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Mac - java - X11

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Paolo Maiuri

Mac - java - X11

Dear Users,

I tried to connect via ssh -X from a Linux computer to a Mac OS X server. Some easy test, like xclock, worked fine, but when I tried to run ImageJ I got this message:

java -jar ij.jar
Exception in thread "main" java.lang.InternalError: Can't connect to window server - not enough permissions.
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1822)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1723)
at java.lang.Runtime.loadLibrary0(Runtime.java:822)
at java.lang.System.loadLibrary(System.java:993)
at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.NativeLibLoader.loadLibraries(NativeLibLoader.java:38)
at sun.awt.DebugHelper.<clinit>(DebugHelper.java:29)
at java.awt.Component.<clinit>(Component.java:547)

Does somebady know were is the problem or have any suggestion?

Thanks,
Paolo.

simon andrews (BI)

Re: Mac - java - X11

On 14 Oct 2008, at 14:07, Paolo Maiuri wrote:

> Dear Users,
>
> I tried to connect via ssh -X from a Linux computer to a Mac OS X
> server. Some easy test, like xclock, worked fine, but when I tried
> to run ImageJ I got this message:
>
> java -jar ij.jar
> Exception in thread "main" java.lang.InternalError: Can't connect
> to window server - not enough permissions.

You might need to use trusted X. Try ssh -Y.

Simon.

Paolo Maiuri

Re: Mac - java - X11

Thanks Simon for the quick reply,
actually I already tried it without any change.....

Thanks,
Paolo.

----- Original Message -----
From: "Simon Andrews" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, October 14, 2008 3:18 PM
Subject: Re: Mac - java - X11

> On 14 Oct 2008, at 14:07, Paolo Maiuri wrote:
>
>> Dear Users,
>>
>> I tried to connect via ssh -X from a Linux computer to a Mac OS X
>> server. Some easy test, like xclock, worked fine, but when I tried
>> to run ImageJ I got this message:
>>
>> java -jar ij.jar
>> Exception in thread "main" java.lang.InternalError: Can't connect
>> to window server - not enough permissions.
>
> You might need to use trusted X. Try ssh -Y.
>
> Simon.

karo03

Re: Mac - java - X11

In reply to this post by Paolo Maiuri

Typically a server does not have any active window open, nobody have
to be loggeg in! Where should ImageJ open its window? Try a remote
Desktop or VNC Connection!
Regards
Karsten

Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:

> I tried to connect via ssh -X from a Linux computer to a Mac OS X
> server. Some easy test, like xclock, worked fine, but when I tried
> to run ImageJ I got this message:
>
> java -jar ij.jar
> Exception in thread "main" java.lang.InternalError: Can't connect to
> window server - not enough permissions.

Stephan Saalfeld

Re: Mac - java - X11

Karsten,

ImageJ invoked from inside an ssh session with X forwarding opens its
window at the display of the session (as any other program does as
well). This worked for me for Linux to Linux and Windows to Linux
connections. VNC is nice but not what Paolo was asking for.

Paolo,

actually Java is complaining about missing permissions which I don't
understand. Is your DISPLAY set properly?

echo $DISPLAY

should say something like

localhost:10.0

Otherwise, sorry for not being able to help you :(

Best regards,
Stephan

On Tue, 2008-10-14 at 15:51 +0200, Karsten Rodenacker wrote:

> Typically a server does not have any active window open, nobody have
> to be loggeg in! Where should ImageJ open its window? Try a remote
> Desktop or VNC Connection!
> Regards
> Karsten
>
> Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:
>
> > I tried to connect via ssh -X from a Linux computer to a Mac OS X
> > server. Some easy test, like xclock, worked fine, but when I tried
> > to run ImageJ I got this message:
> >
> > java -jar ij.jar
> > Exception in thread "main" java.lang.InternalError: Can't connect to
> > window server - not enough permissions.

Paolo Maiuri

Re: Mac - java - X11

Thanks Stephan,
yes, my DISPLAY is set properly:
"
echo $DISPLAY
localhost:11.0
"
and xclock and xcalc work correctly.

Regards,
Paolo.

