determining depth via tilt

[Michael Shaffer-3]

[ ... my apologies for sending this twice.  This is my 1st post from this
address and I received no confirmation that it had been sent at all.  Is
this list configured for the OP seeing the original post? ...]

We would like to measure the depths of laser ablated pits, and other
softwares do not seem up to the job because of their reliance on detail.
Altho we considered even the expense of these softwares, it would seem
they're not up to a task a simple as ours (plus the fact the original
surface nor the pit provide much detail).

That said, there is enough detail for determining the 2 planes, top and
bottom ... ie, user intervention could supply the locations of 3 points on
the original surface and pit bottom that would be defined for each tilt.  It
would seem that 3 points would be all that is required for defining the 2
planes, and the location movements relative to eachother for defining the
depth(?)

Is there such a plugin for ImageJ?

cheerios, michael shaffer  :o)
SEM-MLA Research Coodinator
INCO Innovation Centre
Memorial University
St. John's Newfoundland
  http://www.mun.ca/creait/maf/

[dscho]

Hi,

On Tue, 15 Jan 2008, Michael Shaffer wrote:

> [ ... my apologies for sending this twice.  This is my 1st post from
> this address and I received no confirmation that it had been sent at
> all.  Is this list configured for the OP seeing the original post? ...]
>
> We would like to measure the depths of laser ablated pits, and other
> softwares do not seem up to the job because of their reliance on detail.
> Altho we considered even the expense of these softwares, it would seem
> they're not up to a task a simple as ours (plus the fact the original
> surface nor the pit provide much detail).
>
> That said, there is enough detail for determining the 2 planes, top and
> bottom ... ie, user intervention could supply the locations of 3 points
> on the original surface and pit bottom that would be defined for each
> tilt.  It would seem that 3 points would be all that is required for
> defining the 2 planes, and the location movements relative to eachother
> for defining the depth(?)

I am not quite sure about some important details:

- what does your data look like? (grayscale, 2d/3d, ...)
- what precision is required?

If you want to work with manual registration (which this boils down to),
the precision might be not good enough to give sensible results.

> Is there such a plugin for ImageJ?

I am quite certain there is none.

Ciao,
Dscho

[Baggerly, ROY G]

I would suggest that an optical surface profiler might be the way to
measure pit size and depth. Some instruments work on white light
interferometry where the vertical resolution is less than a nanometer
and they provide a two dimensional image. I would be very interested in
your work and would be willing to provide measurements on a sample of
your material or a typical image of pits on the internal surface of a
titanium tube.
 
Roy G. Baggerly
M&PT
TEL:  [phone]
FAX: [phone]
2-122.2 Bldg; Column E5
 "It is clearly the perception of failure in existing technology
 that drives inventors, designers, and engineers to modify what
others may find perfectly adequate, or at least useable."
Evolution of Useful Things

-----Original Message-----
From: Michael Shaffer [mailto:[hidden email]]
Sent: Tuesday, January 15, 2008 4:18 AM
To: [hidden email]
Subject: determining depth via tilt

[ ... my apologies for sending this twice.  This is my 1st post from
this
address and I received no confirmation that it had been sent at all.  Is
this list configured for the OP seeing the original post? ...]

We would like to measure the depths of laser ablated pits, and other
softwares do not seem up to the job because of their reliance on detail.
Altho we considered even the expense of these softwares, it would seem
they're not up to a task a simple as ours (plus the fact the original
surface nor the pit provide much detail).

That said, there is enough detail for determining the 2 planes, top and
bottom ... ie, user intervention could supply the locations of 3 points
on
the original surface and pit bottom that would be defined for each tilt.
It
would seem that 3 points would be all that is required for defining the
2
planes, and the location movements relative to eachother for defining
the
depth(?)

Is there such a plugin for ImageJ?

cheerios, michael shaffer  :o)
SEM-MLA Research Coodinator
INCO Innovation Centre
Memorial University
St. John's Newfoundland
  http://www.mun.ca/creait/maf/

[Adam Hacking]

Dear Michael,

We have looked for a similar solution and there are some under development by two different ImageJ groups (Gary Chinga, Emerson Lucena).

A bit of background, WLI is a very accurate tool for vertical resolution over a large vertical range and a relatively large sampling area. This is generally where we have found benefit over AFM.

