Colocalisation

[Daniel James White]

Hi

Looking for yellow is a really bad way to asess colocalisation. Its is  
very subjective and usually misleading.



You should use the imagej colocalisation plugins. And read and  
understand the papers they reference. Especially coates et al. And  
landers et al 1992. I can send you these if you like.


The Two dimensional histogram described in these papers is much more  
informative than a colour merge image.

Dr. Daniel J. White
Light Microscopy Facility
MPI-CBG
Dresden 01307
Germany
[phone]
[hidden email]
http://www.bioimagexd.net

[Kirmse Robert]

Hi Daniel,

I would be interested in both papers,
It would be great if you could send me a copy.

Thank you in advance
Best
Robert

-----Ursprüngliche Nachricht-----
Von: ImageJ Interest Group [mailto:[hidden email]] Im Auftrag von Dan White
Gesendet: Dienstag, 22. April 2008 12:02
An: [hidden email]
Betreff: Colocalisation

Hi

Looking for yellow is a really bad way to asess colocalisation. Its is very subjective and usually misleading.



You should use the imagej colocalisation plugins. And read and understand the papers they reference. Especially coates et al. And landers et al 1992. I can send you these if you like.


The Two dimensional histogram described in these papers is much more informative than a colour merge image.

Dr. Daniel J. White
Light Microscopy Facility
MPI-CBG
Dresden 01307
Germany
[phone]
[hidden email]
http://www.bioimagexd.net

[Franklin Shaffer-2]

I have tracked particles through stacks of images from a high speed camera.
 
MTrackJ is an excellent plugin to draw and edit trajectories, but I also need to draw velocity vectors on the images.
 
Does anyone know of any capability in ImageJ to draw velocity vectors ?
 
Thanks,
Frank Shaffer
USDOE National Energy Technology Lab

[Joachim Wesner]

Hi list,

just wondering, is it (already?) possible to run a plugin from the macro
language
while simultaneously passing the String arg to the run method?

(II´m not talking about the Dialog options)

I think this might be useful (not just for me) and could be implemented
quite easily
via the call interface, but I wonder if it probably is already implemented
in some form!?
(Or should be added to the macro language!?)

Sincerely

Joachim




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[William O'Connell-3]

Joachim,
I've passed an argument string from one plugin1 to plugin2 successfully.
plugin1
,,,,,,,,,,,,,,,,,,,,
   IJ.run("plugin1", "argument1");
....................

plugin2
............................
    String str =  Macro.getOptions();
............................

This might well work running the plugin from a macro.  Wayne offered this
method in a user reply some time ago.
Cheers, Bill



On Tue, Apr 22, 2008 at 2:03 PM, Joachim Wesner <
[hidden email]> wrote:

> Hi list,
>
> just wondering, is it (already?) possible to run a plugin from the macro
> language
> while simultaneously passing the String arg to the run method?
>
> (II´m not talking about the Dialog options)
>
> I think this might be useful (not just for me) and could be implemented
> quite easily
> via the call interface, but I wonder if it probably is already implemented
> in some form!?
> (Or should be added to the macro language!?)
>
> Sincerely
>
> Joachim
>
>
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>

[Joachim Wesner]

Hi William,

hmmm, I see, but this is the "options" string I mentioned that is also used
to passed Dialog options.
In my special case I could pretty easily rewrite the macro to do what I
want, (only one extra "option arg),
but it´s not the arg string that the run()  method gets. Any way to
directly set up that?

Maybe one way would be to use a special "Arg=" keyword in the argument
string, together with the
macro recorder/replayer, in that case the fields will not be passed to any
dialog field when replayed,
but to the arg string?

I.e.

   IJ.run("plugin1", "Arg=xxx Open=yyy Dialogopt=dlg");

"Arg=xxx" will be cutoff and given to the arg string, the rest will
work as before!

Just an idea

Thanx a lot.



                                                                           
             William O'Connell                                            
             <oconnell.w@GMAIL                                            
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Joachim,
I've passed an argument string from one plugin1 to plugin2 successfully.
plugin1
,,,,,,,,,,,,,,,,,,,,
   IJ.run("plugin1", "argument1");
....................

plugin2
............................
    String str =  Macro.getOptions();
............................

This might well work running the plugin from a macro.  Wayne offered this
method in a user reply some time ago.
Cheers, Bill



On Tue, Apr 22, 2008 at 2:03 PM, Joachim Wesner <
[hidden email]> wrote:

> Hi list,
>
> just wondering, is it (already?) possible to run a plugin from the macro
> language
> while simultaneously passing the String arg to the run method?
>
> (II´m not talking about the Dialog options)
>
> I think this might be useful (not just for me) and could be implemented
> quite easily
> via the call interface, but I wonder if it probably is already

implemented

> in some form!?
> (Or should be added to the macro language!?)
>
> Sincerely
>
> Joachim
>
>
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________
>

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[Albert Cardona]

Joachim,


 From the macro language you can call static methods on classes. Thus:

call("IJ.runPlugIn", "My_PlugIn_ClassName", "some arg here);


Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Ben Tupper]

On Apr 23, 2008, at 2:58 AM, Albert Cardona wrote:

> Joachim,
>
>
> From the macro language you can call static methods on classes. Thus:
>
> call("IJ.runPlugIn", "My_PlugIn_ClassName", "some arg here);
>
>


Hi,

Oooo, your approach provides an interesting twist.  The call() macro  
command is expecting a static class method - see ....

http://rsb.info.nih.gov/ij/developer/macro/functions.html#C

In my mind I had always drawn a straight line between my macro and my  
plugin (via a static plugin method).  Your trick is quite clever  
since the user plugin doesn't have to have a static method.  Neato.  
Thanks for sharing that.

Cheers,
Ben





Ben Tupper
[hidden email]

I GoodSearch for Ashwood Waldorf School.

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[Joachim Wesner]

Thanx for the different suggestions, after a little experimenting, I found
out
that what I suggested already works with the macro-recorder/replayer:

If you add extra args in the "options" string to IJ.run, that do not
correspond
to any dialog entries, they are simply ignored and you can extract and use
those
for special purposes wit Macro.getOptions(), other dialog options still
work
as before.

Very nice, that solved my problem!

Joachim

ImageJ Interest Group <[hidden email]> schrieb am 23.04.2008 08:23:38:

> Hi William,
>
> hmmm, I see, but this is the "options" string I mentioned that is also
used
> to passed Dialog options.
> In my special case I could pretty easily rewrite the macro to do what I
> want, (only one extra "option arg),
> but it´s not the arg string that the run()  method gets. Any way to
> directly set up that?
>
> Maybe one way would be to use a special "Arg=" keyword in the argument
> string, together with the
> macro recorder/replayer, in that case the fields will not be passed to
any

> dialog field when replayed,
> but to the arg string?
>
> I.e.
>
>    IJ.run("plugin1", "Arg=xxx Open=yyy Dialogopt=dlg");
>
> "Arg=xxx" will be cutoff and given to the arg string, the rest will
> work as before!
>
> Just an idea
>
> Thanx a lot.
>
> Joachim,

> I've passed an argument string from one plugin1 to plugin2 successfully.
> plugin1
> ,,,,,,,,,,,,,,,,,,,,
>    IJ.run("plugin1", "argument1");
> ....................
>
> plugin2
> ............................
>     String str =  Macro.getOptions();
> ............................
>
> This might well work running the plugin from a macro.  Wayne offered this
> method in a user reply some time ago.
> Cheers, Bill
>

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