Particles volume measurement

[Frédéric Carlier]

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]

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]
Fax. : [phone]

Consultez mes disponibilités sur http://www.google.com/calendar/embed?src=fabrice.cordelieres%40gmail.com

[Frédéric Carlier]

On Fri, 6 Feb 2009 18:38:34 +0100, Fabrice Cordelières
<[hidden email]> 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
>

GREAT ! Simply perfect.

Thanks
FC

[Michael Schmid]

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]
> Fax. : [phone]
>
> Consultez mes disponibilités sur http://www.google.com/calendar/ 
> embed?src=fabrice.cordelieres%40gmail.com