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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 1

Fossil Reconstruction and Visualisationfrom CT scans

INRIA-FUTURS-DigiPlanteCIRAD-BIOS-AMAP

Marc Jaegerjaeger@inria.fr , marcjaeg@gmail.com

Interdisciplinary Workshop on

3D Paleo-Anthropology, Anatomy, Computer Science &Engineering- Synergies for the Future -

June, 19-20 - Muséum de Toulouse, France

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 2

UMR AMAP. (CIRAD-INRA-CNRS-UM2-IRD) Research axes (90 people)

Evolution of plant form and function, systematics, floristics:morphological evolution;biomechanics, evolution and ecology;systematics, taxonomy and floristics.

Plant architecture and development:diversity and plasticity of plant architecture;integrated analysis and modelling of plant architecture and function;volumic imaging.

Organisation and dynamics of populations and landscapes:diversity and dynamics of heterogeneous forest communities;structure and dynamics of the plant communities;landscape spatial dynamics and ecological engineering.

Transversal activity in the field of mathematics and informtics applied :the modeling and the simulation of the growth and the architecture of the plants;analysis and statistical processing of information;software engineering.

http://amap.cirad.fr/

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 3

Volume imaging at AMAP. Some projects (1988-2003)Volume imaging at AMAP. Some projects (1988-2003)

=> Application to Paleoanthropology

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 4

Advanced medical imaging methods forHominid Morphology studies.

- LIAMA project 01-08 - “VPaleo” (2002-2004)

Chinese VPaleo Co-ordinator Prof Hanqing Lu (NLPR)

http://liama.ia.ac.cn

1997: CAS and INRIAhub and founding Agency

2000: CIRAD and CNRSwith permanent staff

2005: CASIA + INRA and BrgmTowards a international Lab.

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 5

Some Challenges of volume imaging in PaleoAnthropology

Very limited number of skull fossilsAll Data nearly confidential.High heterogeneity due to high time schedule and past conditionsNo standard acquisition rules

Only hard tissues (bones and teeth)But information on smooth tissues wanted (example: endocast volume)

Data strongly alteredMissing or broken parts, deformations, artificial materials (sand, glue)Data highly mineralized : X ray responses may no more be discriminantFusion of mineral elements with biological ones

=> Try to develop generic methods stable to data variations

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 6

LIAMA 01-08: a multidisciplinary Project

Disciplines Project partners (French/Chinese)

Computer Sciences:Medical Image processing NLPRVolume rendering CIRAD- LIAMAGeometrical characterization CIRAD- LIAMA, INRIA- Immédiat

PaleoAnthropology:Study of hominid evolution Bordeaux I, CAS- IVPP BeijingStudy of animal evolution IVPP Beijing

Medecine :Radiology C. Pasteur (Toulouse) Beijing PMUC HospitalMaxillofacial Biometry CIRAD - C.Pasteur Univ. Sabatier (Toulouse)

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 7

LIAMA 01-08: Virtual PaleoAnthropology

Aim : Morphology studies of hominid skulls from CT scan exams

Data collection and conversion

Advanced visualisation tools

Skull geometrical characterization.

Deformable 2D and 3D models

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 8

Visualisation Isosurface vs Volume Ray tracing rendering

Transfer function Transparency table

[IEEE Computer Graphics, June 2001] Colour table

Rendering example on STS5 fossil.Data courtesy J. Braga

Isovalue: one value among grey levels

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 9

Rendering example on Broken Hill fossil.Data courtesy J. Braga

Other Ray traced Volume visualisations

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 10

Rendering example on Broken Hill fossil.Data courtesy J. Braga

Other Ray traced Volume visualisations

Specific Rendering Average, MIP, Gradiant

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 11

Towards realistic views ?

Rendering example on TM1517 fossil.Data courtesy J. Braga

A simple case: Bone brown color

Teeth ‘high densities “ white

Add illumination (light) and shadows

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 12

Step 2. Geometrical characterisation. Approaches

User guided anatomical point selection: cephalometric constructionAutomatic skeleton extraction from unorganized clouds of pointsSpherical conversions

Skeleton from mandibular surface 3D Cephalometry landmarks and Teeth PCA(A. Verroust, INRIA) (J. Treil, Pasteur)

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 13

Volume spherical characterisation (Skull)Idea: transform coordinates voxels in spherical : R, θ, ϕ

Define center from anatomical points (use cephalometric construction)Transform also cephalometric construction for comparisonsBuild Images as output

Broken Hill skull (θ, ϕ) , (R, ϕ) and (θ,R) output images.

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 14

Registration and charactisation. Tools.

Library of free tools. DICOM converters, 3D viewer, slicers

Evolution of house tool (reconstruction, spherical charcterisation)

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 15

Some reconstructions of CT scan hominid.

SK3978 SK55 SK62 SK64

Bodo BrokenHill Guattari

SK847 TM1517 STS24 STS5

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 16

Urumchi CT scanned momies

In the frame of sino-french projectsleaded byC. Debaine-Francfort (CNRS-UMR7041)A. Idriss (Institute of Archaeological andHeritage in Xinjiang, IPAX )

October 2003

7 scans on GE Scannerresolution: 2 mm

=>Up to 990 slices per exam

=> Difficulties: sand

XinJiang Momies

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 17

Hominid collection. Momies

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 18

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 19

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 20

The first skull of the earliest giant panda

CT Scan,Image registration3D reconstruction

[ PNAS, 2007 ]

Institute of Vertebrate Paleontology and Paleoanthropology, CAS (ChangZhu Jin, Wei Dong)

Renmin Hospital, Peking University (Qizhi Zhu)

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10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 21

Applications of spherical characterisationSymetry analysis, Symetry missing part filling

Symetry map Green+ White= Red-

[ Dong Wei et al, Reconstruction and remedy of Virtual 3D Images of Fossils, 2004 ]

Interactive multilevel VRML output

Filling missing parts by symetry

10:26Inter-disciplinary Workshop 3d Paleo .... CS, Toulouse, 2008, June 19-20, 3D Fossils from CT scans 22

Actual human and hominid (STS5) qualitative comparisons

- symmetrical aspects

- match landmarks and visualize both together

Applications of spherical characterisation