Plugin to Export 3D Meshes

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Plugin to Export 3D Meshes

Anne Jorstad
Hi - does anybody know if a Fiji plugin already exists to export TrakEM2 area lists to Wavefront (.obj) files?  That is, exactly the operation of the script found on the TrakEM2 scripting page https://imagej.net/TrakEM2_Scripting under "Generate a 3D mesh for an AreaList" (but looping over all area lists, without a separate popup for each).  We use a modified version of this script with success, but it's a bit cumbersome when exporting lots of area lists from lots of files, and it would be very helpful to be able to do this with an efficient plugin.

(Yes, this is for Macs that can't run the 3D viewer, and for whom all the work-arounds regarding java 6 vs java 8 don't seem to work on more recent Mac operating systems.)

Thanks for your help!

Anne Jorstad, PhD
Data Visualization Scientist
BioEM Facility, EPFL

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Re: Plugin to Export 3D Meshes

Albert Cardona-2
Hi Anne,
Which is the cumbersome part in the script? What does your script do now, and what would you want instead?
Best,
Albert

> On May 1, 2020, at 11:49 AM, Jorstad Anne Alison <[hidden email]> wrote:
>
> Hi - does anybody know if a Fiji plugin already exists to export TrakEM2 area lists to Wavefront (.obj) files?  That is, exactly the operation of the script found on the TrakEM2 scripting page https://imagej.net/TrakEM2_Scripting under "Generate a 3D mesh for an AreaList" (but looping over all area lists, without a separate popup for each).  We use a modified version of this script with success, but it's a bit cumbersome when exporting lots of area lists from lots of files, and it would be very helpful to be able to do this with an efficient plugin.
>
> (Yes, this is for Macs that can't run the 3D viewer, and for whom all the work-arounds regarding java 6 vs java 8 don't seem to work on more recent Mac operating systems.)
>
> Thanks for your help!
>
> Anne Jorstad, PhD
> Data Visualization Scientist
> BioEM Facility, EPFL
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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Re: Plugin to Export 3D Meshes

Anne Jorstad
In reply to this post by Anne Jorstad
Hi Albert-

Thanks for your reply. As the ‘View in 3D’ function no longer works in TrakEM2 we are pursuing other options to simply export a 3D model. This script is one way to do this, but would be convenient if it could be used as a plugin. This would be quicker than having to run a script each time. If you have any suggestion we would be grateful.

Thanks,
--Anne

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Re: Plugin to Export 3D Meshes

Albert Cardona-2
Hi Anne,
TrakEM2 has a plugin system, so that when you load TrakEM2, its
plugins appear in the display's contextual menu. Write a plugin that
implements https://javadoc.scijava.org/Fiji/ini/trakem2/plugin/TPlugIn.html
and then put its compiled classes in a jar file, with also a text file
for the plugin menu configuration (like that of ImageJ's plugins)
whose name ends in ".trakem2"--so that TrakEM2 can find it. See the
parsing of this text config file here:
https://github.com/trakem2/TrakEM2/blob/master/src/main/java/ini/trakem2/Project.java#L129

Or, you could assign a hotkey in Fiji to run your script. That's the
easiest: ever since scripts exists in Fiji/ImageJ, I haven't had the
need to write a TPlugin ever.

Or, you could write a regular Fiji/ImageJ plugin (see example here
https://www.ini.uzh.ch/~acardona/trakem2_manual.html#plugins_howto )
and run that: it can access all the data of an open TrakEM2 project.
This can also be assigned a hotkey, or, upon invocation, setup a menu
within TrakEM2's windows.

Best,

Albert

Missatge de Anne Jorstad <[hidden email]> del dia dv., 8 de maig
2020 a les 8:16:

>
> Hi Albert-
>
> Thanks for your reply. As the ‘View in 3D’ function no longer works in TrakEM2 we are pursuing other options to simply export a 3D model. This script is one way to do this, but would be convenient if it could be used as a plugin. This would be quicker than having to run a script each time. If you have any suggestion we would be grateful.
>
> Thanks,
> --Anne
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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