----- Original Message -----
From: "Stephan Saalfeld" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, October 14, 2008 4:11 PM
Subject: Re: Mac - java - X11

> Karsten,
>
> ImageJ invoked from inside an ssh session with X forwarding opens its
> window at the display of the session (as any other program does as
> well). This worked for me for Linux to Linux and Windows to Linux
> connections. VNC is nice but not what Paolo was asking for.
>
> Paolo,
>
> actually Java is complaining about missing permissions which I don't
> understand. Is your DISPLAY set properly?
>
> echo $DISPLAY
>
> should say something like
>
> localhost:10.0
>
> Otherwise, sorry for not being able to help you :(
>
> Best regards,
> Stephan
>
>
> On Tue, 2008-10-14 at 15:51 +0200, Karsten Rodenacker wrote:
>> Typically a server does not have any active window open, nobody have
>> to be loggeg in! Where should ImageJ open its window? Try a remote
>> Desktop or VNC Connection!
>> Regards
>> Karsten
>>
>> Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:
>>
>> > I tried to connect via ssh -X from a Linux computer to a Mac OS X
>> > server. Some easy test, like xclock, worked fine, but when I tried
>> > to run ImageJ I got this message:
>> >
>> > java -jar ij.jar
>> > Exception in thread "main" java.lang.InternalError: Can't connect to
>> > window server - not enough permissions.

karo03

Re: Mac - java - X11

In reply to this post by Stephan Saalfeld

Very interesting. "java -jar ij.jar" in a ssh -X/Y opens on my remote
Mac a MacOSX window, not X11. Possibly the cmd needs some more options
to use X11. linux to Mac is something different, what I suppose.
Karsten

Am 14.10.2008 um 16:11 schrieb Stephan Saalfeld:

> ImageJ invoked from inside an ssh session with X forwarding opens its
> window at the display of the session (as any other program does as
> well). This worked for me for Linux to Linux and Windows to Linux
> connections.

Jeffrey B. Woodward

Re: Mac - java - X11

In reply to this post by Paolo Maiuri

I believe that Java on OSX is a native Aqua application and not X
Windows application. Unfortunately, Aqua can't be tunneled (to my
knowledge). See this thread:
http://forums.macosxhints.com/showthread.php?t=92457. Perhaps times have
changed and there is now a workaround.

Good luck,

-Woody

Paolo Maiuri wrote:

> Dear Users,
>
> I tried to connect via ssh -X from a Linux computer to a Mac OS X server. Some easy test, like xclock, worked fine, but when I tried to run ImageJ I got this message:
>
> java -jar ij.jar
> Exception in thread "main" java.lang.InternalError: Can't connect to window server - not enough permissions.
> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1822)
> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1723)
> at java.lang.Runtime.loadLibrary0(Runtime.java:822)
> at java.lang.System.loadLibrary(System.java:993)
> at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
> at java.security.AccessController.doPrivileged(Native Method)
> at sun.awt.NativeLibLoader.loadLibraries(NativeLibLoader.java:38)
> at sun.awt.DebugHelper.<clinit>(DebugHelper.java:29)
> at java.awt.Component.<clinit>(Component.java:547)
>
> Does somebady know were is the problem or have any suggestion?
>
> Thanks,
> Paolo.
>
>
>

Mathieu Marchand-2

Re: Mac - java - X11

You may want to try using SoyLatte on your mac server, a X11 mac port
of BSD java 6:
http://landonf.bikemonkey.org/static/soylatte/

I don't know how much SoyLatte is compatible with imageJ

MM

On Tue, Oct 14, 2008 at 10:31 AM, Jeffrey B. Woodward
<[hidden email]> wrote:

> I believe that Java on OSX is a native Aqua application and not X Windows
> application. Unfortunately, Aqua can't be tunneled (to my knowledge). See
> this thread: http://forums.macosxhints.com/showthread.php?t=92457. Perhaps
> times have changed and there is now a workaround.
>
> Good luck,
>
> -Woody
>
>
> Paolo Maiuri wrote:
>>
>> Dear Users,
>>
>> I tried to connect via ssh -X from a Linux computer to a Mac OS X server.
>> Some easy test, like xclock, worked fine, but when I tried to run ImageJ I
>> got this message:
>>
>> java -jar ij.jar
>> Exception in thread "main" java.lang.InternalError: Can't connect to
>> window server - not enough permissions.
>> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
>> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1822)
>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1723)
>> at java.lang.Runtime.loadLibrary0(Runtime.java:822)
>> at java.lang.System.loadLibrary(System.java:993)
>> at
>> sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
>> at java.security.AccessController.doPrivileged(Native Method)
>> at sun.awt.NativeLibLoader.loadLibraries(NativeLibLoader.java:38)
>> at sun.awt.DebugHelper.<clinit>(DebugHelper.java:29)
>> at java.awt.Component.<clinit>(Component.java:547)
>>
>> Does somebady know were is the problem or have any suggestion?
>>
>> Thanks,
>> Paolo.
>>
>>
>>
>

--
Mathieu Marchand
--
Bio-Imaging Resource Center, The Rockefeller University
1230 York Avenue, box 209, New York, NY 10021
http://www.rockefeller.edu/bioimaging .
+1-212-327-7487 (7489 for fax)
+1-646-457-0430 (cell)

pgp public key:
http://mmarchand.googlepages.com/pgp.txt

simon andrews (BI)

Re: Mac - java - X11

In reply to this post by Paolo Maiuri

How are you launching imageJ? Have you tried referencing the jar
file directly and seeing if that works?

java -jar ij.jar

from inside the imagej install folder.

