TrakEM2 - 3D Viewer

[mandue]

Dear Mailing-List,

I have two questions concerning the TrakEM2 plugin and the associated 3D Viewer - thanks for your input!

I

I used TrakEM2 to organize EM-images of serial sections. Then I segmented cells as arealists on these serial sections and used the Shift+mouse-click option to fill these arealists. The 3D Viewer nicely represents the segmented volume in 3D. However, I want to make use of another representation of the segmented arealists: I would like to see the segmented cell outlines only as outlines, without any filling.

I found already a way to reuse the segmented arealists for this:

- I export the arealist as labels (tif), and use the edge detection function and a thresholding to get a binary image of the cell outline. 

- I save this cell outline (serial sections) as a tif-image stack.

- This image stack is then imported to the canvas of the TrakEM2 plugin as an arealist.

- The representation of the cell outline works perfectly within the display on the various layers.

- However, when I want to display this new imported cell-outline arealist in the 3D viewer, it automatically fills the contours, such that the view is the same of the newly imported cell-outline arealist and the arealist that was used for the export.

—> It would be great if you had advise on how I can prevent the 3D viewer to create the filling of the arealist. 

—> Or do you have other suggestions on how I could create outline of the segmented arealists and display it in the 3D Viewer.

II

Also, I wonder if one can label certain arealists within the 3D Viewer display?

Thanks a lot for your suggestions,

best wishes,

Mandy

[Albert Cardona-2]

Hi Mandy,

Within TrakEM2 there are options to visualize AreaLists as outlines rather
than as filled areas. Also to alter their transparency. Select an AreaList,
right-click and choose "Properties...".

In the 3D Viewer you can't have outlines. What you can have is a wireframe
instead of a solid mesh, or a transparent mesh, or a transparent wireframe
mesh. To render the meshes as wireframes there are options in the 3D
Viewer: click on a mesh, right-click and edit its properties.

Best,

Albert



2016-02-09 6:30 GMT-05:00 mandue <[hidden email]>:

> Dear Mailing-List,
>
> I have two questions concerning the TrakEM2 plugin and the associated 3D
> Viewer - thanks for your input!
>
> I
>
> I used TrakEM2 to organize EM-images of serial sections. Then I segmented
> cells as arealists on these serial sections and used the Shift+mouse-click
> option to fill these arealists. The 3D Viewer nicely represents the
> segmented volume in 3D. However, I want to make use of another
> representation of the segmented arealists: I would like to see the
> segmented cell outlines only as outlines, without any filling.
> I found already a way to reuse the segmented arealists for this:
> - I export the arealist as labels (tif), and use the edge detection
> function and a thresholding to get a binary image of the cell outline.
> - I save this cell outline (serial sections) as a tif-image stack.
> - This image stack is then imported to the canvas of the TrakEM2 plugin as
> an arealist.
> - The representation of the cell outline works perfectly within the
> display on the various layers.
> - However, when I want to display this new imported cell-outline arealist
> in the 3D viewer, it automatically fills the contours, such that the view
> is the same of the newly imported cell-outline arealist and the arealist
> that was used for the export.
>
> —> It would be great if you had advise on how I can prevent the 3D viewer
> to create the filling of the arealist.
> —> Or do you have other suggestions on how I could create outline of the
> segmented arealists and display it in the 3D Viewer.
>
> II
>
> Also, I wonder if one can label certain arealists within the 3D Viewer
> display?
>
>
> Thanks a lot for your suggestions,
> best wishes,
> Mandy
>
>
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/TrakEM2-3D-Viewer-tp5015581.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
http://albert.rierol.net
http://www.janelia.org/lab/cardona-lab
http://www.ini.uzh.ch/~acardona/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html