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new linux version

Johan Henriksson-2
I have switched the distribution of ubuntu/debian packages to my own repository. This means that the package will be available from synaptic, and so will updates. dependencies are taken care of automatically (by synaptic) so overall there should be less headache. I also now compile for both i386 and ***amd64*** (ie also normal intel)

this is tested on ubuntu 9.10. if anyone runs into problems with debian, let me know

http://endrov.net/downloadPublic/debs/micromanager/
^ current URL from micromanager website

/Johan

--
-----------------------------------------------------------
Johan Henriksson
PhD student, Karolinska Institutet
http://mahogny.areta.org  http://www.endrov.net

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Re: new linux version

Philippe GENDRE
Hello Johan,

I followed your instructions to install µManager on my PC.

OS is Ubuntu 9.10 freshly installed.

I have installed from Synaptic the following packages :
- imagej (version 1.43b-1ubuntu1)
- micromanager-ij (version 1.43a)
- micromanager (version 1.43a).

When I launch imagej, I have a message "This plugin requires ImageJ 1.43j or later" and the µmanager studio doesn't open.

If I launch µManager from the plugins menu of ImageJ, µManager starts and works ! But I meet some problems which seems to be link with the management of 32 bits images.

The object of this email concerns the message "This plugin requires ImageJ 1.43j or later". I searched for Image 1.43j for Linux but I did not find it.

Could you help me to improve the behaviour of µManager launching ?

Best regards.

Philippe

2010/1/8 Johan Henriksson <[hidden email]>
I have switched the distribution of ubuntu/debian packages to my own repository. This means that the package will be available from synaptic, and so will updates. dependencies are taken care of automatically (by synaptic) so overall there should be less headache. I also now compile for both i386 and ***amd64*** (ie also normal intel)

this is tested on ubuntu 9.10. if anyone runs into problems with debian, let me know

http://endrov.net/downloadPublic/debs/micromanager/
^ current URL from micromanager website

/Johan

--
-----------------------------------------------------------
Johan Henriksson
PhD student, Karolinska Institutet
http://mahogny.areta.org  http://www.endrov.net

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Re: new linux version

Daniel Jones-3
Hi Phillipe,

When you launch ImageJ, go to Help -> Update ImageJ. This should allow
you to get the most recent version. I'm not sure why it's not just
available on ImageJ's website.

Daniel

On Wed, Jan 13, 2010 at 10:50 AM, Philippe GENDRE <[hidden email]> wrote:

> Hello Johan,
>
> I followed your instructions to install µManager on my PC.
>
> OS is Ubuntu 9.10 freshly installed.
>
> I have installed from Synaptic the following packages :
> - imagej (version 1.43b-1ubuntu1)
> - micromanager-ij (version 1.43a)
> - micromanager (version 1.43a).
>
> When I launch imagej, I have a message "This plugin requires ImageJ 1.43j or
> later" and the µmanager studio doesn't open.
>
> If I launch µManager from the plugins menu of ImageJ, µManager starts and
> works ! But I meet some problems which seems to be link with the management
> of 32 bits images.
>
> The object of this email concerns the message "This plugin requires ImageJ
> 1.43j or later". I searched for Image 1.43j for Linux but I did not find it.
>
> Could you help me to improve the behaviour of µManager launching ?
>
> Best regards.
>
> Philippe
>
> 2010/1/8 Johan Henriksson <[hidden email]>
>>
>> I have switched the distribution of ubuntu/debian packages to my own
>> repository. This means that the package will be available from synaptic, and
>> so will updates. dependencies are taken care of automatically (by synaptic)
>> so overall there should be less headache. I also now compile for both i386
>> and ***amd64*** (ie also normal intel)
>>
>> this is tested on ubuntu 9.10. if anyone runs into problems with debian,
>> let me know
>>
>> http://endrov.net/downloadPublic/debs/micromanager/
>> ^ current URL from micromanager website
>>
>> /Johan
>>
>> --
>> -----------------------------------------------------------
>> Johan Henriksson
>> PhD student, Karolinska Institutet
>> http://mahogny.areta.org  http://www.endrov.net
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast and
>> easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>
>

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Re: new linux version

Nico Stuurman
Administrator
> When you launch ImageJ, go to Help -> Update ImageJ. This should allow
> you to get the most recent version. I'm not sure why it's not just
> available on ImageJ's website.

http://rsb.info.nih.gov/ij/ij.jar



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Re: new linux version + bugs for nico(!)

