Fully Automatic Blood vessel Branch Labeling

Lei Chen

Supervisors:Ir. Jan BruijnsProf. Bart M. ter Haar Romeny

Biomedical Engineering PAGE 221-04-23

Content

• Pathophysiology background− Brain aneurysm− Coronary artery disease (CAD)

• Therapy with medical imaging technology− 3D rotational angiography (3DRA)

• Research software environment− The demo program

• My research questions− Faster blood vessel analysis

− Surface wave propagation− Faster branch labeling

Background- Pathophysiology

• Aneurysm• 1/15 people in the United States• Rupture-bleeding into the brain

From www.nhlbi.nih.govPAGE 321-04-23

Background- Pathophysiology

• CAD - atherosclerosis• Blood clots block blood

vessel to cause a heart attack

From www.nhlbi.nih.gov PAGE 421-04-23

Medical Imaging Technology

• Diagnosis of aneurysms and CAD

• 3D rotational angiography (3DRA)

(From www.brainaneurysm.com) PAGE 521-04-23

Therapy with 3DRA

• Treatment • Brain aneurysms

• Endovascular Coiling

• Surgical Clipping

• CAD• Place a stent

(From www.brainaneurysm.com)PAGE 621-04-23

Software Environment

• Research tools• Linux system• Made by C++• Display window• Control window

− Seven sub-windows with interaction sub-sets

Biomedical Engineering PAGE 721-04-23

Biomedical Engineering PAGE 821-04-23

Research Questions

• Blood vessel analysis – Shape parameters extraction− Aneurysm volume, Stenosis size, etc.− Original analysis algorithm:

− Fully automatic branch labeling of Voxel Vessel Structures

• My work: improved branch labeling algorithm− Surface wave propagation− Centerlines extraction− Bifurcations detection

Research Questions

• Shape parameters extraction

Biomedical Engineering PAGE 921-04-23

Input datasets

Segmentation

Branches Labeling

Computer-Aided Treatment Planning

Original Algorithm

• Fully automatic branch labeling of voxel vessel structures

Biomedical Engineering PAGE 1021-04-23

Detect extremities

Extract skeleton

Labeling branches

Create vessel graphs

Create node geometry

Original Algorithm: 1st Step - The Extremities Detection

• Wave propagation algorithm• Double and multiple Zahlten waves

Biomedical Engineering PAGE 1121-04-23

Find seeds

Initial wave

Double or multiple Waves

Direction adjustment

Get extremities

Wave propagation

• The volume wave propagation

Biomedical Engineering PAGE 1221-04-23

My work: Faster wave propagation-Task 1

• Acceleration algorithms• Down sampling

− Resize the datasets

− Drawbacks

− Lost information

− Decrease accuracy

• Surface wave propagation− Propagate on the surface of the

blood vessel− Seed point selection− Extremities detection

Biomedical Engineering PAGE 1321-04-23

Faster Wave Propagation : Down Sampling

• Acceleration algorithm• Down sampling

− 2*2*2 original voxels -> 1 new voxel

− Original volume -> smaller

• Method: Average as threshold

Biomedical Engineering PAGE 1421-04-23

}}8,...,1,0{{,))(( ,,

12

2

12

2

12

2,,,,

kji

i

ip

j

jq

k

krrqpkji SoS

1:?)( ,,,, xTSn kjikji

Processing

Down Sampling Result Analysis

• Down sampling• Result: the false and the lost extremity• Comparison:

− The saving computation time

− The number and position of the extremities

Biomedical Engineering PAGE 1521-04-23

Datasets

Old / New methodFalse/Lost

extremities

Improved

speed/ratioExtremities elapsed time

128*128*128

Aneurysm

phantom7 / 5 0.457 / 0.342s 0/2 0.115s/25%

Stenosis1 22 / 20 0.337 / 0.281s 1/3 0.06s/17%

Stenosis1_po

st54 / 53 0.512 / 0.461s 6/1 0.05s/10%

256*256*256

Large_ane02 59 / 48 24.119 / 8.375s 12/23 15.74s/65%

Large_ane50 179 / 180 5.510 / 4.487s 27/82 1.02s/19 %

Large_ane51 177 / 93 33.770 / 14.969s 18/103 18.8s/56%

Faster Wave Propagation : Surface Wave Propagation

Biomedical Engineering PAGE 1621-04-23

• Seed point selection− Detect seed points on the boundary layers− Initialize the 1st wave

