3D Viewer and exporting STL files

[White, Stuart]

I am trying to export an STL file of a surface rendering of a fossil wolf skull made in 3D Viewer. The 3D view of the skull looks great but when I go to: File / Export surfaces / STL (binary or ASCII) the result is the message; “No meshes to export!”  What am I doing wrong?

Thanks in advance for any help,

Stuart White

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[dscho]

Hi Stuart,

On Tue, 29 Jul 2014, White, Stuart wrote:

> I am trying to export an STL file of a surface rendering of a fossil
> wolf skull made in 3D Viewer. The 3D view of the skull looks great but
> when I go to: File / Export surfaces / STL (binary or ASCII) the result
> is the message; “No meshes to export!”  What am I doing wrong?

Are you looking at a volume rendering (the default mode of the 3d viewer)?
If so, give the isosurface a try. For details, see the paper, and look for
the description of the different visualisation modes.

Ciao,
Johannes

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[Michael Doube-4]

Hi Stuart,

On 29/07/14 01:31, White, Stuart wrote:
> I am trying to export an STL file of a surface rendering of a fossil wolf skull made in 3D Viewer.

You might find the Isosurface command in BoneJ convenient. It is just a little plugin which uses the 3D Viewer's API.

http://bonej.org/isosurface

I've composed a bit of code which will make a binary STL straight from an open stack (or virtual stack) without needing to visualise it, which can be handy if you are making too many triangles for your suffering GPU. It's not released, because the code is embarrassingly cut-and-pasted rather than nicely reusing methods (needed a quick solution at the time and haven't got back to fix it properly). Let me know off-list if you'd like a copy.

Michael


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[White, Stuart]

Hi Johannes,

Thanks for the tip. Indeed, when I construct a surface rendering and not a volume rendering, the result saves as an STL file.

What is the paper you refer to for details? I would like to read it.

Best,

Stuart





On Jul 28, 2014, at 7:41 PM, Johannes Schindelin <[hidden email]> wrote:

> Hi Stuart,
>
> On Tue, 29 Jul 2014, White, Stuart wrote:
>
>> I am trying to export an STL file of a surface rendering of a fossil
>> wolf skull made in 3D Viewer. The 3D view of the skull looks great but
>> when I go to: File / Export surfaces / STL (binary or ASCII) the result
>> is the message; “No meshes to export!”  What am I doing wrong?
>
> Are you looking at a volume rendering (the default mode of the 3d viewer)?
> If so, give the isosurface a try. For details, see the paper, and look for
> the description of the different visualisation modes.
>
> Ciao,
> Johannes

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[Albert Cardona-2]

2014-07-29 15:12 GMT-04:00 White, Stuart <[hidden email]>:

> Hi Johannes,
>
> Thanks for the tip. Indeed, when I construct a surface rendering and not a
> volume rendering, the result saves as an STL file.
>
> What is the paper you refer to for details? I would like to read it.
>
> Best,
>
> Stuart
>

I think Johannes refers to his:

"A high-level 3D visualization API for Java and ImageJ"
http://www.biomedcentral.com/1471-2105/11/274/


Albert

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[Kenneth Sloan-2]

I have one of those, too - I just wanted to note that it’s convenient to also
make sure the STL file is “manifold”.  On difficulty is that the “right” way to
do this is domain-specific.

If memory serves, I ended up writing one of these for case of a complete Stack, and another
for the special case of a single image.   We do a lot or work where it is convenient to convert
a single binary image into a (one voxel thick) slab.


--
Kenneth Sloan
[hidden email]


On Jul 29, 2014, at 15:12 , White, Stuart <[hidden email]> wrote:

> Hi Johannes,
>
> Thanks for the tip. Indeed, when I construct a surface rendering and not a volume rendering, the result saves as an STL file.
>
> What is the paper you refer to for details? I would like to read it.
>
> Best,
>
> Stuart
>
>
>
>
>
> On Jul 28, 2014, at 7:41 PM, Johannes Schindelin <[hidden email]> wrote:
>
>> Hi Stuart,
>>
>> On Tue, 29 Jul 2014, White, Stuart wrote:
>>
>>> I am trying to export an STL file of a surface rendering of a fossil
>>> wolf skull made in 3D Viewer. The 3D view of the skull looks great but
>>> when I go to: File / Export surfaces / STL (binary or ASCII) the result
>>> is the message; “No meshes to export!”  What am I doing wrong?
>>
>> Are you looking at a volume rendering (the default mode of the 3d viewer)?
>> If so, give the isosurface a try. For details, see the paper, and look for
>> the description of the different visualisation modes.
>>
>> Ciao,
>> Johannes
>
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> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[dscho]

Hi Stuart,

On Tue, 29 Jul 2014, White, Stuart wrote:

> What is the paper you refer to for details? I would like to read it.

I am on a phone right now; please go to PubMed and search for authors B
Schmid and J Schindelin and you should find it.

Thank you,
Johannes

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[ndr.ferrari]

Hi Michael,

i am trying to export a big surface mesh (STL) and i have many visualization problems. Can you please send me your script, i think it will be very usefull.

thanks

andrea