how to run multiple copies of ImageJ?

[Cammer, Michael]

We used to be able to run multiple ImageJs simultaneously.  Now we cannot.  Is this a necessary change with newer versions or is there a way we may run multiple ImageJ programs simultaneously as we used to?

Thank you.

________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]


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[Nikolay]

Just copy ij.jar --> ij_1.jar, ij_2.jar, and ij_n.jar and you can run
them simultaneously.

--
Rogoshchenkov Nikolay


On Fri, Mar 1, 2013 at 2:43 PM, Cammer, Michael
<[hidden email]>wrote:

> We used to be able to run multiple ImageJs simultaneously.  Now we cannot.
>  Is this a necessary change with newer versions or is there a way we may
> run multiple ImageJ programs simultaneously as we used to?
>
> Thank you.
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Nikolay]

:) I'm sorry, it's not neccessary. Just run ij.jar, instead of ImageJ.exe
(if you are under Windows).

--
Rogoshchenkov Nikolay


On Fri, Mar 1, 2013 at 2:55 PM, Nikolay Rogoshchenkov
<[hidden email]>wrote:

> Just copy ij.jar --> ij_1.jar, ij_2.jar, and ij_n.jar and you can run
> them simultaneously.
>
> --
> Rogoshchenkov Nikolay
>
>
> On Fri, Mar 1, 2013 at 2:43 PM, Cammer, Michael <
> [hidden email]> wrote:
>
>> We used to be able to run multiple ImageJs simultaneously.  Now we
>> cannot.  Is this a necessary change with newer versions or is there a way
>> we may run multiple ImageJ programs simultaneously as we used to?
>>
>> Thank you.
>>
>> ________________________________________________________
>> Michael Cammer, Assistant Research Scientist
>> Skirball Institute of Biomolecular Medicine
>> Lab: [phone]  Cell: [phone]
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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

[Cammer, Michael]

Thank you!  Command line works fine.

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Nikolay Rogoshchenkov
Sent: Friday, March 01, 2013 2:58 PM
To: [hidden email]
Subject: Re: how to run multiple copies of ImageJ?

:) I'm sorry, it's not neccessary. Just run ij.jar, instead of ImageJ.exe (if you are under Windows).

--
Rogoshchenkov Nikolay


On Fri, Mar 1, 2013 at 2:55 PM, Nikolay Rogoshchenkov
<[hidden email]>wrote:

> Just copy ij.jar --> ij_1.jar, ij_2.jar, and ij_n.jar and you can run
> them simultaneously.
>
> --
> Rogoshchenkov Nikolay
>
>
> On Fri, Mar 1, 2013 at 2:43 PM, Cammer, Michael <
> [hidden email]> wrote:
>
>> We used to be able to run multiple ImageJs simultaneously.  Now we
>> cannot.  Is this a necessary change with newer versions or is there a
>> way we may run multiple ImageJ programs simultaneously as we used to?
>>
>> Thank you.
>>
>> ________________________________________________________
>> Michael Cammer, Assistant Research Scientist Skirball Institute of
>> Biomolecular Medicine
>> Lab: [phone]  Cell: [phone]
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
>

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[Ion Andronache]

Dear Sir,
You can download and use the Fiji version without jre (http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip)   but until  must be installed separatelly jre (jre-7u15-windows-x64.exe form site:  http://www.oracle.com/technetwork/java/javase/downloads/jre7-downloads-1880261.html). In this situatiion update works.
About second email: yes, is possible to use more version of ImageJ, but  you must use jar version, no exe version. You must download and use http://developer.imagej.net/2012/12/27/imagej-v200-beta6 toghether with http://jenkins.imagej.net/job/Stable-Fiji/lastSuccessfulBuild/artifact/fiji-nojre.zip and http://en.sourceforge.jp/frs/g_redir.php?m=jaist&f=%2Fimageja%2Fimageja%2F1.45q%2Fij-1.45q.jar or http://rsb.info.nih.gov/ij/ij.jar
Respectfuly,
Ion Andronache.



01.03.2013, 21:43, "Cammer, Michael" <[hidden email]>:

> We used to be able to run multiple ImageJs simultaneously.  Now we cannot.  Is this a necessary change with newer versions or is there a way we may run multiple ImageJ programs simultaneously as we used to?
>
> Thank you.
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[dscho]

Hi Michael,

On Fri, 1 Mar 2013, Cammer, Michael wrote:

> We used to be able to run multiple ImageJs simultaneously.  Now we
> cannot.  Is this a necessary change with newer versions or is there a
> way we may run multiple ImageJ programs simultaneously as we used to?

