Scanning electron microscope image to 3D print

[dksamuel]

Respected Imagej Researchers. I want to make a 3D print. Can I directly
convert a single image to *.STL and print. Or do I need an Image stack for
3D printing . I am confused on how to make an image stack using SEM. With
regards Samuel IIHR Bangalore, India

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[Robert Baer]

On 2/18/2017 10:30 AM, Duleep Samuel wrote:
> Respected Imagej Researchers. I want to make a 3D print. Can I directly
> convert a single image to *.STL and print.
No, not if by single image you mean a 2 dimensional image.  If you mean
a single file, and you have the equivalent of an image stack, maybe.

> Or do I need an Image stack for
> 3D printing . I am confused on how to make an image stack using SEM.
This depends entirely on the format in which the SEM information was
saved.  Your first task will be to learn about the format.  Was it a
stack of images in a .tiff container or some other 3D container? If you
have a folder of single 2D images at different z-depths (penetration
depths) you can combine them into a stack inside imageJ.  You will need
to know the relative spacing of these images to get a decent printable
3D result.

With all that said, when you print, you need a surface mesh with minimum
holes.  This may mean that you have to do some significant re-topology
work on the results of your image stack to get something that is
printable in the physical world.  This is unlikely to be a simple scan
and print process.

> With
> regards Samuel IIHR Bangalore, India
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Robert W. Baer, Ph.D.
Professor of Physiology
Kirksville College of Osteopathic Medicine
A T Still University of Health Sciences
800 W. Jefferson St
Kirksville, MO 63501
660-626-2321 Department
660-626-2965 FAX

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[Kenneth Sloan-2]

First - there are many styles of "3D print". Either a single image, you an
treat the image as a height map. I have produced many of these.

You can also produce a solid from a single image by thresholding ( or
otherwise segmenting) and layering this on a solid base (another image with
a constant value)

Second - making a stack out of several (aligned) images is easy. If you are
stuck st this point, you need to concentrate on that problem before
considering 3D printing.

Third - the comments about topology are spot on. You need a connected,
manifold mesh. When I last checked, the standard ImageJ tools will produce
a mesh, but do not guarantee that the mesh is manifold. I ended up writing
a plugin to enforce this. There are also mesh-processing programs that can
help, but I found that the good ones were expensive and the free ones were
clunky and not very good.

I recently retired, but before that I taught 3D printing and ran a small 3D
print facility. One if the first exercises for students was to produce a
solid object from a single image (treating it as a height map). But - you
won't find this as a standard ImageJ tool.

On Mon, Feb 20, 2017 at 09:29 Robert Baer <[hidden email]> wrote:

> On 2/18/2017 10:30 AM, Duleep Samuel wrote:
> > Respected Imagej Researchers. I want to make a 3D print. Can I directly
> > convert a single image to *.STL and print.
> No, not if by single image you mean a 2 dimensional image.  If you mean
> a single file, and you have the equivalent of an image stack, maybe.
>
> > Or do I need an Image stack for
> > 3D printing . I am confused on how to make an image stack using SEM.
> This depends entirely on the format in which the SEM information was
> saved.  Your first task will be to learn about the format.  Was it a
> stack of images in a .tiff container or some other 3D container? If you
> have a folder of single 2D images at different z-depths (penetration
> depths) you can combine them into a stack inside imageJ.  You will need
> to know the relative spacing of these images to get a decent printable
> 3D result.
>
> With all that said, when you print, you need a surface mesh with minimum
> holes.  This may mean that you have to do some significant re-topology
> work on the results of your image stack to get something that is
> printable in the physical world.  This is unlikely to be a simple scan
> and print process.
>
> > With
> > regards Samuel IIHR Bangalore, India
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
>
>
> --
> Robert W. Baer, Ph.D.
> Professor of Physiology
> Kirksville College of Osteopathic Medicine
> A T Still University of Health Sciences
> 800 W. Jefferson St
> Kirksville, MO 63501
> 660-626-2321 Department
> 660-626-2965 FAX
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Michael Schmid]

On 18/02/2017 17:30, Duleep Samuel wrote:
> Respected Imagej Researchers. I want to make a 3D print. Can I directly
> convert a single image to *.STL and print. Or do I need an Image stack for
> 3D printing . I am confused on how to make an image stack using SEM. With
> regards Samuel IIHR Bangalore, India


Hi Samuel,

there is no way to derive 3D information from one SEM image.
In principle, it is possible to derive a 3D structure from images taken
under different sample angles (e.g. a stereo image pair), but it might
be difficult.

Two articles as starting point from a previous post
   https://list.nih.gov/cgi-bin/wa.exe?A2=ind0910&L=IMAGEJ&P=R17599

Kuroda, Ikeuchi Nakade, Inoue, Kitagawa
Vacuum (2002) Volume 65 Pages 541-546. doi: 10.1016/S0042-207X(01)00469-9

Stampfl, Scherer, Gruber, et al.
Appl. Phys. A (1996) Volume 63 p 341. doi:10.1007/BF01567324

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If you get a height map from this, it should be possible to create a 3D
print from it.  I am not aware of a height-map to STL converter for
ImageJ, but there are several image-to-STL converters around; any
internet search engine will find a few.


Michael

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