Simon.

On 14 Oct 2008, at 15:26, Paolo Maiuri wrote:

> Thanks Stephan,
> yes, my DISPLAY is set properly:
> "
> echo $DISPLAY
> localhost:11.0
> "
> and xclock and xcalc work correctly.
>
> Regards,
> Paolo.
>
>
> ----- Original Message ----- From: "Stephan Saalfeld" <saalfeld@MPI-
> CBG.DE>
> To: <[hidden email]>
> Sent: Tuesday, October 14, 2008 4:11 PM
> Subject: Re: Mac - java - X11
>
>
>> Karsten,
>> ImageJ invoked from inside an ssh session with X forwarding opens its
>> window at the display of the session (as any other program does as
>> well). This worked for me for Linux to Linux and Windows to Linux
>> connections. VNC is nice but not what Paolo was asking for.
>> Paolo,
>> actually Java is complaining about missing permissions which I don't
>> understand. Is your DISPLAY set properly?
>> echo $DISPLAY
>> should say something like
>> localhost:10.0
>> Otherwise, sorry for not being able to help you :(
>> Best regards,
>> Stephan
>> On Tue, 2008-10-14 at 15:51 +0200, Karsten Rodenacker wrote:
>>> Typically a server does not have any active window open, nobody
>>> have to be loggeg in! Where should ImageJ open its window? Try a
>>> remote Desktop or VNC Connection!
>>> Regards
>>> Karsten
>>> Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:
>>> > I tried to connect via ssh -X from a Linux computer to a Mac OS
>>> X > server. Some easy test, like xclock, worked fine, but when I
>>> tried > to run ImageJ I got this message:
>>> >
>>> > java -jar ij.jar
>>> > Exception in thread "main" java.lang.InternalError: Can't
>>> connect to > window server - not enough permissions.

Paolo Maiuri

Re: Mac - java - X11

Hi Stephan,

on the Mac computer (not via ssh, but directly at the console) 'java -jar
ij.jar' works fine..

I think that Mathieu Marchand is in the right direction, and now I am trying
his solution

Regard,
Paolo.

----- Original Message -----
From: "Simon Andrews" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, October 14, 2008 4:54 PM
Subject: Re: Mac - java - X11

> How are you launching imageJ? Have you tried referencing the jar file
> directly and seeing if that works?
>
> java -jar ij.jar
>
> from inside the imagej install folder.
>
> Simon.
>
> On 14 Oct 2008, at 15:26, Paolo Maiuri wrote:
>
>> Thanks Stephan,
>> yes, my DISPLAY is set properly:
>> "
>> echo $DISPLAY
>> localhost:11.0
>> "
>> and xclock and xcalc work correctly.
>>
>> Regards,
>> Paolo.
>>
>>
>> ----- Original Message ----- From: "Stephan Saalfeld" <saalfeld@MPI-
>> CBG.DE>
>> To: <[hidden email]>
>> Sent: Tuesday, October 14, 2008 4:11 PM
>> Subject: Re: Mac - java - X11
>>
>>
>>> Karsten,
>>> ImageJ invoked from inside an ssh session with X forwarding opens its
>>> window at the display of the session (as any other program does as
>>> well). This worked for me for Linux to Linux and Windows to Linux
>>> connections. VNC is nice but not what Paolo was asking for.
>>> Paolo,
>>> actually Java is complaining about missing permissions which I don't
>>> understand. Is your DISPLAY set properly?
>>> echo $DISPLAY
>>> should say something like
>>> localhost:10.0
>>> Otherwise, sorry for not being able to help you :(
>>> Best regards,
>>> Stephan
>>> On Tue, 2008-10-14 at 15:51 +0200, Karsten Rodenacker wrote:
>>>> Typically a server does not have any active window open, nobody have
>>>> to be loggeg in! Where should ImageJ open its window? Try a remote
>>>> Desktop or VNC Connection!
>>>> Regards
>>>> Karsten
>>>> Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:
>>>> > I tried to connect via ssh -X from a Linux computer to a Mac OS
>>>> X > server. Some easy test, like xclock, worked fine, but when I
>>>> tried > to run ImageJ I got this message:
>>>> >
>>>> > java -jar ij.jar
>>>> > Exception in thread "main" java.lang.InternalError: Can't
>>>> connect to > window server - not enough permissions.

dscho

Re: Mac - java - X11

In reply to this post by Mathieu Marchand-2

Hi,

On Tue, 14 Oct 2008, Mathieu Marchand wrote:

> You may want to try using SoyLatte on your mac server, a X11 mac port of
> BSD java 6: http://landonf.bikemonkey.org/static/soylatte/

Keep in mind that most people are not allowed as per the license to use
SoyLatte.