There is an option in Edit>Options>Misc... called "Run single instance
listener". If you check this off, you should be able to run multiple
instances.

It is not necessary to copy ij.jar to run multiple instances.

You can also use the command-line option -port0 to force this behavior.

Ciao,
Johannes

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[Nikolay]

"Run single instance listener" did not not works for me, if use ImageJ.exe.

--
Rogoshchenkov Nikolay


On Fri, Mar 1, 2013 at 3:24 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Michael,
>
> On Fri, 1 Mar 2013, Cammer, Michael wrote:
>
> > We used to be able to run multiple ImageJs simultaneously.  Now we
> > cannot.  Is this a necessary change with newer versions or is there a
> > way we may run multiple ImageJ programs simultaneously as we used to?
>
> There is an option in Edit>Options>Misc... called "Run single instance
> listener". If you check this off, you should be able to run multiple
> instances.
>
> It is not necessary to copy ij.jar to run multiple instances.
>
> You can also use the command-line option -port0 to force this behavior.
>
> Ciao,
> Johannes
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[damienrj]

Hello Johannes,

I am using Fiji on a mac, and do not see the option you mentioned. Is there a way to get two instances to work on the mac?

Best,
Damien

[cudmore]

I am also trying to run multiple instances of Fiji/ImageJ on the mac and can not get it working.

There is no 'Run single instance listener' available in 'Edit>Options>Misc...'

I tried running Fiji from the command line using '/Fiji.app/Contents/MacOS/ImageJ-macosx --allow-multiple'. This does not work either and I get '[INFO] Detected existing ImageJ; passing arguments along' at my command prompt.

Fiji version: 2.0.0-rc-49/1.51d, Build e01a259e5d, Date 2016-05-06

I am tring to run multiple instances of a plugin so I can make my batch processing faster. In particular I want to run MultiStackReg on a number of .tif files at the same time. It appears MultiStackReg (and the underlying Stackreg) is not multithread aware? This is why I am trying to run multiple copies of Fiji at the same time.

How can we run multiple instance of fiji at the same time? I want to do this from a python script as follows. 'testspawn_.py' is my fiji code that will call MultiStackReg.

    import subprocess

    fijipath = '/Users/cudmore/Fiji_20160914.app/Contents/MacOS/ImageJ-macosx'
    switches = '--run' # do not use -macro
    plugin = '/mydirectory/testspawn_.py'
    args = 'tiffile="mytif.tif"'
    subprocess.Popen([fijipath, switches, plugin, args])

bob

[Brandon Hurr]

I do this when I have similar needs too. I split the images into separate
folders using the following:

#takes files in a directory and breaks them up into folders based upon your
number (1000 files per folder)

ls|xargs -n 1000|awk ' {i++;system("mkdir dir"i);system("mv "$0" -t dir"i)}'

Then I created multiple folders (ImageJ 1, ImageJ 2, etc...) and ran each
one with the same macro. It's not automated like you want, but it saves a
lot of time, especially if you have a 4+ core chip.

Brandon

On Sun, Oct 9, 2016 at 1:10 PM, cudmore <[hidden email]> wrote:

> I am also trying to run multiple instances of Fiji/ImageJ on the mac and
> can
> not get it working.
>
> There is no 'Run single instance listener' available in
> 'Edit>Options>Misc...'
>
> I tried running Fiji from the command line using
> '/Fiji.app/Contents/MacOS/ImageJ-macosx --allow-multiple'. This does not
> work either and I get '[INFO] Detected existing ImageJ; passing arguments
> along' at my command prompt.
>
> Fiji version: 2.0.0-rc-49/1.51d, Build e01a259e5d, Date 2016-05-06
>
> I am tring to run multiple instances of a plugin so I can make my batch
> processing faster. In particular I want to run MultiStackReg on a number of
> .tif files at the same time. It appears MultiStackReg (and the underlying
> Stackreg) is not multithread aware? This is why I am trying to run multiple
> copies of Fiji at the same time.
>
> How can we run multiple instance of fiji at the same time? I want to do
> this
> from a python script as follows. 'testspawn_.py' is my fiji code that will
> call MultiStackReg.
>
>     import subprocess
>
>     fijipath =
> '/Users/cudmore/Fiji_20160914.app/Contents/MacOS/ImageJ-macosx'
>     switches = '--run' # do not use -macro
>     plugin = '/mydirectory/testspawn_.py'
>     args = 'tiffile="mytif.tif"'
>     subprocess.Popen([fijipath, switches, plugin, args])
>
> bob
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.
> com/how-to-run-multiple-copies-of-ImageJ-tp5001939p5017326.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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