Re: Segmentation Question

Posted by Ahmed Khwaja on May 17, 2006; 2:23pm
URL: http://imagej.273.s1.nabble.com/Segment-Measurement-Question-tp3702739p3702745.html

Hi Leon,
YAWI2D works great. Thank you for your help. I'll look more into 3D editing tool from Albert Cardona.
I appreciate your support.
Best,
Ahmed

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Leon Espinosa
Sent: Wednesday, 17 May, 2006 9:08 AM
To: [hidden email]
Subject: Re: Segmentation Question

Hello, I agree with the fact that the wand tool needs some way to increase or decrease the selected region by changing the "tolerance"  
for gray levels.

The threshold approach is not good because each region of the image needs different settings !

The "YAWI2D" works better because it don't need threshold and its tolerance good, but for good contrast images (MRI) but not "noisy fluorescence".

The 3D editing tools from Albert Cardona have a wand tool that works very good, but in my system everything crash after few seconds (?? G5 mac OS X 10.4.6).

Somme commercial IA softwares have a very nice command linked to the wand tool: after click you can increase or decrease tolerance with the mouse wheel (or up/down arrows) and make open/close transformation of the selected region with left/right arrows, and even "morphological separation" for region with "8" shape" (shortcut "s")...

I have tried to modify the Wand tool source code but it was to high for my java knowledge...

Some ideas... ?


All the best, Leon




Le 17 mai 06 à 13:18, jarek a écrit :

> Ahmed Khwaja napisał(a):
>> Hi Chamot,
>>
>> For some reason, the wand tool is not working properly in ImageJ.  
>> I just
>> tried Adobe Photoshop and I'm getting good results.
>>
>> Thanks for your help.
>>
>> Ahmed
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>> CHAMOT Christophe
>> Sent: Wednesday, 17 May, 2006 4:09 AM
>> To: [hidden email]
>> Subject: Re: Segmentation Question
>>
>> Ahmed Khwaja a écrit :
>>
>>> Hi,
>>>
>>> I have a stack of RGB segmented images. I would like to remove the
>>> area outside a closed segmented loop that is marked in red color.
>>> The segmented line can be loaded from a different image.
>>>
>>> Is there any tool in Imagej that can remove the area outside the
>>> segmented loop.
>>>
>>> Thanks for the help.
>>>
>>> Ahmed
>>>
>>>
>>
>> Hello Ahmed and listers,
>>
>> Can't you just use the magic wand on your loop and Edit > Clear
>> outside?
>>
>> Regards,
>>
>> --
>> CHAMOT Christophe
>> ---------------------------------------------------------------------
>> Plate-Forme de Recherche IFR117
>> "Imageries des Processus Dynamiques
>> en Biologie Cellulaire et Biologie du Développement "
>> Institut Jacques Monod, CNRS, Universités Paris 6 et 7 2, place
>> Jussieu - Tour 43
>> 75251 Paris cedex 05
>> Tel: [phone]
>> http://www.ijm.jussieu.fr/
>> ---------------------------------------------------------------------
>>
>>
>>
>>
> hello to all,
> i want to change a bit this topic. i work on x-ray images of plant
> tissues with imagej and the best for manual analysis would be the wand
> tool just like in adobe photoshop, where one can set the tolerance and
> select just a part of image. of course one can adjust treshold and try
> extract the ROI with ij-wand tool, but it is not exactly how i would
> imagine this operation. x-ray images of microdamages of plant tissue
> are commonly slightly contrasted so it is difficult to properly select
> ROI based on treshold adjustation.
> so, if someone has any clue how to get a plug working like a wand in
> photoshop-big respect and lots of thanks because it would made my life
> easier ;-)
>
> please do not hesitate, if anyone know this kind of plugin, maybe i
> missed in plugins list on ij homepage? please let me know.
>
> with best regards,
> Jarek Grodek
>
> p.s. wish i was on Conference in Tudor Rechere Centre....
>

Leon Espinosa
[hidden email]

Laboratoire des Rickettsies du Pr. RAOULT UMR CNRS 6020 Fac. de Medecine de la Timone
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