Ciao,
Dscho

Paolo Maiuri

thanks Re: Mac - java - X11

In reply to this post by Mathieu Marchand-2

Thanks to everybody for the kind answers, and specially to Mathieu Marchand
that solved the problem.

Best Regards,

Paolo.

----- Original Message -----
From: "Mathieu Marchand" <[hidden email]>
To: <[hidden email]>
Sent: Tuesday, October 14, 2008 4:52 PM
Subject: Re: Mac - java - X11

> You may want to try using SoyLatte on your mac server, a X11 mac port
> of BSD java 6:
> http://landonf.bikemonkey.org/static/soylatte/
>
> I don't know how much SoyLatte is compatible with imageJ
>
> MM
>
>
> On Tue, Oct 14, 2008 at 10:31 AM, Jeffrey B. Woodward
> <[hidden email]> wrote:
>> I believe that Java on OSX is a native Aqua application and not X Windows
>> application. Unfortunately, Aqua can't be tunneled (to my knowledge). See
>> this thread: http://forums.macosxhints.com/showthread.php?t=92457.
>> Perhaps
>> times have changed and there is now a workaround.
>>
>> Good luck,
>>
>> -Woody
>>
>>
>> Paolo Maiuri wrote:
>>>
>>> Dear Users,
>>>
>>> I tried to connect via ssh -X from a Linux computer to a Mac OS X
>>> server.
>>> Some easy test, like xclock, worked fine, but when I tried to run ImageJ
>>> I
>>> got this message:
>>>
>>> java -jar ij.jar
>>> Exception in thread "main" java.lang.InternalError: Can't connect to
>>> window server - not enough permissions.
>>> at java.lang.ClassLoader$NativeLibrary.load(Native Method)
>>> at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1822)
>>> at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1723)
>>> at java.lang.Runtime.loadLibrary0(Runtime.java:822)
>>> at java.lang.System.loadLibrary(System.java:993)
>>> at
>>> sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
>>> at java.security.AccessController.doPrivileged(Native Method)
>>> at sun.awt.NativeLibLoader.loadLibraries(NativeLibLoader.java:38)
>>> at sun.awt.DebugHelper.<clinit>(DebugHelper.java:29)
>>> at java.awt.Component.<clinit>(Component.java:547)
>>>
>>> Does somebady know were is the problem or have any suggestion?
>>>
>>> Thanks,
>>> Paolo.
>>>
>>>
>>>
>>
>
>
>
> --
> Mathieu Marchand
> --
> Bio-Imaging Resource Center, The Rockefeller University
> 1230 York Avenue, box 209, New York, NY 10021
> http://www.rockefeller.edu/bioimaging .
> +1-212-327-7487 (7489 for fax)
> +1-646-457-0430 (cell)
>
>
>
>
>
>
>
>
> pgp public key:
> http://mmarchand.googlepages.com/pgp.txt

Laura Lucia Prieto Godino

pixel counting in RGB stack

In reply to this post by Paolo Maiuri

Hi,

I send an email before and I got no reply...Does anybody know how to
get the pixels^3 of each of the different colors from a stack of RGB
images with a total of 8 colours?

Thank you for your help,

Lucia

This is a bit more detailed what i need to do

I have an RGB stack originated by the merge of 3 channels. Each
channel is a binary file, so the whole set of stacks only has 8
colour: red, green, blue, yellow (colocalization of red+green), white
(blue+red+green), magenta (red+blue),light blue (green+blue) and black.
I need to know how many pixels of each color i have in the total stack
so that I can calculate the volumes in µm^3 of each of the colors. I
found that with the colocalization analisys I can do this for stacks
with only 4 colours (red, green, black, yellow) ,but it only admits 2
channel not three and therefore, i coulnd't find a way of doing it
with three colors at the same time and it is especially important for
me to know the volume of the white pixels. (I know that otherwise I
could just calculate separately first red+blue, and I would get: red,
blue and magenta; and red+green, to get red, green and yellow; and
green+blue, to get light blue) but I could get a way of knowing which
one is the volume of white pixels.

