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RE: [Seg3D] Interpolate for ROIs?


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  • From: <Leon.Driessen@radboudumc.nl>
  • To: <jess@sci.utah.edu>, <hilatzipora@gmail.com>
  • Cc: <seg3d@sci.utah.edu>
  • Subject: RE: [Seg3D] Interpolate for ROIs?
  • Date: Mon, 25 Sep 2017 05:59:07 +0000
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Hi Jess,

It's a pitty that this function isn't available in Seg3D (yet?). This would
make segmenting large objects só much easier and faster! Especially when you
combine this with a threshold setting. I myself use this function a lot in
Mimics.
If you are interested in how it works, just let me know. Maybe you'll like
it. ;)

Léon Driessen

-----Original Message-----
From: seg3d-request@sci.utah.edu [mailto:seg3d-request@sci.utah.edu] On
Behalf Of Jess
Sent: zondag 24 september 2017 21:02
To: hilatzipora@gmail.com
Cc: seg3d@sci.utah.edu
Subject: Re: [Seg3D] Interpolate for ROIs?

Hi,

That isn’t really implemented in Seg3D.

You can try using the fast binary dilate and erode filter. If you make the
radius greater than half the distance between the slices, then it should
close off the distance. This will also smooth the image and you will need to
be careful to not hit the boundaries of the volume (you can use the pad tool
to make it bigger).

Another tool that might help you is the implicit surface tool. If you place
contour points every several slices and run it, it will try to fit a radial
basis function to the points to make a smooth surface segmentation. This
tool works best to start with sparse points and fill int eh detail as needed.

cheers,
Jess




> On Sep 24, 2017, at 8:02 PM, hilatzipora@gmail.com wrote:
>
> Is there any way to interpolate a region (volume) of interest from
> selected regions on slices throughout a volume? I.e. choosing the
> region every 10 slices through a volume instead of selecting the 2D
> region on every slice in the stack.
>
> Thanks!
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