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Shape data modelling and analysisas a support in the diagnosis ofvascular diseases

M. Attene, M. Mortara, G. PatanèCNR-IMATI Ge

Speaker: Michela Mortaramichela@ge.imati.cnr.it

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Shape Modelling

Aquisition Reconstruction Processing …

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Shape Analysis

Characterization Segmentation Structuring …

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In the following…

Tailor

Plumber

Convex Approximation

ShapeAnnotator

with possible applications in the medical field

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Tailor

Use a curvature analysis to compute themain features of a given shape and organizethem into an abstract representation

Automate processes likematching, retrieval, comparisonof shapes.

M.Mortara, G.Patané, M.Spagnuolo, B.Falcidieno, J.Rossignac "Blowing Bubbles for the multiscaledecomposition of triangle meshes" Algorithmica - special issue on shape algorithms. Vol 38, (1), pp. 227-248,Springer, 2003.

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Tailor Label of v at scale i ←

configuration of theintersection between themesh and a sphere havingradius Ri and centred in v.

Curvature

Topology

Geometric attributes

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Classification criteria

Number of connected components: 1,2, 3 or more

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Classification criteria

One intersection curve Curvature characterization:

Sharp

Rounded

Blend

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GC(v)=L/R ∈[0, +∞) On a plane: GC(v)=2π On a spike: GC(v)< 2π →0 On a blend: GC(v)>2π → +∞

No distinction betweenconvex and concave

R

R

α

l

Pl : α = 2πR : 2πα = l / RΣ αi = L / R

Multi-scale curvature on meshes

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Classification criteria

Two intersection curves Relative length characterization:

Cylindrical Lmax≤ 2 Lmin

Conic otherwise

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Classification criteria

Status: One int. Convex Concave

More int. Full Empty

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Final classification

HOLLOWSPLITWELLFUNNELJOINTLIMBBLEND

DIPPITMOUNTTIP

TipTip TipTip

CylindricalCylindricalSaddleSaddle

ConicConic

SmoothSmooth

CylindricalCylindrical

ConcaveConcave

BranchingBranching

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Query Language

Each vertex isdescribed by avector of labels

The ith labelcorresponds to thevertexcharacterization atscale Ri

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Multi-scale Morphological analysis of the cortex

Tailor results

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Curvature-based Skeleton

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ProTailor Parallel implementation on a Linux Beowulf Cluster of

16 PCs 2.66 GHz Pentium IV processor 1 GB of Ram 2 EIDE 80 GB disks interfaced in RAID 0 by Antonella Galizia,IMATI

The scalability of thealgorithm is almostlinear(molecule model, 35MB,31 minutes -> 2 minutes)

M.Mortara, A.Galizia “ProTailor: a paralle operator for extremely fast shape analysis in Bioinformatics applications”in Proceedings of PDP2009, special session on Bioinformatics applications.

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Tailor on volumes

on tetrahedral meshes, computes the spheresurface inside the volume

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Plumber

Segmentation into tubular features and“bodies”

Is based on the Tailor characterization

Works in a multi-scale fashion wrt tubesection size

Computes axis and sections of eachtubular feature

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PlumberThe algorithm works in the following

steps:

Selection of the scale R

Classification of vertices andidentification of seed limb region

Tubular feature extraction

Increase R and repeat

M. Mortara, G. Patané, M. Spagnuolo, B. Falcidieno, and J. Rossignac. Plumber: A Multi-scale Decomposition of 3D Shapes into Tubular Primitives and Bodies, Proc. of SolidModeling and Applications, 2004

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Plumber

A sphere is centredin the barycentre ofthe medial loop.

The sphere rolls in the two possibledirections until a halting condition occurs.

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Plumber

At each step, the sphere generates a newcross section and a new axis point.

Stop when: The tube ends Curve length over threshold Bifurcation

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Results

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Results

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Plumber on Point Clouds

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Identification of human body parts

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Generalization of the hierarchical face clustering(Garland et al. 01)

Automatic generation of a binary tree of clusters,each fitted to one of the availableprimitives: planes, spheres and cylinders At the first step, each triangle is

considered to be a cluster Then, adjacent triangles are

clustered according tocluster-to-primitive fitting

M. Attene, B. Falcidieno, and M. Spagnuolo. Hierarchical Mesh Segmentation based onFitting Primitives. The Visual Computer, 22, 2006

Fitting Primitives

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Segments a shape into a hierarchy of nearlyconvex parts

Works on tetrahedra Applications:

fast region selectionfrom complex models

shape segmentation shape approximation deformation, editing

Hierarchical Convex Approximation

Marco Attene, Michela Mortara, Michela Spagnuolo and Bianca Falcidieno “Hierarchical Convex Approximationof 3D Shapes for Fast Region Selection” Computer Graphics Forum, Vol. 27, No. 5 (SGP'08 Procs.), pp. 1323-1333, 2008

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Region selection The tree of clusters can be traversed

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Complex Selections

Tracking cuttinglines or surfacestrokes can becomplicated Difficult topology Occlusions

Here the heart is connected with multiple vessels and tissues, and is tightly occluded bythe chest, thus selecting it through cutting lines would be rather unpractical.Through our mechanism the selection required just a mouse click and a wheel rotation.

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Annotation Psychological surveys show that humans “understand”

shapes by recognizing interesting sub-parts and theirstructure (Marr 1982, Biederman 1987). Shape Segmentation

For specific contexts, it is possible to describe what these“features” are and how they are structured. Geometric Description of the features Structural Description of the shape Semantic Annotation

cylinder

plane

CylinderIN plane

ThroughHole

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ShapeAnnotator

ShapeA surface mesh

DomainAn OWL ontology

CG ToolsSegmentation Plug-ins

Shape

Annotator

ExpertExpert Knowledge Base

AbstractedShape

A segmented mesh

Instance Instance

User knowledge → usable explicit content

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ShapeAnnotator The ShapeAnnotator is an open-source software

project hosted by sourceforge.net http://shapeannotator.sourceforge.net

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Scenario

Aquisition/reconstruction

Meshsimplification

Part selection

Annotation Analysis

Search/retrievalComparison

Sharing…

…

………

…

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Monitoring shape changes over time

Comparison of the shape of anatomical regionsamong patients

Semantic rendering of anatomical regions andsurgery planning

Analysis, automatic extraction of metadata,automatic or supported annotation of anatomicalregions for future retrieval, comparison and analysisof collected data.

Applications