surface profile from confocal stacks?

[Stanislav Vitha]

Hi,
I am attempting surface topology (profilometry). I have confocal
z-stacks taken with small z-steps (20-50 nm). The signal comes only
from the surface and drops off as the surface is getting out of
focus. So for each XY position, the Z intensity profile is
essentially a gaussian peak; the position of the peak then indicates
where the sample surface is.
I would like to perform some smoothing of the z-profiles to remove
noise and then either generate a topographical image (where the pixel
intensity corresponds to the surface height (i.e., position of the
peak in z-profile) or  export the peak coordinates as CSV (comma
separated values) x, y, z.

I have tried the Extended Depth of Field plugin,  but that is a bit
slow (and I need just the topology output). My stacks are generally
640 x 640 x 500 or bigger.

Thanks in advance.

Stan




Dr. Stanislav Vitha      [hidden email]
Microscopy and Imaging Center
Texas A&M University
BSBW 119
College Station, TX 77843-2257

tel: [phone] (main desk)
tel: [phone] (direct link)
fax: [phone]

[David Hovis]

I've written a plugin that I call TopoJ for just such a purpose.  It  
is quite simple and very fast.

Email me off the list if you are interested and I will send you a copy  
with instructions.  I'm happy to open source it if anyone is interested.

--David

----------------------------------------
David Hovis
Senior Research Associate
Department of Materials Science
Case Western Reserve University
[hidden email]

On Nov 15, 2007, at 11:57 AM, Stanislav Vitha wrote:

> Hi,
> I am attempting surface topology (profilometry). I have confocal z-
> stacks taken with small z-steps (20-50 nm). The signal comes only  
> from the surface and drops off as the surface is getting out of  
> focus. So for each XY position, the Z intensity profile is  
> essentially a gaussian peak; the position of the peak then indicates  
> where the sample surface is.
> I would like to perform some smoothing of the z-profiles to remove  
> noise and then either generate a topographical image (where the  
> pixel intensity corresponds to the surface height (i.e., position of  
> the peak in z-profile) or  export the peak coordinates as CSV (comma  
> separated values) x, y, z.
>
> I have tried the Extended Depth of Field plugin,  but that is a bit  
> slow (and I need just the topology output). My stacks are generally  
> 640 x 640 x 500 or bigger.
>
> Thanks in advance.
>
> Stan
>
>
>
>
> Dr. Stanislav Vitha      [hidden email]
> Microscopy and Imaging Center
> Texas A&M University
> BSBW 119
> College Station, TX 77843-2257
>
> tel: [phone] (main desk)
> tel: [phone] (direct link)
> fax: [phone]