then please delete it from your system. Any use, disclosure, copying or distribution of the contents of this communication by a not-intended recipient or in violation of the purposes of this communication is strictly prohibited and may be unlawful. The transmission technology used to send this mail can grant neither the sender identity nor the data integrity


________________________________

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Re: R: JaCoP Tools

djw23
Hi there,

I would very much like to access this tool as I'm having trouble trying to write a macro for batch processing my images.  However, after updating BIOP and downloading the action bar and putting it in the plugins folder, I can't access the Jacop tools.  This is the error message I get:
java.lang.UnsupportedClassVersionError: BIOP_LibInstaller : Unsupported major.minor version 52.0
        at java.lang.ClassLoader.defineClass1(Native Method)
        at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
        at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
        at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
        at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
        at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
        at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:296)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at ij.macro.Functions.call(Functions.java:4070)
        at ij.macro.Functions.getStringFunction(Functions.java:272)
        at ij.macro.Interpreter.getStringTerm(Interpreter.java:1293)
        at ij.macro.Interpreter.getString(Interpreter.java:1272)
        at ij.macro.Interpreter.doStatement(Interpreter.java:281)
        at ij.macro.Interpreter.doStatements(Interpreter.java:218)
        at ij.macro.Interpreter.run(Interpreter.java:115)
        at ij.macro.Interpreter.run(Interpreter.java:85)
        at ij.macro.Interpreter.run(Interpreter.java:96)
        at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
        at ij.plugin.Macro_Runner.runMacroFromJar(Macro_Runner.java:198)
        at ij.plugin.Macro_Runner.run(Macro_Runner.java:44)
        at ij.IJ.runPlugIn(IJ.java:187)
        at ij.Executer.runCommand(Executer.java:137)
        at ij.Executer.run(Executer.java:66)
        at java.lang.Thread.run(Thread.java:662)


Could someone help me please?

Thanks,

David
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Re: R: JaCoP Tools

ctrueden
Hi David,

> java.lang.UnsupportedClassVersionError: BIOP_LibInstaller :
> Unsupported major.minor version 52.0

That error means that Java 8 is required, but you are running an older
version of Java.

If you update to Java 8, that error should go away.

If you are using ImageJ 1.x, you can download a version bundled with Java 8
from here:
    https://imagej.nih.gov/ij/download.html

If you are using ImageJ2 (what the Fiji distribution of ImageJ is built
on), then you can download a fresh version of Fiji bundled with Java 8 from
here:
    https://fiji.sc/#download

Unfortunately, most ImageJ2 and Fiji web services are currently down for
emergency maintenance, as we deal with a failing hard drive. Hopefully we
will have it restored by/over the weekend.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Fri, Jan 13, 2017 at 9:15 AM, djw23 <[hidden email]> wrote:

> Hi there,
>
> I would very much like to access this tool as I'm having trouble trying to
> write a macro for batch processing my images.  However, after updating BIOP
> and downloading the action bar and putting it in the plugins folder, I
> can't
> access the Jacop tools.  This is the error message I get:
> java.lang.UnsupportedClassVersionError: BIOP_LibInstaller : Unsupported
> major.minor version 52.0
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>         at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:296)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>         at ij.macro.Functions.call(Functions.java:4070)
>         at ij.macro.Functions.getStringFunction(Functions.java:272)
>         at ij.macro.Interpreter.getStringTerm(Interpreter.java:1293)
>         at ij.macro.Interpreter.getString(Interpreter.java:1272)
>         at ij.macro.Interpreter.doStatement(Interpreter.java:281)
>         at ij.macro.Interpreter.doStatements(Interpreter.java:218)
>         at ij.macro.Interpreter.run(Interpreter.java:115)
>         at ij.macro.Interpreter.run(Interpreter.java:85)
>         at ij.macro.Interpreter.run(Interpreter.java:96)
>         at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
>         at ij.plugin.Macro_Runner.runMacroFromJar(Macro_Runner.java:198)
>         at ij.plugin.Macro_Runner.run(Macro_Runner.java:44)
>         at ij.IJ.runPlugIn(IJ.java:187)
>         at ij.Executer.runCommand(Executer.java:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:662)
>
>
> Could someone help me please?
>
> Thanks,
>
> David
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/JaCoP-Tools-tp5013499p5017880.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: R: JaCoP Tools

djw23
Hi Curtis,

My Java is already at the latest version though.  I'll try the fresh download you suggested and see how I get on.

Thanks,

David

On 13 January 2017 at 16:02, ctrueden [via ImageJ] <[hidden email]> wrote:
Hi David,

> java.lang.UnsupportedClassVersionError: BIOP_LibInstaller :
> Unsupported major.minor version 52.0

That error means that Java 8 is required, but you are running an older
version of Java.

If you update to Java 8, that error should go away.

If you are using ImageJ 1.x, you can download a version bundled with Java 8
from here:
    https://imagej.nih.gov/ij/download.html

If you are using ImageJ2 (what the Fiji distribution of ImageJ is built
on), then you can download a fresh version of Fiji bundled with Java 8 from
here:
    https://fiji.sc/#download

Unfortunately, most ImageJ2 and Fiji web services are currently down for
emergency maintenance, as we deal with a failing hard drive. Hopefully we
will have it restored by/over the weekend.

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/



On Fri, Jan 13, 2017 at 9:15 AM, djw23 <[hidden email]> wrote:

> Hi there,
>
> I would very much like to access this tool as I'm having trouble trying to
> write a macro for batch processing my images.  However, after updating BIOP
> and downloading the action bar and putting it in the plugins folder, I
> can't
> access the Jacop tools.  This is the error message I get:
> java.lang.UnsupportedClassVersionError: BIOP_LibInstaller : Unsupported
> major.minor version 52.0
>         at java.lang.ClassLoader.defineClass1(Native Method)
>         at java.lang.ClassLoader.defineClassCond(ClassLoader.java:632)
>         at java.lang.ClassLoader.defineClass(ClassLoader.java:616)
>         at java.security.SecureClassLoader.defineClass(
> SecureClassLoader.java:141)
>         at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
>         at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
>         at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
>         at java.security.AccessController.doPrivileged(Native Method)
>         at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
>         at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:296)
>         at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
>         at ij.macro.Functions.call(Functions.java:4070)
>         at ij.macro.Functions.getStringFunction(Functions.java:272)
>         at ij.macro.Interpreter.getStringTerm(Interpreter.java:1293)
>         at ij.macro.Interpreter.getString(Interpreter.java:1272)
>         at ij.macro.Interpreter.doStatement(Interpreter.java:281)
>         at ij.macro.Interpreter.doStatements(Interpreter.java:218)
>         at ij.macro.Interpreter.run(Interpreter.java:115)
>         at ij.macro.Interpreter.run(Interpreter.java:85)
>         at ij.macro.Interpreter.run(Interpreter.java:96)
>         at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:155)
>         at ij.plugin.Macro_Runner.runMacroFromJar(Macro_Runner.java:198)
>         at ij.plugin.Macro_Runner.run(Macro_Runner.java:44)
>         at ij.IJ.runPlugIn(IJ.java:187)
>         at ij.Executer.runCommand(Executer.java:137)
>         at ij.Executer.run(Executer.java:66)
>         at java.lang.Thread.run(Thread.java:662)
>
>
> Could someone help me please?
>
> Thanks,
>
> David
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/JaCoP-Tools-tp5013499p5017880.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
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--
David J. Walker MSc BSc Hons
PhD Research Student
School of Psychology & Neuroscience
University of St Andrews
St Mary's Quad,
South Street,
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