Johan Henriksson-4
In reply to this post by Philippe GENDRE
thanks, you are right. you can get a newer version of imagej from
unstable Debian:

http://packages.debian.org/sid/all/imagej/download

this revealed some more problems with the config creator though (just
pulled from svn)

==========

mmstudio cannot find the html help files. digging the source:

checking src/org/micromanager/conf/ConfiguratorDlg.java

         File curDir = new File(".");
         String helpFileName = pages_[curPage_].getHelpFileName();
         if (helpFileName == null)
            return;
         helpURL = new java.net.URL("file:///" +
curDir.getCanonicalPath() + "/" + helpFileName);
         if (helpURL != null)
            helpTextPane_.setPage(helpURL);

this won't do; File(".") can be anywhere for unix imagej, it need not be
the imagej root directory. unless there is a chdir() I am missing?
checking the windows version (wine), I see that all the html files are
in the root. I think this is rather dirty :/

on windows/mac I would prefer "plugins/Micro-manager/html"
on unix "/usr/share/micro-manager/html/"

could this be changed? currently not so needed for mac/windows, but by
all means needed for unix. currently the jars and shared objects go to
different places (/usr/lib/micro-manager and /usr/share/java); neither
of these is a good place for data files, which is what
/usr/share/<program> is for.

ALTERNATIVE, OS-independent, less of a hassle:
put the html-files into MMJ_.jar. use something like
Xyz.class.getResource("foo.html")
to get the content (Xyz class in the same directory/package as the html).



====

next bug, have not investigated a lot but managed to get a demo camera &
shutter. success upon init, but:

LOG(2010-01-13T23:43:30.093899, 8636, 140584515463440:): All devices
unloaded.
LOG(2010-01-13T23:43:31.079110, 8636, 140584515463440:): Device DCam
loaded from DemoCamera and labeled as DCam
LOG(2010-01-13T23:43:31.079138, 8636, 140584515463440:): Device DCam set
as default camera.
LOG(2010-01-13T23:43:31.079298, 8636, 140584515463440:): Device DShutter
loaded from DemoCamera and labeled as DShutter
LOG(2010-01-13T23:43:31.079314, 8636, 140584515463440:): Device DShutter
set as default shutter.
LOG(2010-01-13T23:43:31.079352, 8636, 140584515463440:): Auto shutter ON.
LOG(2010-01-13T23:43:31.079457, 8636, 140584515463440:): System state
cache updated.

LOG(2010-01-13T23:43:39.888323, 8636, 140584515463440:): Error occured.
Device MMCore::loadDevice. Error code: 16
DCam
Specified device label already in use.

LOG(2010-01-13T23:43:39.888419, 8636, 140584515463440:): Error occured.
Device MMCore::loadDevice. Error code: 16
DShutter
Specified device label already in use.

LOG(2010-01-13T23:43:39.888473, 8636, 140584515463440:): Auto shutter ON.
LOG(2010-01-13T23:43:40.020561, 8636, 140584515463440:): >
Error code: 39
Line 7: Device,DCam,DemoCamera,DCam
Error code: 16
DCam
Specified device label already in use.

Line 8: Device,DShutter,DemoCamera,DShutter
Error code: 16
DShutter
Specified device label already in use.


 in Thread[AWT-EventQueue-0,6,main]
java.lang.Exception: Error code: 39
Line 7: Device,DCam,DemoCamera,DCam
Error code: 16
DCam
Specified device label already in use.

Line 8: Device,DShutter,DemoCamera,DShutter
Error code: 16
DShutter
Specified device label already in use.


/Johan



Philippe GENDRE wrote:

> Hello Johan,
>
> I followed your instructions to install µManager on my PC.
>
> OS is Ubuntu 9.10 freshly installed.
>
> I have installed from Synaptic the following packages :
> - imagej (version 1.43b-1ubuntu1)
> - micromanager-ij (version 1.43a)
> - micromanager (version 1.43a).
>
> When I launch imagej, I have a message "This plugin requires ImageJ 1.43j or
> later" and the µmanager studio doesn't open.
>
> If I launch µManager from the plugins menu of ImageJ, µManager starts and
> works ! But I meet some problems which seems to be link with the management
> of 32 bits images.
>
> The object of this email concerns the message "This plugin requires ImageJ
> 1.43j or later". I searched for Image 1.43j for Linux but I did not find it.
>
> Could you help me to improve the behaviour of µManager launching ?
>
> Best regards.
>
> Philippe
>
> 2010/1/8 Johan Henriksson <[hidden email]>
>
>  
>> I have switched the distribution of ubuntu/debian packages to my own
>> repository. This means that the package will be available from synaptic, and
>> so will updates. dependencies are taken care of automatically (by synaptic)
>> so overall there should be less headache. I also now compile for both i386
>> and ***amd64*** (ie also normal intel)
>>
>> this is tested on ubuntu 9.10. if anyone runs into problems with debian,
>> let me know
>>
>> http://endrov.net/downloadPublic/debs/micromanager/
>> ^ current URL from micromanager website
>>
>> /Johan
>>
>> --
>> -----------------------------------------------------------
>> Johan Henriksson
>> PhD student, Karolinska Institutet
>> http://mahogny.areta.org  http://www.endrov.net
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast and
>> easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>>    
>
>  
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev 
> ------------------------------------------------------------------------
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>  


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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Re: new linux version + bugs for nico(!)

Philippe GENDRE
The launching problem is solved with a newer version of ij.jar.

Thanks at all.

As mentionned in my first email, I meet a problem with 32 bits images but this problem is probably an imagej (or java) bug. I have never met this problem with ImageJ+µManager under Windows OS.

If I generate a 32 bits image (by different ways : in a plugin or from the imagej menu), it is impossible to close it after :
- clicking on the "close" icon on the image window opens a dialog box with "Save changes to .... ?" but the buttons (Yes, No, Cancel) of the dialog box seems to be inactive except that the dialog box is closed,
- Imagej cannot be closed,

Need help. Maybe I have to report on ImageJ mailing list ?

Philippe
- I need to restart the PC.


 



2010/1/14 Johan Henriksson <[hidden email]>
thanks, you are right. you can get a newer version of imagej from
unstable Debian:

http://packages.debian.org/sid/all/imagej/download

this revealed some more problems with the config creator though (just
pulled from svn)

==========

mmstudio cannot find the html help files. digging the source:

checking src/org/micromanager/conf/ConfiguratorDlg.java

        File curDir = new File(".");
        String helpFileName = pages_[curPage_].getHelpFileName();
        if (helpFileName == null)
           return;
        helpURL = new java.net.URL("file:///" +
curDir.getCanonicalPath() + "/" + helpFileName);
        if (helpURL != null)
           helpTextPane_.setPage(helpURL);

this won't do; File(".") can be anywhere for unix imagej, it need not be
the imagej root directory. unless there is a chdir() I am missing?
checking the windows version (wine), I see that all the html files are
in the root. I think this is rather dirty :/

on windows/mac I would prefer "plugins/Micro-manager/html"
on unix "/usr/share/micro-manager/html/"

could this be changed? currently not so needed for mac/windows, but by
all means needed for unix. currently the jars and shared objects go to
different places (/usr/lib/micro-manager and /usr/share/java); neither
of these is a good place for data files, which is what
/usr/share/<program> is for.

ALTERNATIVE, OS-independent, less of a hassle:
put the html-files into MMJ_.jar. use something like
Xyz.class.getResource("foo.html")
to get the content (Xyz class in the same directory/package as the html).



====

next bug, have not investigated a lot but managed to get a demo camera &
shutter. success upon init, but:

LOG(2010-01-13T23:43:30.093899, 8636, 140584515463440:): All devices
unloaded.
LOG(2010-01-13T23:43:31.079110, 8636, 140584515463440:): Device DCam
loaded from DemoCamera and labeled as DCam
LOG(2010-01-13T23:43:31.079138, 8636, 140584515463440:): Device DCam set
as default camera.
LOG(2010-01-13T23:43:31.079298, 8636, 140584515463440:): Device DShutter
loaded from DemoCamera and labeled as DShutter
LOG(2010-01-13T23:43:31.079314, 8636, 140584515463440:): Device DShutter
set as default shutter.
LOG(2010-01-13T23:43:31.079352, 8636, 140584515463440:): Auto shutter ON.
LOG(2010-01-13T23:43:31.079457, 8636, 140584515463440:): System state
cache updated.

