Re: Particles volume measurement

Posted by Michael Schmid on Feb 09, 2009; 10:35am
URL: http://imagej.273.s1.nabble.com/Particles-volume-measurement-tp3693803p3693805.html

Hi Fabrice,

my guess is that your AFM data are not really 3D data (in the sense  
of data as a function of x,y,z) but rather height as a function of  
(x,y).
So what you have to do is probably the following:

- Convert the data to 32-bit (nless you have done so),
- Level them so that the substrate has an average value of 0. YOu can  
use, e.g., the Fit Polynomial Plugin
http://imagejdocu.tudor.lu/doku.php?
id=plugin:filter:fit_polynomial:start

With the particle analyzer, measure "integrate density". For a  
definition, see
http://rsb.info.nih.gov/ij/docs/menus/analyze.html#set

You can use the "Redirect To" feature of the Particle analyzer to use  
the segmentation (derived from Watershed, Find Maxima or whatever)  
for the areas measured.

Michael
________________________________________________________________

On 6 Feb 2009, at 18:38, Fabrice Cordelières wrote:

> Hi Frederic,
>
> Have a look at 3D Object counter on http://imagejdocu.tudor.lu/ 
> doku.php?id=plugin:analysis:3d_object_counter:start
> Once installed, you have 2 entries within the 3D OC section under  
> plugins. Open the 2 images, the mask and the image to analyze. Have  
> a look at the "Set measurements" entry and under "redirect to"  
> select the image to analyze. Close "Set Measurements". Now select  
> the mask, be sure that your image is well calibrated (if not, use  
> Image/Properties to do that) and launch the "3D Object counter"  
> plugin. In the result window, you will have access to the volume.
>
> I hope this is what you've been looking for.
>
> Fabrice
>
>
> Le 6 févr. 09 à 15:46, Frederic Carlier a écrit :
>
>> Hi all,
>>
>> I have an AFM image of particles grown on a surface. I make a  
>> segmentation
>> of the image to identify the particles. This, I know how to  
>> (watershed, etc.).
>> I have two images : original and segmented. I would like to  
>> integrate the z
>> signal in the original image and for each particle of the  
>> segmented image to
>> obtain (if x,y,z are correctly calibrated) the particles' volume.
>>
>> A kind of "cross Analyze particles".
>>
>> I donnot know where to look for. Any help would be greatly  
>> appreciated.
>>
>> Thanks in advance
>> FC
>>
>
>
> Fabrice Cordelières, PhD
>
> Institut Curie - Section de recherche/ CNRS UMR 146
> Plateforme d'Imagerie Cellulaire et Tissulaire
> Bâtiment 112 - Centre universitaire
> 91405 Orsay Cedex
> FRANCE
>
> Tél. : [phone]
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>
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