As well I thought that I might be able to do it with the tool Object
counter 3D, but I don't know why it doesn't work for me, whenever I
try to use it, the following error pops out:

java.lang.ClassFormatError: Incompatible magic value -1095041334 in
class file Object_Counter3D
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
at java.lang.ClassLoader.defineClass(ClassLoader.java:520)
at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:246)
at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:209)
at ij.IJ.runUserPlugIn(IJ.java:156)
at ij.IJ.runPlugIn(IJ.java:124)
at ij.Executer.runCommand(Executer.java:104)
at ij.Executer.run(Executer.java:58)
at java.lang.Thread.run(Thread.java:613)

On 14 Oct 2008, at 16:14, Paolo Maiuri wrote:

> Hi Stephan,
>
> on the Mac computer (not via ssh, but directly at the console) 'java
> -jar ij.jar' works fine..
>
> I think that Mathieu Marchand is in the right direction, and now I
> am trying his solution
>
> Regard,
> Paolo.
>
>
> ----- Original Message ----- From: "Simon Andrews" <[hidden email]
> >
> To: <[hidden email]>
> Sent: Tuesday, October 14, 2008 4:54 PM
> Subject: Re: Mac - java - X11
>
>
>> How are you launching imageJ? Have you tried referencing the jar
>> file directly and seeing if that works?
>>
>> java -jar ij.jar
>>
>> from inside the imagej install folder.
>>
>> Simon.
>>
>> On 14 Oct 2008, at 15:26, Paolo Maiuri wrote:
>>
>>> Thanks Stephan,
>>> yes, my DISPLAY is set properly:
>>> "
>>> echo $DISPLAY
>>> localhost:11.0
>>> "
>>> and xclock and xcalc work correctly.
>>>
>>> Regards,
>>> Paolo.
>>>
>>>
>>> ----- Original Message ----- From: "Stephan Saalfeld"
>>> <saalfeld@MPI- CBG.DE>
>>> To: <[hidden email]>
>>> Sent: Tuesday, October 14, 2008 4:11 PM
>>> Subject: Re: Mac - java - X11
>>>
>>>
>>>> Karsten,
>>>> ImageJ invoked from inside an ssh session with X forwarding opens
>>>> its
>>>> window at the display of the session (as any other program does as
>>>> well). This worked for me for Linux to Linux and Windows to Linux
>>>> connections. VNC is nice but not what Paolo was asking for.
>>>> Paolo,
>>>> actually Java is complaining about missing permissions which I
>>>> don't
>>>> understand. Is your DISPLAY set properly?
>>>> echo $DISPLAY
>>>> should say something like
>>>> localhost:10.0
>>>> Otherwise, sorry for not being able to help you :(
>>>> Best regards,
>>>> Stephan
>>>> On Tue, 2008-10-14 at 15:51 +0200, Karsten Rodenacker wrote:
>>>>> Typically a server does not have any active window open, nobody
>>>>> have to be loggeg in! Where should ImageJ open its window? Try
>>>>> a remote Desktop or VNC Connection!
>>>>> Regards
>>>>> Karsten
>>>>> Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:
>>>>> > I tried to connect via ssh -X from a Linux computer to a Mac OS
>>>>> X > server. Some easy test, like xclock, worked fine, but when
>>>>> I tried > to run ImageJ I got this message:
>>>>> >
>>>>> > java -jar ij.jar
>>>>> > Exception in thread "main" java.lang.InternalError: Can't
>>>>> connect to > window server - not enough permissions.

Lucia Prieto Godino, PhD student
Department of Zoology, University of Cambridge
Downing street CB23EJ Cambridge, UK

Gluender-2

Re: pixel counting in RGB stack

Could you please be more specific.

An RGB-image--as the name implies--has only three
colours, namely red, green and blue!

How do you represent the mentioned 8 colours?

>Hi,
>
>I send an email before and I got no reply...Does
>anybody know how to get the pixels^3 of each of
>the different colors from a stack of RGB images
>with a total of 8 colours?
>
>Thank you for your help,
>
>Lucia
>
>This is a bit more detailed what i need to do
>
>I have an RGB stack originated by the merge of 3
>channels. Each channel is a binary file, so the
>whole set of stacks only has 8 colour: red,
>green, blue, yellow (colocalization of
>red+green), white (blue+red+green), magenta
>(red+blue),light blue (green+blue) and black.
>I need to know how many pixels of each color i
>have in the total stack so that I can calculate
>the volumes in µm^3 of each of the colors. I
>found that with the colocalization analisys I
>can do this for stacks with only 4 colours (red,
>green, black, yellow) ,but it only admits 2
>channel not three and therefore, i coulnd't find
>a way of doing it with three colors at the same
>time and it is especially important for me to
>know the volume of the white pixels. (I know
>that otherwise I could just calculate separately
>first red+blue, and I would get: red, blue and
>magenta; and red+green, to get red, green and
>yellow; and green+blue, to get light blue) but I
>could get a way of knowing which one is the
>volume of white pixels.
>
>As well I thought that I might be able to do it
>with the tool Object counter 3D, but I don't
>know why it doesn't work for me, whenever I try
>to use it, the following error pops out:
>
>java.lang.ClassFormatError: Incompatible magic
>value -1095041334 in class file Object_Counter3D
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:520)
> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:246)
> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:209)
> at ij.IJ.runUserPlugIn(IJ.java:156)
> at ij.IJ.runPlugIn(IJ.java:124)
> at ij.Executer.runCommand(Executer.java:104)
> at ij.Executer.run(Executer.java:58)
> at java.lang.Thread.run(Thread.java:613)
>
>Lucia Prieto Godino, PhD student
>Department of Zoology, University of Cambridge
>Downing street CB23EJ Cambridge, UK

