did anyone implement a 3D watershed?

[Albert Cardona]

I would appreciate some pointers to source and web pages relating to 3D
watershed plugins or java implementations.

What I want to do: segment nuclei from a confocal stack.

Thank you for any hints.


Albert

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

[Thomas Boudier]

Hi Albert,

I have updated my 3D filters plugins which includes 3D watershed :  
http://imagejdocu.tudor.lu/Members/tboudier/plonearticle.2007-01-08.6704298355/ 


Thomas

> I would appreciate some pointers to source and web pages relating to
> 3D watershed plugins or java implementations.
>
> What I want to do: segment nuclei from a confocal stack.
>
> Thank you for any hints.
>
>
> Albert
>

--
/*****************************************************/
 Thomas Boudier, MCU Université Pierre et Marie Curie
 UMR 7101 / IFR 83. Bat A 328, Campus Jussieu
 Tél : [phone]  Fax : [phone]
/*****************************************************/


 

[Albert Cardona]

Hi Thomas,

I run the 3D watershed on an 8-bit stack and I get:

- a copy of the stack
- the message: "Command 005-random not found"
- the original stack is left locked.

I opened the source code and I found that, within the run method, an
IJ.run call is issued for the "005-random" command. Which plugin
implements this functionality?

Also, a general recommendation: your plugins are not thread safe. Such
IJ.run call assumes that the WindowManager will have, as the currently
active image, the copy of the stack that you just created and opened,
which can easily not be the case. I suggest you use the ImagePlus
pointer directly to pass to the 005-random.


Albert

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

[Thomas Boudier]

Hello,

The "005-random" refers to a lut that is distributed in new versions of
imageJ. I have removed this colouring of the result so the plugin should
not lock the image.

Thomas

>
> Hi Thomas,
>
> I run the 3D watershed on an 8-bit stack and I get:
>
> - a copy of the stack
> - the message: "Command 005-random not found"
> - the original stack is left locked.
>
> I opened the source code and I found that, within the run method, an
> IJ.run call is issued for the "005-random" command. Which plugin
> implements this functionality?
>
> Also, a general recommendation: your plugins are not thread safe. Such
> IJ.run call assumes that the WindowManager will have, as the currently
> active image, the copy of the stack that you just created and opened,
> which can easily not be the case. I suggest you use the ImagePlus
> pointer directly to pass to the 005-random.
>
>
> Albert
>

--
/*****************************************************/
 Thomas Boudier, MCU Université Pierre et Marie Curie
 UMR 7101 / IFR 83. Bat A 328, Campus Jussieu
 Tél : [phone]  Fax : [phone]
/*****************************************************/


 

[Joachim Wesner]

Hi List,

I just tried the dynamic profiler plugin and like it a lot. However, I
would wish that it also updates its contents, when the underlying window
(the one with the ROI it "listens" to) is redrawn (updateAndDraw() etc),
because I would like to have a profile plot of another "dynamic" window
that changes its contents.

I would add this to the existing plugin source code myself, but I do not
yet understand enough about the inner workings of ImageJ and/or Java
to do it. Any hints? Any Chance to "hook" into some event that occurs with
the redraw?

Sincerely

Joachim Wesner


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[Michael Schmid]

Hi Joachim,

yes, I have a version that includes the ImageListener interface.
When hooked to an image, it updates the plot on changes to the
image. E.g., if preview of a filter is active, you can see how
the filter parameters would change the linescan.

I still have to do some checks and polishing of the code (which
is on a different computer than the one I am currently using),
but for the meanwhile I can put the class file online:

http://www.iap.tuwien.ac.at/www/surface/tmp/Dynamic_Profiler.class

If you find any errors or have trouble with it, let me know.

Michael
________________________________________________________________

On 19 Nov 2007, at 13:25, Joachim Wesner wrote:

> Hi List,
>
> I just tried the dynamic profiler plugin and like it a lot. However, I
> would wish that it also updates its contents, when the underlying  
> window
> (the one with the ROI it "listens" to) is redrawn (updateAndDraw()  
> etc),
> because I would like to have a profile plot of another "dynamic"  
> window
> that changes its contents.
>
> I would add this to the existing plugin source code myself, but I  
> do not
> yet understand enough about the inner workings of ImageJ and/or Java
> to do it. Any hints? Any Chance to "hook" into some event that  
> occurs with
> the redraw?
>
> Sincerely
>
> Joachim Wesner
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
> ______________________________________________________________________