Surface Nets

Constrained Elastic SurfaceNets:
generating smooth surfaces from binary segmented data
Sarah F. F. Gibson
MERL - A Mitsubishi Electric Research Lab
Binary Data
binary
segmentation produces rough, unrealistic models
need
models with smooth surfaces for high quality rendering and for modeling physical interactions MERL - A Mitsubishi Electric Research Lab
Artifacts from Binary Data
polygon rendered medial meniscus from MRI @ 0.27x0.27x0.25 mm resolution volume rendered knee bones from MRI @ 0.27x0.27x1.4 mm resolution
Surface Smoothing
existing
techniques:
1) local smoothing (e.g. low pass filtering of the binary data) and then surface construction using an algorithm such as Marching Cubes 2) global smoothing by warping a parameterized surface to fit the binary surface
Low-pass Filtering
low
pass filtering smoothes local features but does not remove terraces unless the filter size is quite large
Problems with Local Smoothing

low
pass filtering removes fine detail indiscriminately filtering does not remove terracing artifacts unless the filter size is large smoothing and decimation of the Marching Cubes surface is done without reference to the original data
local
additional
Global Smoothing
global
smoothing by warping a parameterized surface to find a minimum energy surface
example from I. Takanahi et al, SUNY-SB

Problems with Global Smoothing

choosing
the number of grid points in the parameterized model depends on the amount of detail in the surface
tradeoffs
between smoothness and surface detail is made by setting global parameters
Constrained Elastic SurfaceNets
Constrained Elastic SurfaceNets

initialize
an elastic net of surface nodes at the resolution of the data to fit the binary surface the net to smooth the surface while constraining the nodes using the binary data a globally smooth surface that is locally faithful to the original segmentation
relax
attain
Algorithm in 2D
sample point
cell
interior data sample
Algorithm in 2D
surface cell
interior data sample
1)
locate surface cells

Algorithm in 2D
X X X X X X X X X
interior data sample SurfaceNet node
2)
place a SurfaceNet node at the center of each surface cell

Algorithm in 2D
X X X X X X X X X
interior data sample SurfaceNet node SurfaceNet link
3)
establish links between 4-connected surface nodes

Algorithm in 2D
X X X X X X X X X
interior data sample SurfaceNet node SurfaceNet link
4)
adjust node positions to relax the SurfaceNet while remaining within the original surface cell
2D Examples
initial
initial
2D Examples
initial
1 iteration
initial
1 iteration
2D Examples
initial
1 iteration
30 iterations
initial
1 iteration
20 iterations
Topological Considerations
For
ambiguous surface topologies:
Marching
Cubes makes arbitrary decisions about surface topology
10
Marching
Cubes makes arbitrary decisions about surface topology
Surface
Nets maintain surface ambiguity for later high level processing

X X X X X X X X
11
3D Algorithm
1)
locate surface cells 2) place a SurfaceNet node at the center of each surface cell
3)
establish links between 6-connected surface nodes 4) adjust node positions to relax the SurfaceNet while remaining within the original surface cell
3D Examples
original surface
1 relaxation
2 relaxations
3 relaxations
4 relaxations
5 relaxations
6 relaxations
7 relaxations
8 relaxations
9 relaxations
Binary sphere: radius 30 voxels

10 relaxations 15 relaxations
12
3D Examples
original surface
1 relaxation
12 relaxations
Femur, 0.27 x 0.27 x 1.0 mm resolution

Building a Surface Triangle Model

Nice
Properties of SurfaceNets:
1) surface triangles can be generated automatically from the structure of the SurfaceNet 2) the triangle model only needs to be constructed once
as the surface relaxes, the topology is maintained and only the triangle vertex positions and normals change
13
Surface Triangulation
each
SurfaceNet node has 6 possible links and hence 12 possible triangles

top front left back
x
bottom
right
front-back
face
top front
left back
x
bottom
right
14
left-right
face
top front left back
x
bottom
right
top-bottom face
top front left back
x
bottom
right
15
construct
the triangles for each node based on the presence or absence of links to the nodes 6 possible neighbors triangles to point out of the segmented object by referencing the binary segmentation
orient
Examples
brain atlas, segmented data courtesy of SPL, Brigham and Womens Hospital
16
Examples
volume rendered brain from smoothed SurfaceNet

Examples
surface model of the femur after low-pass filtering, Marching Cubes, and rendering with Vtk
surface model of the femur from SurfaceNets, rendered with OpenGL
17
Examples
abdominal arteries, segmented data courtesy of SPL, Brigham and Womens Hospital
SurfaceNets
Binary Segmentation Smooth Surface Model
SurfaceNets:
removes terracing artifacts preserves fine detail remains faithful to the original segmentation
Volume Rendering
Polygon Rendering
18
Thanks
data and binary segementations from the Surgical Planning Lab, Brigham and Womens Hospital Mike Leventon for Vtk and Marching Cubes example
19
Why Use Binary Segmented Data?
20

Surface Nets

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Surface Nets

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Constrained Elastic SurfaceNets:

generating smooth surfaces from binary segmented data

segmentation produces rough, unrealistic models

Artifacts from Binary Data

MERL - A Mitsubishi Electric Research Lab

Problems with Local Smoothing

smoothing by warping a parameterized surface to find a minimum energy surface

example from I. Takanahi et al, SUNY-SB

Problems with Global Smoothing

between smoothness and surface detail is made by setting global parameters

MERL - A Mitsubishi Electric Research Lab

Constrained Elastic SurfaceNets

MERL - A Mitsubishi Electric Research Lab

Constrained Elastic SurfaceNets

interior data sample

MERL - A Mitsubishi Electric Research Lab

interior data sample

locate surface cells

place a SurfaceNet node at the center of each surface cell

establish links between 4-connected surface nodes

ambiguous surface topologies:

MERL - A Mitsubishi Electric Research Lab

Cubes makes arbitrary decisions about surface topology

MERL - A Mitsubishi Electric Research Lab

Cubes makes arbitrary decisions about surface topology

MERL - A Mitsubishi Electric Research Lab

Nets maintain surface ambiguity for later high level processing

MERL - A Mitsubishi Electric Research Lab

Binary sphere: radius 30 voxels

Femur, 0.27 x 0.27 x 1.0 mm resolution

Building a Surface Triangle Model

SurfaceNet node has 6 possible links and hence 12 possible triangles

MERL - A Mitsubishi Electric Research Lab

MERL - A Mitsubishi Electric Research Lab

MERL - A Mitsubishi Electric Research Lab

MERL - A Mitsubishi Electric Research Lab

MERL - A Mitsubishi Electric Research Lab

volume rendered brain from smoothed SurfaceNet

surface model of the femur from SurfaceNets, rendered with OpenGL

MERL - A Mitsubishi Electric Research Lab

MERL - A Mitsubishi Electric Research Lab

MERL - A Mitsubishi Electric Research Lab

Why Use Binary Segmented Data?

MERL - A Mitsubishi Electric Research Lab

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