Best
--

Herbie

------------------------
<http://www.gluender.de>

Laura Lucia Prieto Godino

Re: pixel counting in RGB stack

I create the RGB image by merging 3 different sets of stacks ( image-
> colour->RGB merge) each of which is a 8bit binary file (so the
pixels are either black or white). Therefore when I merge the 3
different stacks I assign one colour to each (red, blue and green),
because in some places of the picture the pixels overlap, I end up
having 8 different colours (red, blue, green, black, yellow (red
+green), magenta (blue+red), lgith blue (green+blue) and white (red
+blue+green)) when usuing the plugin colour counter it says number of
colours : 8. As well with the colour inspector 3D i can do it for a
single plane, but I need to know the volume for the whole set of stack.

Thank you for your help and the fast reply,

best,

lucia

On 14 Oct 2008, at 18:52, Gluender wrote:

> Could you please be more specific.
>
> An RGB-image--as the name implies--has only three colours, namely
> red, green and blue!
>
> How do you represent the mentioned 8 colours?
>
>
>> Hi,
>>
>> I send an email before and I got no reply...Does anybody know how
>> to get the pixels^3 of each of the different colors from a stack of
>> RGB images with a total of 8 colours?
>>
>> Thank you for your help,
>>
>> Lucia
>>
>> This is a bit more detailed what i need to do
>>
>> I have an RGB stack originated by the merge of 3 channels. Each
>> channel is a binary file, so the whole set of stacks only has 8
>> colour: red, green, blue, yellow (colocalization of red+green),
>> white (blue+red+green), magenta (red+blue),light blue (green+blue)
>> and black.
>> I need to know how many pixels of each color i have in the total
>> stack so that I can calculate the volumes in µm^3 of each of the
>> colors. I
>> found that with the colocalization analisys I can do this for
>> stacks with only 4 colours (red, green, black, yellow) ,but it only
>> admits 2 channel not three and therefore, i coulnd't find a way of
>> doing it with three colors at the same time and it is especially
>> important for me to know the volume of the white pixels. (I know
>> that otherwise I could just calculate separately first red+blue,
>> and I would get: red, blue and magenta; and red+green, to get red,
>> green and yellow; and green+blue, to get light blue) but I could
>> get a way of knowing which one is the volume of white pixels.
>>
>> As well I thought that I might be able to do it with the tool
>> Object counter 3D, but I don't know why it doesn't work for me,
>> whenever I try to use it, the following error pops out:
>>
>> java.lang.ClassFormatError: Incompatible magic value -1095041334 in
>> class file Object_Counter3D
>> at java.lang.ClassLoader.defineClass1(Native Method)
>> at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
>> at java.lang.ClassLoader.defineClass(ClassLoader.java:520)
>> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:246)
>> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:209)
>> at ij.IJ.runUserPlugIn(IJ.java:156)
>> at ij.IJ.runPlugIn(IJ.java:124)
>> at ij.Executer.runCommand(Executer.java:104)
>> at ij.Executer.run(Executer.java:58)
>> at java.lang.Thread.run(Thread.java:613)
>>
>> Lucia Prieto Godino, PhD student
>> Department of Zoology, University of Cambridge
>> Downing street CB23EJ Cambridge, UK
>
> Best
> --
>
> Herbie
>
> ------------------------
> <http://www.gluender.de>

Lucia Prieto Godino, PhD student
Department of Zoology, University of Cambridge
Downing street CB23EJ Cambridge, UK

Laura Lucia Prieto Godino

Re: pixel counting in RGB stack

In reply to this post by Gluender-2

I realized that I guess what i need is somethig like the voxel counter
but for RGB stacks.

Any ideas?

thanks!

On 14 Oct 2008, at 18:52, Gluender wrote:

Lucia Prieto Godino, PhD student
Department of Zoology, University of Cambridge
Downing street CB23EJ Cambridge, UK

Michael Doube

Re: pixel counting in RGB stack

In reply to this post by Laura Lucia Prieto Godino

How timely...

Lucia, you could modify the plugin I just posted so that instead of
counting between thresholds, you count the specific values, e.g. in an
array with 8 counters, or in 8 different int counters. What are the
pixel values that correspond to your colours?

