Fuhai Li, Ph.D.BBP-TMHRI, Feb 7 2011

3D Tumor Stem Cell Niche Image Analysis

http://www.methodisthealth.com/icbp

NCI-ICBP CMCD U54 Progress Report

Tumor Stem Cell Niche

J Rosen, BCM

From 2D to 3D

From center grant proposal

DAPI GFP

Dextran Superimposed .44 μm X .44 μm X 1 μm

Specific Aim

Digitize 3D images of tumor stem cell niche & provide quantitative data for

• Tumor modeling• Blood vessel tracing• Nuclei segmentation

What information is expected?Anything we can see, image,

and imagine! E.g.,

• Spatial distributions (in normal and tumor, before and after treatment) of blood vessels, stem cells, stroma, etc.

• Cell morphology, proliferation and death

From John, Tegy, Mei Zhang, Michael T. Lewis

Blood Vessel and Nuclei Segmentation

Blood Vessel Segmentation

(Tracing)

Technical Challenges:

Noise Signal

Broken Points and Vessel Crossing

3D Blood Vessel Image

Maximum Intensity Projection (MIP)

Validation of Available Segmentation Software

http://research.mssm.edu/cnic/tools-ns.html

NeuronStudio

http://research.mssm.edu/cnic/tools-ns.html

V3D

http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html

FARSIGHT

http://www.farsight-toolkit.org/wiki/Main_Page

Multi-scale Filtering and Optimal Linking Based Approach

Multiscale Vessel Enhancement Filtering

2

2

2

, ,

, ,

, ,

I I Ix y x zx

I I IH I y x y zy

I I Iz x z y z

Hessian Matrix

Multiscale means image filtering with Gaussian filters (with different sigmas)The eigenvalues of Hessian matrix tell us where are the vessels

A. Frangi, et. al, MICCAI, 1998

Binary Image of MIP (Original)

Multiscale Vessel Enhancement Filtering

Removal of Debris

Skeleton Extraction

T.C. Lee, et. al, GVGIP, 1994

Binary

3D View

Optimal Linking by Integer Programming (ongoing)

1

, ,i i

i i

p p ip p

v p q I p

argmax ,all possible broken pairs

v p q

Cost function:

,p q can only be linked to at most to once!subject to:

Fitness termsmoothness term

Solving:

Nuclei Segmentation

Technical Challenges:

Uneven Intensity and Cell Clustering

3D View

FARSIGHT

3D Analysis

Flowchart of Nuclei Segmentation

Z-Series 2D Images

Adaptive Thresholding

Distance Transform(Shape Info.)

Seed Image(Non-Maximum Suppression)

LoG Filtering(Intensity Info.)

Level Set Segmentation

2D Image Analysis

TT

Proposed

3D Analysis

Refine & Define Nuclei by Ellipsoid Fitting

Low Z resolution

digital 3D tumor stem cell nichenucleus = {o, a, b, c, α, β}

Ongoing Work

1. Blood vessel smoothing & broken points linking

2. Nuclei ellipsoid fitting, Image quantification & dividing cell identification

3. Process large volumes of image data to derive information for tumor modeling

4. Graphic user interface (GUI) tools for image analysis, visualization & tumor simulation

TT

Normal

Breast

Tissue

From Dr. Michael T. Lewis (John David Acquired)

Acknowledgements

BBP-TMHRI:

Stephen Wong

Xiaofeng Xia

Hong Zhao

Derek Cridebring

BCM:

Michael Lewis

Mei Zhang

Mary Dickinson

John Landua

Tegy Vadakkan

Wei Wei

NIH NCI-ICBP U54 Grant Support