Mac - java - X11

[Laura Lucia Prieto Godino]

Hi Wayne,
thanks...I know colour counter is supposed to do that, it was the  
first thing I tried, but when I have  my stack and i go plugins-
 >colour counter...the only thing that appears is a result window that  
reads colour count: 8. And that's it, there is no info about the  
number of pixels for each colour. I wonder if there is a problem with  
the version of imajeJ i have. I am using ImageJ64 on a mac that runs  
leopard.

Any idea what the problem might be?

Thank you very very much!

Lucia

On 14 Oct 2008, at 21:14, Wayne Rasband wrote:

>> 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
>>

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

[Fabrice Senger]

Laura Lucia Prieto Godino a écrit :

> Hi Wayne,
> thanks...I know colour counter is supposed to do that, it was the
> first thing I tried, but when I have  my stack and i go
> plugins->colour counter...the only thing that appears is a result
> window that reads colour count: 8. And that's it, there is no info
> about the number of pixels for each colour. I wonder if there is a
> problem with the version of imajeJ i have. I am using ImageJ64 on a
> mac that runs leopard.
>
> Any idea what the problem might be?
>
> Thank you very very much!
>
> Lucia
>
> On 14 Oct 2008, at 21:14, Wayne Rasband wrote:
>
>>> 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
>>>
>
> Lucia Prieto Godino, PhD student
> Department of Zoology, University of Cambridge
> Downing street CB23EJ Cambridge, UK

Hello,

you may try thomas boudier's FISH3D.

Fabrice.

--
Senger Fabrice

[Patrick Pirrotte]

Hello,

I updated the "The ImageJ Eclipse Howto" on the new ImageJ documentation
wiki.

It now includes a step-by-step description on how to setup Eclipse to debug
ImageJ plugins.

http://imagejdocu.tudor.lu/doku.php?id=howto:plugins:the_imagej_eclipse_howt
o

Regards,

Patrick

[Michael Schmid]

Hi Lucia,

maybe the following procedure may help:
- split the color channels
- divide the green channel by 2, the red channel by 4, the blue  
channel by 8.
- add the three channels
Now you will have the following pixel values:

(the table is meant for a monospace font such as Courier)

---original---          ---added---
green   red     blue
0       0       0          0
0       0       255        32
0       255     0          64
0       255     255        32+64=96
255     0       0          128
255     0       255        128+32=160
255     255     0          128+64=192
255     255     255        128+64+32=224

Then you can simply use the histogram function to get the result.

Michael
________________________________________________________________

On 14 Oct 2008, at 22:43, Laura Lucia Prieto Godino wrote:

> Hi Wayne,
> thanks...I know colour counter is supposed to do that, it was the  
> first thing I tried, but when I have  my stack and i go plugins-
> >colour counter...the only thing that appears is a result window  
> that reads colour count: 8. And that's it, there is no info about  
> the number of pixels for each colour. I wonder if there is a  
> problem with the version of imajeJ i have. I am using ImageJ64 on a  
> mac that runs leopard.
>
> Any idea what the problem might be?
>
> Thank you very very much!
>
> Lucia
>
> On 14 Oct 2008, at 21:14, Wayne Rasband wrote:
>
>>> 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
>>>
>
> Lucia Prieto Godino, PhD student
> Department of Zoology, University of Cambridge
> Downing street CB23EJ Cambridge, UK