Mike

Laura Lucia Prieto Godino wrote:

> I create the RGB image by merging 3 different sets of stacks ( image->
> colour->RGB merge) each of which is a 8bit binary file (so the pixels
> are either black or white). Therefore when I merge the 3 different
> stacks I assign one colour to each (red, blue and green), because in
> some places of the picture the pixels overlap, I end up having 8
> different colours (red, blue, green, black, yellow (red+green), magenta
> (blue+red), lgith blue (green+blue) and white (red+blue+green)) when
> usuing the plugin colour counter it says number of colours : 8. As well
> with the colour inspector 3D i can do it for a single plane, but I need
> to know the volume for the whole set of stack.
>
> Thank you for your help and the fast reply,
>
> best,
>
> lucia
>
> On 14 Oct 2008, at 18:52, Gluender wrote:
>
>> Could you please be more specific.
>>
>> An RGB-image--as the name implies--has only three colours, namely red,
>> green and blue!
>>
>> How do you represent the mentioned 8 colours?
>>
>>
>>> Hi,
>>>
>>> I send an email before and I got no reply...Does anybody know how to
>>> get the pixels^3 of each of the different colors from a stack of RGB
>>> images with a total of 8 colours?
>>>
>>> Thank you for your help,
>>>
>>> Lucia
>>>
>>> This is a bit more detailed what i need to do
>>>
>>> I have an RGB stack originated by the merge of 3 channels. Each
>>> channel is a binary file, so the whole set of stacks only has 8
>>> colour: red, green, blue, yellow (colocalization of red+green), white
>>> (blue+red+green), magenta (red+blue),light blue (green+blue) and black.
>>> I need to know how many pixels of each color i have in the total
>>> stack so that I can calculate the volumes in µm^3 of each of the
>>> colors. I
>>> found that with the colocalization analisys I can do this for stacks
>>> with only 4 colours (red, green, black, yellow) ,but it only admits 2
>>> channel not three and therefore, i coulnd't find a way of doing it
>>> with three colors at the same time and it is especially important for
>>> me to know the volume of the white pixels. (I know that otherwise I
>>> could just calculate separately first red+blue, and I would get: red,
>>> blue and magenta; and red+green, to get red, green and yellow; and
>>> green+blue, to get light blue) but I could get a way of knowing which
>>> one is the volume of white pixels.
>>>
>>> As well I thought that I might be able to do it with the tool Object
>>> counter 3D, but I don't know why it doesn't work for me, whenever I
>>> try to use it, the following error pops out:
>>>
>>> java.lang.ClassFormatError: Incompatible magic value -1095041334 in
>>> class file Object_Counter3D
>>> at java.lang.ClassLoader.defineClass1(Native Method)
>>> at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
>>> at java.lang.ClassLoader.defineClass(ClassLoader.java:520)
>>> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:246)
>>> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:209)
>>> at ij.IJ.runUserPlugIn(IJ.java:156)
>>> at ij.IJ.runPlugIn(IJ.java:124)
>>> at ij.Executer.runCommand(Executer.java:104)
>>> at ij.Executer.run(Executer.java:58)
>>> at java.lang.Thread.run(Thread.java:613)
>>>
>>> Lucia Prieto Godino, PhD student
>>> Department of Zoology, University of Cambridge
>>> Downing street CB23EJ Cambridge, UK
>>
>> Best
>> --
>>
>> Herbie
>>
>> ------------------------
>> <http://www.gluender.de>
>
> Lucia Prieto Godino, PhD student
> Department of Zoology, University of Cambridge
> Downing street CB23EJ Cambridge, UK

--
Dr Michael Doube BPhil BVSc PhD MRCVS
Research Associate
Department of Bioengineering
Imperial College London
South Kensington Campus
London SW7 2AZ
United Kingdom

Laura Lucia Prieto Godino

Re: pixel counting in RGB stack

yeah..thanks mike sounds perfect...just...I am new in all this
sorry...I really don't know how to change the code yet...and..what do
you mean by the question "what are the pixel values that correspond to
my colours?" If I understood properly, what i usually get is:

green red blue
green 255 0 0
red 0 255 0
blue 0 0 255
white 255 255 255
yellow 255 255 0
magenta 0 255 255

So...can you give me a little more detail on how to do it?

Thanks a lot for all your help

lucia

On 14 Oct 2008, at 20:22, Michael Doube wrote:

> mo

Lucia Prieto Godino, PhD student
Department of Zoology, University of Cambridge
Downing street CB23EJ Cambridge, UK

Wayne Rasband

Re: pixel counting in RGB stack

In reply to this post by Laura Lucia Prieto Godino

> Hi,
>
> I send an email before and I got no reply...Does anybody know how to
> get the pixels^3 of each of the different colors from a stack of RGB
> images with a total of 8 colours?

The Color Counter plugin
(http://rsb.info.nih.gov/ij/plugins/color-counter.html) will do this.

