Fuhai Li, Ph.D. BBP-TMHRI, Feb 7 2011 3D Tumor Stem Cell Niche Image Analysis NCI-ICBP CMCD U54...
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![Page 1: Fuhai Li, Ph.D. BBP-TMHRI, Feb 7 2011 3D Tumor Stem Cell Niche Image Analysis NCI-ICBP CMCD U54 Progress Report.](https://reader036.fdocument.pub/reader036/viewer/2022062518/56649ee85503460f94bf9366/html5/thumbnails/1.jpg)
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
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Tumor Stem Cell Niche
J Rosen, BCM
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From 2D to 3D
From center grant proposal
DAPI GFP
Dextran Superimposed .44 μm X .44 μm X 1 μm
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Specific Aim
Digitize 3D images of tumor stem cell niche & provide quantitative data for
• Tumor modeling• Blood vessel tracing• Nuclei segmentation
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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
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Blood Vessel and Nuclei Segmentation
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Blood Vessel Segmentation
(Tracing)
Technical Challenges:
Noise Signal
Broken Points and Vessel Crossing
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3D Blood Vessel Image
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Maximum Intensity Projection (MIP)
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Validation of Available Segmentation Software
http://research.mssm.edu/cnic/tools-ns.html
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NeuronStudio
http://research.mssm.edu/cnic/tools-ns.html
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V3D
http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html
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FARSIGHT
http://www.farsight-toolkit.org/wiki/Main_Page
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Multi-scale Filtering and Optimal Linking Based Approach
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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
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Binary Image of MIP (Original)
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Multiscale Vessel Enhancement Filtering
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Removal of Debris
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Skeleton Extraction
T.C. Lee, et. al, GVGIP, 1994
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Binary
3D View
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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:
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Nuclei Segmentation
Technical Challenges:
Uneven Intensity and Cell Clustering
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3D View
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FARSIGHT
3D Analysis
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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
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2D Image Analysis
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TT
Proposed
3D Analysis
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Refine & Define Nuclei by Ellipsoid Fitting
Low Z resolution
digital 3D tumor stem cell nichenucleus = {o, a, b, c, α, β}
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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
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TT
Normal
Breast
Tissue
From Dr. Michael T. Lewis (John David Acquired)
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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