LOG(2010-01-13T23:43:39.888323, 8636, 140584515463440:): Error occured.
Device MMCore::loadDevice. Error code: 16
DCam
Specified device label already in use.

LOG(2010-01-13T23:43:39.888419, 8636, 140584515463440:): Error occured.
Device MMCore::loadDevice. Error code: 16
DShutter
Specified device label already in use.

LOG(2010-01-13T23:43:39.888473, 8636, 140584515463440:): Auto shutter ON.
LOG(2010-01-13T23:43:40.020561, 8636, 140584515463440:): >
Error code: 39
Line 7: Device,DCam,DemoCamera,DCam
Error code: 16
DCam
Specified device label already in use.

Line 8: Device,DShutter,DemoCamera,DShutter
Error code: 16
DShutter
Specified device label already in use.


 in Thread[AWT-EventQueue-0,6,main]
java.lang.Exception: Error code: 39
Line 7: Device,DCam,DemoCamera,DCam
Error code: 16
DCam
Specified device label already in use.

Line 8: Device,DShutter,DemoCamera,DShutter
Error code: 16
DShutter
Specified device label already in use.


/Johan



Philippe GENDRE wrote:
> Hello Johan,
>
> I followed your instructions to install µManager on my PC.
>
> OS is Ubuntu 9.10 freshly installed.
>
> I have installed from Synaptic the following packages :
> - imagej (version 1.43b-1ubuntu1)
> - micromanager-ij (version 1.43a)
> - micromanager (version 1.43a).
>
> When I launch imagej, I have a message "This plugin requires ImageJ 1.43j or
> later" and the µmanager studio doesn't open.
>
> If I launch µManager from the plugins menu of ImageJ, µManager starts and
> works ! But I meet some problems which seems to be link with the management
> of 32 bits images.
>
> The object of this email concerns the message "This plugin requires ImageJ
> 1.43j or later". I searched for Image 1.43j for Linux but I did not find it.
>
> Could you help me to improve the behaviour of µManager launching ?
>
> Best regards.
>
> Philippe
>
> 2010/1/8 Johan Henriksson <[hidden email]>
>
>
>> I have switched the distribution of ubuntu/debian packages to my own
>> repository. This means that the package will be available from synaptic, and
>> so will updates. dependencies are taken care of automatically (by synaptic)
>> so overall there should be less headache. I also now compile for both i386
>> and ***amd64*** (ie also normal intel)
>>
>> this is tested on ubuntu 9.10. if anyone runs into problems with debian,
>> let me know
>>
>> http://endrov.net/downloadPublic/debs/micromanager/
>> ^ current URL from micromanager website
>>
>> /Johan
>>
>> --
>> -----------------------------------------------------------
>> Johan Henriksson
>> PhD student, Karolinska Institutet
>> http://mahogny.areta.org  http://www.endrov.net
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Verizon Developer Community
>> Take advantage of Verizon's best-in-class app development support
>> A streamlined, 14 day to market process makes app distribution fast and
>> easy
>> Join now and get one step closer to millions of Verizon customers
>> http://p.sf.net/sfu/verizon-dev2dev
>> _______________________________________________
>> micro-manager-general mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>>
>>
>>
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> ------------------------------------------------------------------------
>
> _______________________________________________
> micro-manager-general mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/micro-manager-general
>


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
_______________________________________________
micro-manager-general mailing list
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https://lists.sourceforge.net/lists/listinfo/micro-manager-general


------------------------------------------------------------------------------
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world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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Re: new linux version + bugs for nico(!)

Nico Stuurman-4
In reply to this post by Johan Henriksson-4
> mmstudio cannot find the html help files. digging the source:
>
> this won't do; File(".") can be anywhere for unix imagej, it need  
> not be
> the imagej root directory. unless there is a chdir() I am missing?
> checking the windows version (wine), I see that all the html files are
> in the root. I think this is rather dirty :/
>
> ALTERNATIVE, OS-independent, less of a hassle:
> put the html-files into MMJ_.jar. use something like
> Xyz.class.getResource("foo.html")
> to get the content (Xyz class in the same directory/package as the  
> html).

I like that solution.

> next bug, have not investigated a lot but managed to get a demo  
> camera &
> shutter. success upon init, but:
>
>
> LOG(2010-01-13T23:43:39.888323, 8636, 140584515463440:): Error  
> occured.
> Device MMCore::loadDevice. Error code: 16
> DCam
> Specified device label already in use.