-wayne

> Thank you for your help,
>
> Lucia
>
>
>
>
> This is a bit more detailed what i need to do
>
>
> I have an RGB stack originated by the merge of 3 channels. Each
> channel is a binary file, so the whole set of stacks only has 8
> colour: red, green, blue, yellow (colocalization of red+green), white
> (blue+red+green), magenta (red+blue),light blue (green+blue) and
> black.
> I need to know how many pixels of each color i have in the total stack
> so that I can calculate the volumes in µm^3 of each of the colors. I
> found that with the colocalization analisys I can do this for stacks
> with only 4 colours (red, green, black, yellow) ,but it only admits 2
> channel not three and therefore, i coulnd't find a way of doing it
> with three colors at the same time and it is especially important for
> me to know the volume of the white pixels. (I know that otherwise I
> could just calculate separately first red+blue, and I would get: red,
> blue and magenta; and red+green, to get red, green and yellow; and
> green+blue, to get light blue) but I could get a way of knowing which
> one is the volume of white pixels.
>
> As well I thought that I might be able to do it with the tool Object
> counter 3D, but I don't know why it doesn't work for me, whenever I
> try to use it, the following error pops out:
>
> java.lang.ClassFormatError: Incompatible magic value -1095041334 in
> class file Object_Counter3D
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:675)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:520)
> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:246)
> at ij.io.PluginClassLoader.loadClass(PluginClassLoader.java:209)
> at ij.IJ.runUserPlugIn(IJ.java:156)
> at ij.IJ.runPlugIn(IJ.java:124)
> at ij.Executer.runCommand(Executer.java:104)
> at ij.Executer.run(Executer.java:58)
> at java.lang.Thread.run(Thread.java:613)
>
>
>
> On 14 Oct 2008, at 16:14, Paolo Maiuri wrote:
>
>> Hi Stephan,
>>
>> on the Mac computer (not via ssh, but directly at the console) 'java
>> -jar ij.jar' works fine..
>>
>> I think that Mathieu Marchand is in the right direction, and now I am
>> trying his solution
>>
>> Regard,
>> Paolo.
>>
>>
>> ----- Original Message ----- From: "Simon Andrews"
>> <[hidden email]>
>> To: <[hidden email]>
>> Sent: Tuesday, October 14, 2008 4:54 PM
>> Subject: Re: Mac - java - X11
>>
>>
>>> How are you launching imageJ? Have you tried referencing the jar
>>> file directly and seeing if that works?
>>>
>>> java -jar ij.jar
>>>
>>> from inside the imagej install folder.
>>>
>>> Simon.
>>>
>>> On 14 Oct 2008, at 15:26, Paolo Maiuri wrote:
>>>
>>>> Thanks Stephan,
>>>> yes, my DISPLAY is set properly:
>>>> "
>>>> echo $DISPLAY
>>>> localhost:11.0
>>>> "
>>>> and xclock and xcalc work correctly.
>>>>
>>>> Regards,
>>>> Paolo.
>>>>
>>>>
>>>> ----- Original Message ----- From: "Stephan Saalfeld"
>>>> <saalfeld@MPI- CBG.DE>
>>>> To: <[hidden email]>
>>>> Sent: Tuesday, October 14, 2008 4:11 PM
>>>> Subject: Re: Mac - java - X11
>>>>
>>>>
>>>>> Karsten,
>>>>> ImageJ invoked from inside an ssh session with X forwarding opens
>>>>> its
>>>>> window at the display of the session (as any other program does as
>>>>> well). This worked for me for Linux to Linux and Windows to Linux
>>>>> connections. VNC is nice but not what Paolo was asking for.
>>>>> Paolo,
>>>>> actually Java is complaining about missing permissions which I
>>>>> don't
>>>>> understand. Is your DISPLAY set properly?
>>>>> echo $DISPLAY
>>>>> should say something like
>>>>> localhost:10.0
>>>>> Otherwise, sorry for not being able to help you :(
>>>>> Best regards,
>>>>> Stephan
>>>>> On Tue, 2008-10-14 at 15:51 +0200, Karsten Rodenacker wrote:
>>>>>> Typically a server does not have any active window open, nobody
>>>>>> have to be loggeg in! Where should ImageJ open its window? Try a
>>>>>> remote Desktop or VNC Connection!
>>>>>> Regards
>>>>>> Karsten
>>>>>> Am 14.10.2008 um 15:07 schrieb Paolo Maiuri:
>>>>>> > I tried to connect via ssh -X from a Linux computer to a Mac OS
>>>>>> X > server. Some easy test, like xclock, worked fine, but when I
>>>>>> tried > to run ImageJ I got this message:
>>>>>> >
>>>>>> > java -jar ij.jar
>>>>>> > Exception in thread "main" java.lang.InternalError: Can't
>>>>>> connect to > window server - not enough permissions.
>
> Lucia Prieto Godino, PhD student
> Department of Zoology, University of Cambridge
> Downing street CB23EJ Cambridge, UK
>