3D modelling software

[Nicolas, Y. (Yves)]

Hello,
Not really a ImageJ question but related...
Are you aware of software that are able to create a 3D model structure
(e.g. particles in matrix) and to convert the 3D model structure into a
stack (2D image stack by slicing the 3D structure)?

Thanks.
Regards,
Yves


"The information contained in this message and its attachments is intended only for the use of the addressee, you may not use, copy or disclose to anyone any information contained in the message and its attachments. If you received the message in error, please advise the sender immediately and destroy or delete the message. E-mail transmission cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the content of this message which arise as a result of e-mail transmission. If verification is required please request a hard copy version."


"De informatie verzonden met dit e-mail bericht en de bijlagen is uitsluitend bestemd voor de geadresseerde(n). Gebruik van deze informatie door anderen dan de geadresseerde(n) is verboden. Indien u dit e-mail bericht bij vergissing heeft ontvangen, wilt u dan de verzender onmiddellijk waarschuwen en het bericht vernietigen. Het gebruik van e-mail is niet gegarandeerd veilig of foutloos; informatie kan worden onderschept, verminkt of verloren gaan; kan te laat of incompleet binnenkomen of virussen bevatten. Om deze reden neemt de verzender geen enkele verantwoordelijkheid voor fouten of wijzigingen in de inhoud van dit bericht als gevolg van het versturen via e-mail. Bij twijfel verzoeken wij u een kopie op te vragen."

[Justin McGrath]

Blender, although it may not be the best tool, can probably do this
through it's API.

www.blender.org

Justin

On 9/17/07, Nicolas, Y. (Yves) <[hidden email]> wrote:

> Hello,
> Not really a ImageJ question but related...
> Are you aware of software that are able to create a 3D model structure
> (e.g. particles in matrix) and to convert the 3D model structure into a
> stack (2D image stack by slicing the 3D structure)?
>
> Thanks.
> Regards,
> Yves
>
>
> "The information contained in this message and its attachments is intended only for the use of the addressee, you may not use, copy or disclose to anyone any information contained in the message and its attachments. If you received the message in error, please advise the sender immediately and destroy or delete the message. E-mail transmission cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the content of this message which arise as a result of e-mail transmission. If verification is required please request a hard copy version."
>
>
> "De informatie verzonden met dit e-mail bericht en de bijlagen is uitsluitend bestemd voor de geadresseerde(n). Gebruik van deze informatie door anderen dan de geadresseerde(n) is verboden. Indien u dit e-mail bericht bij vergissing heeft ontvangen, wilt u dan de verzender onmiddellijk waarschuwen en het bericht vernietigen. Het gebruik van e-mail is niet gegarandeerd veilig of foutloos; informatie kan worden onderschept, verminkt of verloren gaan; kan te laat of incompleet binnenkomen of virussen bevatten. Om deze reden neemt de verzender geen enkele verantwoordelijkheid voor fouten of wijzigingen in de inhoud van dit bericht als gevolg van het versturen via e-mail. Bij twijfel verzoeken wij u een kopie op te vragen."
>

[Bob Nienhuis]

I haven't tried it, but Reconstruct might be worth a look.
See: J.C. Fiala, Reconstruct: a free editor for serial section microscopy,
J. Microscopy,  188, Pt 1, April 2005, pp. 52-61.

Bob

On 9/16/07, Nicolas, Y. (Yves) <[hidden email]> wrote:

>
> Hello,
> Not really a ImageJ question but related...
> Are you aware of software that are able to create a 3D model structure
> (e.g. particles in matrix) and to convert the 3D model structure into a
> stack (2D image stack by slicing the 3D structure)?
>
> Thanks.
> Regards,
> Yves
>
>
> "The information contained in this message and its attachments is intended
> only for the use of the addressee, you may not use, copy or disclose to
> anyone any information contained in the message and its attachments. If you
> received the message in error, please advise the sender immediately and
> destroy or delete the message. E-mail transmission cannot be guaranteed to
> be secure or error free as information could be intercepted, corrupted,
> lost, destroyed, arrive late or incomplete, or contain viruses. The sender
> therefore does not accept liability for any errors or omissions in the
> content of this message which arise as a result of e-mail transmission. If
> verification is required please request a hard copy version."
>
>
> "De informatie verzonden met dit e-mail bericht en de bijlagen is
> uitsluitend bestemd voor de geadresseerde(n). Gebruik van deze informatie
> door anderen dan de geadresseerde(n) is verboden. Indien u dit e-mail
> bericht bij vergissing heeft ontvangen, wilt u dan de verzender onmiddellijk
> waarschuwen en het bericht vernietigen. Het gebruik van e-mail is niet
> gegarandeerd veilig of foutloos; informatie kan worden onderschept, verminkt
> of verloren gaan; kan te laat of incompleet binnenkomen of virussen
> bevatten. Om deze reden neemt de verzender geen enkele verantwoordelijkheid
> voor fouten of wijzigingen in de inhoud van dit bericht als gevolg van het
> versturen via e-mail. Bij twijfel verzoeken wij u een kopie op te vragen."
>

