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Re: [Seg3D] Fwd: Poisson noise and 'black' background removal

Chronological Thread 
  • From: Jess Tate <>
  • To: "" <>
  • Cc:
  • Subject: Re: [Seg3D] Fwd: Poisson noise and 'black' background removal
  • Date: Wed, 22 Jun 2016 11:52:43 -0600

Hi Mike,

The first question you have about removing the background from the 3D view isn’t really possible as I understand what you are asking.  You can remove the slices from the 3D view, and show only the isosurface (An isosurface of this data would be easy to make).  If you have more than one layer, you could play with the opacity to show layers underneath.  Another option is to try the volume rendering (or use the volume rendering in ImageVis3D).  check out the Basic functionality document (search for volume rendering) linked here:

as for your second question, there are a number of filters for smoothing and noise removal.  There is a gaussian blur filter in the Data filters menu, for example.  This noise looks similar to the noise we see in CT scans of the torso, which I usually use the median filter, or curvature anisotropy diffusion filter (in the advanced filter menu) to reduce.  The previously mentioned document provides some descriptions of each of the filters. 


On Jun 22, 2016, at 10:36 AM, Ayla Khan <> wrote:

A couple of Seg3D usage questions. To answer the first, you can change the background color in Preferences under the View tab.


Begin forwarded message:

From: Mike Meyer <>
Subject: Poisson noise and 'black' background removal
Date: June 22, 2016 9:44:12 AM MDT
To: Ayla Khan <>

Hi Ayla,

I was wondering if you could send this out to the list.

HI All,

I have 2 issues, one of which is likely a 'newbie' one:

Problem 1) Removing black background from volume viewer/seeing true 3D data in volume viewer. 

In the attached image 1a you can see the volume view of my data (it is a layered rock) but it is sill showing the black background and the 3-axis. I would like to remove that black background, see this in 3D with the coloring (of the rock layers visible), not just a single color mask.

Problem 2) Poisson Noise removal

Is there a way to lessen this type of noise in Seg3D? you can see in image 2a a look at the axial plane and the cross-hatched artifacts. I know that I won't be able to remove these entirely, but if I could lessen them I could get to some nice data on the interior of the rock.

Please let me know if you have any tips!



Mike Meyer, PhD

Geophysical Laboratory
Carnegie Institution for Science
5251 Broad Branch Rd. NW
Washington, DC 20015-1305, USA

Office: 202-478-8910


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