WLI  is however limited by the wavelength of light and the optics of the instrument. We have found that for accurately depicting steep walled features or for quantifying closely spaced features, the instrument is limited and has a   lateral resolution of ~600nm. This may not be much of a problem if your features are larger and you are just measuring pit to step height and pit diameter. You can get a quick idea of resolution issues by comparing SEM images of the surface to your WLI images and judging the similarity.

If you can get past the Biomaterial slant, this paper offers a nice summary of some of the problems I have touched on.

 Interfacial Shear Strength of Titanium Implants in Bone is Significantly Improved by Surface Topographies With High Pit Density and Microroughness
 Nataliya Deyneka-Dupriez,1 Bora Kocdemir,1 Ulrich Herr,1 Hans-Jo¨ rg Fecht,1
 Hans-Joachim Wilke,2 Lutz Claes2
 
 2007 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater 82B: 305–312, 2007

As a "know-how-make-do-approach" you may consider sectioning the surfaces and measuring the profile in an SEM if feature size permits ?

The AFM as I am sure you are aware may also have a problem measuring your pits, as the pit becomes 'V' shaped as you generate artifacts related to the tip moving over the surface and most have a 5-10um vertical range.

One other solution is stereo SEM which I think that you may be alluding to. We examine micro and nano textured biomaterial surfaces and this seems (in theory) to be a viable option. It should have  very good lateral resolution and good feature resolution, and allows you to image the exact area of quantification, but requires an SEM with a eucentric stage to obtain tilted images. This can be tricky to find.

So far there has been some progress on the imageJ plugins but am not sure if they are ready. We can provide tilted SEM images of NIST standard surfaces if anyone else is interested.

There is commercial software out there, 2 companies that I know of - one is about 4,000 EU the other about $11,000. I can put you in touch off the list if you like.

If there are any other questions, there are some much more capable people than I at McGill working in this area (Prof Srikar Vengallatore, PhD student Guru Sosale) and I would be happy to put you in touch with them.

Best of luck.

Adam Hacking

"Baggerly, ROY G" <[hidden email]> wrote: I would suggest that an optical surface profiler might be the way to
measure pit size and depth. Some instruments work on white light
interferometry where the vertical resolution is less than a nanometer
and they provide a two dimensional image. I would be very interested in
your work and would be willing to provide measurements on a sample of
your material or a typical image of pits on the internal surface of a
titanium tube.
 
Roy G. Baggerly
M&PT
TEL:  [phone]
FAX: [phone]
2-122.2 Bldg; Column E5
 "It is clearly the perception of failure in existing technology
 that drives inventors, designers, and engineers to modify what
others may find perfectly adequate, or at least useable."
Evolution of Useful Things

-----Original Message-----
From: Michael Shaffer [mailto:[hidden email]]
Sent: Tuesday, January 15, 2008 4:18 AM
To: [hidden email]
Subject: determining depth via tilt

[ ... my apologies for sending this twice.  This is my 1st post from
this
address and I received no confirmation that it had been sent at all.  Is
this list configured for the OP seeing the original post? ...]

We would like to measure the depths of laser ablated pits, and other
softwares do not seem up to the job because of their reliance on detail.
Altho we considered even the expense of these softwares, it would seem
they're not up to a task a simple as ours (plus the fact the original
surface nor the pit provide much detail).

That said, there is enough detail for determining the 2 planes, top and
bottom ... ie, user intervention could supply the locations of 3 points
on
the original surface and pit bottom that would be defined for each tilt.
It
would seem that 3 points would be all that is required for defining the
2
planes, and the location movements relative to eachother for defining
the
depth(?)

Is there such a plugin for ImageJ?

cheerios, michael shaffer  :o)
SEM-MLA Research Coodinator
INCO Innovation Centre
Memorial University
St. John's Newfoundland
  http://www.mun.ca/creait/maf/



________________________________________________________________         Dr. S Adam Hacking, Post Doctoral Fellow
JTN Wong Laboratories for Mineralized Tissue Research,
Center for Bone and Periodontal Research,
McGill University     740 Dr. Penfield Ave. Rm. 2300A
Montreal, QC, Canada H3A 1A4
Ph.:  514-398-5112
Fax: [phone]