3d Reconstruction from Stack

[Andrew E. Meyer]

We have an application where we are taking a stack of pictures of a fuel
injector seat and spray orifices, and trying to reconstruct a 3-Dimensional
image for use in verifying that  the hardware was made to spec.  We are
using a microscope with a short focal length, so that the features in the
stack appear to grow in size as we get closer to the object.  (think of a
star field animation, where the nearer stars go racing to the edge of the
picture as the spaceship goes through the star field).

 

First, is there a name for this "star field" effect by which I could search
for information?

 

We have tried using stack focuser and EDF to create a three dimensional map
from our stack with very limited success-the images are very noisy and don't
correspond to the reality which we can measure, so we cannot trust them for
the stuff we cannot measure.  Maybe I'm just not using these extensions
properly?  I'm new to this, but it is my understanding that these techniques
determine position of each point based on how sharp the focus for the point
is, so moving features might be a problem for them.

 

From our stack, it would seem that the three dimensional information we are
looking for could be easily found by tracking the position of each feature
in the photograph from frame to frame-the nearer objects moving outward more
rapidly than the closer objects.  Does anyone know of a routine for this
kind of application?  If not, can someone recommend a place to start with
developing one.  Ideally the 3d image developed would take account of both
the changing position of the features and the changing focus of the
features.

 

I'm a mechanical engineer with a physic minor (Princeton University, '81)
and I'm willing to dig in and learn what I need to, especially if anyone can
give me some leads in where to start developing such an application.  I
could also use some guidance on understanding the physics of the optical
system.

 

Andrew E. Meyer

 President

 Beginnings Technology Inc.

 43 Palmer Drive

 Harpers Ferry, WV 25425

 USA

 

 Tel: [phone]

 Fax: [phone]

 

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[Nathaniel Ryckman]

I Googled around. These look like they might be useful. You could read the papers for background information.

http://www.macbiophotonics.ca/imagej/12_deconvolution.htm
http://bigwww.epfl.ch/algorithms/deconvolutionlab/
http://bigwww.epfl.ch/demo/edf/

If you want to make something custom, you'll unfortunately have to learn how to program (Java) if you don't already know how to.

http://www.imagingbook.com/index.php?id=102
http://rsbweb.nih.gov/ij/developer/index.html

Andrew E. Meyer wrote

We have an application where we are taking a stack of pictures of a fuel
injector seat and spray orifices, and trying to reconstruct a 3-Dimensional
image for use in verifying that  the hardware was made to spec.  We are
using a microscope with a short focal length, so that the features in the
stack appear to grow in size as we get closer to the object.  (think of a
star field animation, where the nearer stars go racing to the edge of the
picture as the spaceship goes through the star field).

 

First, is there a name for this "star field" effect by which I could search
for information?

 

We have tried using stack focuser and EDF to create a three dimensional map
from our stack with very limited success-the images are very noisy and don't
correspond to the reality which we can measure, so we cannot trust them for
the stuff we cannot measure.  Maybe I'm just not using these extensions
properly?  I'm new to this, but it is my understanding that these techniques
determine position of each point based on how sharp the focus for the point
is, so moving features might be a problem for them.

 

From our stack, it would seem that the three dimensional information we are
looking for could be easily found by tracking the position of each feature
in the photograph from frame to frame-the nearer objects moving outward more
rapidly than the closer objects.  Does anyone know of a routine for this
kind of application?  If not, can someone recommend a place to start with
developing one.  Ideally the 3d image developed would take account of both
the changing position of the features and the changing focus of the
features.

 

I'm a mechanical engineer with a physic minor (Princeton University, '81)
and I'm willing to dig in and learn what I need to, especially if anyone can
give me some leads in where to start developing such an application.  I
could also use some guidance on understanding the physics of the optical
system.

 

Andrew E. Meyer

 President

 Beginnings Technology Inc.

 43 Palmer Drive

 Harpers Ferry, WV 25425

 USA

 

 Tel: [phone]

 Fax: [phone]

 

 THE INFORMATION CONTAINED IN THIS E-MAIL COMMUNICATION IS THE PROPERTY

 OF BEGINNINGS TECHNOLOGY INC. AND IS INTENDED ONLY FOR THE USE OF THE

 ABOVE NAMED RECIPIENT(S). If you are not the intended recipient, you

 have received this communication in error. Please destroy the

 transmission and notify us immediately by telephone and/or reply

 e-mail. You are not authorized to use, copy, or in any way disseminate

 any information obtained from this e-mail.