Is this with a configuration file that you created with a MM version  
of a few days ago?  If so, either delete it, or replace all occurences  
of "PropertyItem" in that file with "Property".

Best,

Nico


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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Re: new linux version + bugs for nico(!)

Nico Stuurman-4
In reply to this post by Philippe GENDRE
> As mentionned in my first email, I meet a problem with 32 bits  
> images but this problem is probably an imagej (or java) bug. I have  
> never met this problem with ImageJ+µManager under Windows OS.
>
> If I generate a 32 bits image (by different ways : in a plugin or  
> from the imagej menu), it is impossible to close it after :
> - clicking on the "close" icon on the image window opens a dialog  
> box with "Save changes to .... ?" but the buttons (Yes, No, Cancel)  
> of the dialog box seems to be inactive except that the dialog box is  
> closed,
> - Imagej cannot be closed,

Sounds like an ImageJ bug to me.  Try running ImageJ without starting  
Micro-Manager and see if the same problem occurs.  Then, start ImageJ  
from the command line (java -cp ij.jar ij.ImageJ) and look for output  
in the terminal. If it is indeed an ImageJ problem, it is best to  
report this on the ImageJ list.

Best,

Nico


------------------------------------------------------------------------------
Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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Re: new linux version + bugs for nico(!)

Philippe GENDRE
Hello Nico,

Starting ImageJ from the terminal  leads to the same result : that is the problem I mentionned yesterday. There are no outputs on the terminal. Closing the terminal with the Imagej active processus closes Imagej.

I have installed another version of ImageJ (without Micro-Manager) in my home files, I meet the same problem.

Let me know if I have to report to Imagej mailing list because I'm a little surprised that nobody reports this problem before.

Best regards,

Philippe



2010/1/14 Nico Stuurman <[hidden email]>
> As mentionned in my first email, I meet a problem with 32 bits
> images but this problem is probably an imagej (or java) bug. I have
> never met this problem with ImageJ+µManager under Windows OS.
>
> If I generate a 32 bits image (by different ways : in a plugin or
> from the imagej menu), it is impossible to close it after :
> - clicking on the "close" icon on the image window opens a dialog
> box with "Save changes to .... ?" but the buttons (Yes, No, Cancel)
> of the dialog box seems to be inactive except that the dialog box is
> closed,
> - Imagej cannot be closed,

Sounds like an ImageJ bug to me.  Try running ImageJ without starting
Micro-Manager and see if the same problem occurs.  Then, start ImageJ
from the command line (java -cp ij.jar ij.ImageJ) and look for output
in the terminal. If it is indeed an ImageJ problem, it is best to
report this on the ImageJ list.

Best,

Nico


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Re: new linux version + bugs for nico(!)

Nico Stuurman
Administrator
> Starting ImageJ from the terminal  leads to the same result : that is the problem I mentionned yesterday. There are no outputs on the terminal. Closing the terminal with the Imagej active processus closes Imagej.
>
> I have installed another version of ImageJ (without Micro-Manager) in my home files, I meet the same problem.
>
> Let me know if I have to report to Imagej mailing list because I'm a little surprised that nobody reports this problem before.

Yes, this is an ImageJ issue, and not something we can address in the Micro-Manager code.

best,

Nico


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Re: new linux version + bugs for nico(!)

Philippe GENDRE
Hello,

Some news regarding a problem with the Linux version of µManager (+ImageJ) that I have posted last week.

I have reported this problem to the ImageJ mailing list, see https://list.nih.gov/cgi-bin/wa?A1=ind1001&L=imagej#44.

Best regards,

Philippe

2010/1/14 Nico Stuurman <[hidden email]>
> Starting ImageJ from the terminal  leads to the same result : that is the problem I mentionned yesterday. There are no outputs on the terminal. Closing the terminal with the Imagej active processus closes Imagej.
>
> I have installed another version of ImageJ (without Micro-Manager) in my home files, I meet the same problem.
>
> Let me know if I have to report to Imagej mailing list because I'm a little surprised that nobody reports this problem before.

Yes, this is an ImageJ issue, and not something we can address in the Micro-Manager code.

best,

Nico


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Throughout its 18-year history, RSA Conference consistently attracts the
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attendees to learn about information security's most important issues through
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