Grid for volume density calculation

[Vivek Balasubramaniam]

I am looking for some assistance. we are trying to analyze lung  
slices with a aim to estimate the ratio of the volume density of the  
lung as compared to the airspaces. I would like to overlay a grid of  
crosshairs over an image of the lung and be able to count the number  
of times the grid intersects the lung and the airspaces. We used to  
use a program called Stereology Toolbox for the Mac OS9 to do this  
but would like to use ImageJ so that it could be used cross platform  
and on TIFF images. I am hoping that there is a plug in already  
created out there that can do this, before having to create one.

The problem is that we are dealing with  very small lungs and  
sometimes we cannot fill the entire field of view with the lung slice  
and would like to do a volume density calculation as described in  
Howard and Reed.

thanks in advance,

vivek

Vivek Balasubramaniam, MD
Assistant Professor
Director, Pediatric Heart Lung Center Laboratory
University of Colorado Health Sciences Center
The Children's Hospital
(clinical office) 303-837-2522
(lab) 303-724-4062
(pager) 303-826-8560

[Anda Cornea]

We have used a combination of 2 plugins,  Grid and Cell Counter, for a similar purpose, on brain MRI images. I am not sure that I understand the last paragraph.  Can you change the magnification of image acquisition?

Anda

Anda Cornea Ph.D.
Head of the Imaging and Morphology Core
Oregon National Primate Research Center
Oregon Health & Science University
[phone]

>>> [hidden email] 11/08/05 9:28 PM >>>
I am looking for some assistance. we are trying to analyze lung  
slices with a aim to estimate the ratio of the volume density of the  
lung as compared to the airspaces. I would like to overlay a grid of  
crosshairs over an image of the lung and be able to count the number  
of times the grid intersects the lung and the airspaces. We used to  
use a program called Stereology Toolbox for the Mac OS9 to do this  
but would like to use ImageJ so that it could be used cross platform  
and on TIFF images. I am hoping that there is a plug in already  
created out there that can do this, before having to create one.

The problem is that we are dealing with  very small lungs and  
sometimes we cannot fill the entire field of view with the lung slice  
and would like to do a volume density calculation as described in  
Howard and Reed.

thanks in advance,

vivek

Vivek Balasubramaniam, MD
Assistant Professor
Director, Pediatric Heart Lung Center Laboratory
University of Colorado Health Sciences Center
The Children's Hospital
(clinical office) 303-837-2522
(lab) 303-724-4062
(pager) 303-826-8560

[r.ghezzo]

Hi, we have developed a plugin for computing Lm in mice and human lungs. I will
tell the programmer to send you a copy of the java code with the cross hairs,
we also have one with the Weibull grid of non overlapping segments.
Heberto Ghezzo Ph.D.
Meakins-Christie Labs
McGill Uniuversity
Montreal - canada


Quoting Anda Cornea <[hidden email]>:

> We have used a combination of 2 plugins,  Grid and Cell Counter, for a
> similar purpose, on brain MRI images. I am not sure that I understand the
> last paragraph.  Can you change the magnification of image acquisition?
>
> Anda
>
> Anda Cornea Ph.D.
> Head of the Imaging and Morphology Core
> Oregon National Primate Research Center
> Oregon Health & Science University
> [phone]
>
> >>> [hidden email] 11/08/05 9:28 PM >>>
> I am looking for some assistance. we are trying to analyze lung
> slices with a aim to estimate the ratio of the volume density of the
> lung as compared to the airspaces. I would like to overlay a grid of
> crosshairs over an image of the lung and be able to count the number
> of times the grid intersects the lung and the airspaces. We used to
> use a program called Stereology Toolbox for the Mac OS9 to do this
> but would like to use ImageJ so that it could be used cross platform
> and on TIFF images. I am hoping that there is a plug in already
> created out there that can do this, before having to create one.
>
> The problem is that we are dealing with  very small lungs and
> sometimes we cannot fill the entire field of view with the lung slice
> and would like to do a volume density calculation as described in
> Howard and Reed.
>
> thanks in advance,
>
> vivek
>
> Vivek Balasubramaniam, MD
> Assistant Professor
> Director, Pediatric Heart Lung Center Laboratory
> University of Colorado Health Sciences Center
> The Children's Hospital
> (clinical office) 303-837-2522
> (lab) 303-724-4062
> (pager) 303-826-8560
>

[No Name-4]

I have worked on this same problem in the past. I used the chord length
measurement stereology technique from Jack Elias' lab at Yale. They are
using NIH Image macros so I converted these to ImageJ macros.

Here are the original macros:
http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/nih-image/pub/nih-image/contrib/chord%2520length%25252Fsurface%2520area

Here's a couple of refs:
Anat. Rec. 239:287 (1994)
J. Clin. Invest. 106:1081-1093 (2000).

Let me know if you have any questions.

Jim Deeds
Novartis Institute for BioMedical Research, Inc.
Oncology Target Biomarkers US, Building 600 / 4C-421-01
250 Mass Avenue, Cambridge, MA 02139
[hidden email]
Tel: [phone]




Anda Cornea <[hidden email]>
Sent by: ImageJ Interest Group <[hidden email]>
11/09/2005 01:40 PM
Please respond to ImageJ Interest Group

 
        To:     [hidden email]
        cc:     (bcc: James Deeds/PH/Novartis)
        Subject:        Re: Grid for volume density calculation


We have used a combination of 2 plugins,  Grid and Cell Counter, for a
similar purpose, on brain MRI images. I am not sure that I understand the
last paragraph.  Can you change the magnification of image acquisition?

Anda

Anda Cornea Ph.D.
Head of the Imaging and Morphology Core
Oregon National Primate Research Center
Oregon Health & Science University
[phone]

>>> [hidden email] 11/08/05 9:28 PM >>>
I am looking for some assistance. we are trying to analyze lung
slices with a aim to estimate the ratio of the volume density of the
lung as compared to the airspaces. I would like to overlay a grid of
crosshairs over an image of the lung and be able to count the number
of times the grid intersects the lung and the airspaces. We used to
use a program called Stereology Toolbox for the Mac OS9 to do this
but would like to use ImageJ so that it could be used cross platform
and on TIFF images. I am hoping that there is a plug in already
created out there that can do this, before having to create one.

The problem is that we are dealing with  very small lungs and
sometimes we cannot fill the entire field of view with the lung slice
and would like to do a volume density calculation as described in
Howard and Reed.

thanks in advance,

vivek

Vivek Balasubramaniam, MD
Assistant Professor
Director, Pediatric Heart Lung Center Laboratory
University of Colorado Health Sciences Center
The Children's Hospital
(clinical office) 303-837-2522
(lab) 303-724-4062
(pager) 303-826-8560