[dscho]

Hi Andrew,

On Thu, 23 Jun 2011, Andrew E. Meyer wrote:

> We have an application where we are taking a stack of pictures of a fuel
> injector seat and spray orifices, and trying to reconstruct a
> 3-Dimensional image for use in verifying that the hardware was made to
> spec.  We are using a microscope with a short focal length, so that the
> features in the stack appear to grow in size as we get closer to the
> object.  (think of a star field animation, where the nearer stars go
> racing to the edge of the picture as the spaceship goes through the star
> field).
>
> First, is there a name for this "star field" effect by which I could
> search for information?
>
> We have tried using stack focuser and EDF to create a three dimensional
> map from our stack with very limited success-the images are very noisy
> and don't correspond to the reality which we can measure, so we cannot
> trust them for the stuff we cannot measure.  Maybe I'm just not using
> these extensions properly?  I'm new to this, but it is my understanding
> that these techniques determine position of each point based on how
> sharp the focus for the point is, so moving features might be a problem
> for them.

I imagine the problem is that your stack slices are not really in and out
of focus.

So maybe you need something completely different: you could use SIFT
features in every slice to generate robust landmarks, and then use a
RANSAC to find the most likely 3D locations of the landmarks.

The last step would be an inverse mapping from the recorded stack into a
3D height-field.

Ciao,
Johannes

[Philip Ershler]

On Jul 6, 2011, at 11:09 AM, Johannes Schindelin wrote:

> Hi Andrew,
>
> On Thu, 23 Jun 2011, Andrew E. Meyer wrote:
>
>> We have an application where we are taking a stack of pictures of a fuel
>> injector seat and spray orifices, and trying to reconstruct a
>> 3-Dimensional image for use in verifying that the hardware was made to
>> spec.  We are using a microscope with a short focal length, so that the
>> features in the stack appear to grow in size as we get closer to the
>> object.  (think of a star field animation, where the nearer stars go
>> racing to the edge of the picture as the spaceship goes through the star
>> field).
>>
>> First, is there a name for this "star field" effect by which I could
>> search for information?
>>
>> We have tried using stack focuser and EDF to create a three dimensional
>> map from our stack with very limited success-the images are very noisy
>> and don't correspond to the reality which we can measure, so we cannot
>> trust them for the stuff we cannot measure.  Maybe I'm just not using
>> these extensions properly?  I'm new to this, but it is my understanding
>> that these techniques determine position of each point based on how
>> sharp the focus for the point is, so moving features might be a problem
>> for them.
>
> I imagine the problem is that your stack slices are not really in and out
> of focus.
>
> So maybe you need something completely different: you could use SIFT
> features in every slice to generate robust landmarks, and then use a
> RANSAC to find the most likely 3D locations of the landmarks.
>
> The last step would be an inverse mapping from the recorded stack into a
> 3D height-field.
>

This might be a totally "off the wall" idea, but I'm wondering if a simple cofocal imaging system might be an alternative way to image the spray pattern. If a fluorescent dye were to be used, the pattern could easily be sectioned into slices of predictable thickness. I'm not sure whether correction for point spread issues (a common problem in confocal microscopy) would have to be carried out or not.

Just a thought,

Phil

[Joel Sheffield]

Another pair of thoughts.  There is a plugin (actually 2 of them) called
"Unwarp", that imposes a distortion on one image to match a second one.
Perhaps you can normalize your images with these.  You might have to write a
macro to process all images sequentially.  Additionally, StackReg is another
alternative that has a scaling function.

Joel


On Wed, Jul 6, 2011 at 1:09 PM, Johannes Schindelin <
[hidden email]> wrote:

> Hi Andrew,
>
> On Thu, 23 Jun 2011, Andrew E. Meyer wrote:
>
> > We have an application where we are taking a stack of pictures of a fuel
> > injector seat and spray orifices, and trying to reconstruct a
> > 3-Dimensional image for use in verifying that the hardware was made to
> > spec.  We are using a microscope with a short focal length, so that the
> > features in the stack appear to grow in size as we get closer to the
> > object.  (think of a star field animation, where the nearer stars go
> > racing to the edge of the picture as the spaceship goes through the star
> > field).
> >
> > First, is there a name for this "star field" effect by which I could
> > search for information?
> >
> > We have tried using stack focuser and EDF to create a three dimensional
> > map from our stack with very limited success-the images are very noisy
> > and don't correspond to the reality which we can measure, so we cannot
> > trust them for the stuff we cannot measure.  Maybe I'm just not using
> > these extensions properly?  I'm new to this, but it is my understanding
> > that these techniques determine position of each point based on how
> > sharp the focus for the point is, so moving features might be a problem
> > for them.
>
> I imagine the problem is that your stack slices are not really in and out
> of focus.
>
> So maybe you need something completely different: you could use SIFT
> features in every slice to generate robust landmarks, and then use a
> RANSAC to find the most likely 3D locations of the landmarks.
>
> The last step would be an inverse mapping from the recorded stack into a
> 3D height-field.
>
> Ciao,
> Johannes
>

--


Joel B. Sheffield, Ph.D
Department of Biology
Temple University
Philadelphia, PA 19122
Voice: 215 204 8839
e-mail: [hidden email]
URL:  http://astro.temple.edu/~jbs