• Set special label to the surface voxel• Adjust the extremities selection method

− Keep the waves continuity− Detect the false extremities − A center voxel in the stop wave – an extremity

Wave propagation on surface

Biomedical Engineering PAGE 1721-04-23

• The surface wave propagation

Result of Surface Wave Propagation

• 26 – connected path between the original and new extremities

Biomedical Engineering PAGE 1821-04-23

Acceleration of Branch Labeling – Task 2

• Extract the center lines and the bifurcations• Problem: bifurcation correction - thinning method

• To combine the first two original steps to one

Biomedical Engineering PAGE 1921-04-23

Improved Branch Labeling Algorithm

• The wave moving− Simulation by a probe− Single wave normal calculation

• Methods− Propagate from the root to the branches

− Propagate from the branches to the root

Biomedical Engineering PAGE 2021-04-23

Bifurcation Detection

• Centerlines extraction• Single wave normal calculation

− A plane F (x, y, z) = ax + by + cz + d = 0

− A normal vector (a, b, c)

− The voxel points in a wave put into a linear equations: AX=0

Biomedical Engineering PAGE 2121-04-23

Single wave normal calculation

• Single wave normal calculation

• homogeneous least square problem

• Singular value decomposition

Matrix : A=USV*A: consist of all the voxels

U: m-by-m unitary matrix

S: m-by-n diagonal matrix with nonnegative Eigen values

V: n-by-n unitary matrix include the Eigen vectors

Biomedical Engineering PAGE 2204/21/23

i i i iAx By Cz d

[0 0 0]TN n 2

1 1 1

2

1 1 1

2

1 1 1

N N N

i i i i ii i i

N N N

i i i i ii i i

N N N

i i i i ii i i

x x y x z

N y x y y z

z x z y z

Single wave normal calculation

• Single wave normal result

Biomedical Engineering PAGE 2321-04-23

Center points and Bifurcation Detection

• Method

1. Store the wave parameters, the average diameter etc.

2. Find and label the abnormal wave

3. Detect the disconnected waves

4. Find the bifurcation

− Go back to the abnormal wave to label the bifurcation

5. Store the bifurcation voxels

Biomedical Engineering PAGE 2421-04-23

Move waves

Store wave parameters

Label (abnormal) waves/branch

Label bifurcation

Position bifurcation point

Bifurcation Detection Result

• Propagate from the root to the branch

Biomedical Engineering PAGE 2521-04-23

Bifurcation Detection Validation

• Compare to the original algorithm

Biomedical Engineering PAGE 2621-04-23

Surface Wave Propagation - Validation

• The validation and comparison between the original and new wave propagation− The saving computation time

− The number and position of the extremities− Decidability of the old and new extremity on the same tip: 26 – connected path

Biomedical Engineering PAGE 2704/21/23

Datasets

Old / New methodLost/False extremities

Improve to ratioExtremities Elapsed time

128*128*128

Aneurysm p 7 / 6 0.663 / 0.37s 1/0 44%

Stenosis1 22 / 22 0.328 / 0.18s 0/0 45%

Stenosis1_post 51 / 49 0.297 / 0.19s 3/1 36%

256*256*256

Large_ane02 58 / 53 48.543 / 15.32s 12/18 68%

Large_ane50 155 / 120 7.229 / 4.76s 46/11 34 %

Large_ane52 81 / 68 36.39 / 11.31 18/5 69%

Surface Wave Propagation Validation

• Compare to the original algorithm

Biomedical Engineering PAGE 2821-04-23

Bifurcation Detection Validation

• Compare to the original algorithm

Biomedical Engineering PAGE 2921-04-23

Conclusion

Biomedical Engineering PAGE 3004/21/23

• Surface wave propagation gives correct extremity detection results. the detection time is decreased at 34% to 69%.

• The centerlines and bifurcations extraction gives correct and visually acceptable results.

Future Work

Biomedical Engineering PAGE 3121-04-23

• Detect the bifurcation

• The bifurcation adjustment

• Centerlines validation

Questions?

• Questions?

Biomedical Engineering PAGE 3221-04-23

• Thanks for your attention!