[Wilfred L. Guerin]

There are a large number of cross-section generators that are used in the
rapid-prototyping field as well as engineering analysis... there are a few
open projects, linux CNC amongst others, and a plethora of standard model
definition types, regardless of if you want hull (surface) boundaries (like
what ij's edge finder looks like) or a fully raytraced model to the planar
projection with any depth of field (cat scans, etc with non planar images)
there are standards that exist. Im sure there are plugins for most of the 3d
modeling and rendering systems, as mentioned blender exists (with a not so
functional interface) and likely many more.

Perhaps it would be best to define your target data characteristics, do you
want a literal slice that might have triangle fragments, a mathematically
accurate shell/hull model (rhino3d, etc), or do you want a contiguous
material characteristic (looks like slices on a slide) or all the way up to
depth compressed tiff data like topographies or CT scan slices? How do you
want to generate your test samples? Do you want a realtime simulation or
time based 3d frames, or simply slices of a single instant? Do you want
ICE/fragments or distortions and blurred depth representations of particles
that are not in the slice? (microscope) etc etc etc

Also I should mention, having last made a module over a decade ago now, that
IDX3D still works in java just like it did long ago, is 100% 3d, and
regardless of some minor technical issues in the code due to java
1.1compliance, it very nicely renders 3d models from 3ds/etc imports
through to
realtime data representations with a fairly simple interface... Drawing 3d
graphs as 3d structures is quite simple, and it can export 3ds to your
browser/applet in runtime. I typically use it for abstract data
visualization with vrml style interface capabilities in the applet. IJ
simply should ask for the same getimage call that the applet demos do, and
you can easily load highly complex 3ds/etc models (20 meg body/brain) with
variable transparency and materials characteristics and spatially accurate
representations in multiple (shared as well) instances within an applet or
ij frames with absolutely no external requirements (no opengl or d3d or
other mess)

Peter's IDX3D is still at

http://idx3d.ch/idx3d/_idx3d.html

or http://idx3d.ch as it has been for over a decade now ;)

Let me know if you need help interfacing realtime visualizations, it is
quite simple and we have a ton of partial demos you can look at from other
projects doing all of the above...

-Wilfred
[hidden email]







On 9/17/07, Justin McGrath <[hidden email]> wrote:

>
> Blender, although it may not be the best tool, can probably do this
> through it's API.
>
> www.blender.org
>
> Justin
>
> On 9/17/07, Nicolas, Y. (Yves) <[hidden email]> wrote:
> > Hello,
> > Not really a ImageJ question but related...
> > Are you aware of software that are able to create a 3D model structure
> > (e.g. particles in matrix) and to convert the 3D model structure into a
> > stack (2D image stack by slicing the 3D structure)?
> >
> > Thanks.
> > Regards,
> > Yves
> >
> >
> > "The information contained in this message and its attachments is
> intended only for the use of the addressee, you may not use, copy or
> disclose to anyone any information contained in the message and its
> attachments. If you received the message in error, please advise the sender
> immediately and destroy or delete the message. E-mail transmission cannot be
> guaranteed to be secure or error free as information could be intercepted,
> corrupted, lost, destroyed, arrive late or incomplete, or contain viruses.
> The sender therefore does not accept liability for any errors or omissions
> in the content of this message which arise as a result of e-mail
> transmission. If verification is required please request a hard copy
> version."
> >
> >
> > "De informatie verzonden met dit e-mail bericht en de bijlagen is
> uitsluitend bestemd voor de geadresseerde(n). Gebruik van deze informatie
> door anderen dan de geadresseerde(n) is verboden. Indien u dit e-mail
> bericht bij vergissing heeft ontvangen, wilt u dan de verzender onmiddellijk
> waarschuwen en het bericht vernietigen. Het gebruik van e-mail is niet
> gegarandeerd veilig of foutloos; informatie kan worden onderschept, verminkt
> of verloren gaan; kan te laat of incompleet binnenkomen of virussen
> bevatten. Om deze reden neemt de verzender geen enkele verantwoordelijkheid
> voor fouten of wijzigingen in de inhoud van dit bericht als gevolg van het
> versturen via e-mail. Bij twijfel verzoeken wij u een kopie op te vragen."
> >
>