Progressive extraction of neural models CAD’16 from high...
Transcript of Progressive extraction of neural models CAD’16 from high...
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Progressiveextractionofneuralmodelsfromhigh-resolution3Dimagesofbrain
CAD’16 Vancouver, Canada
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Contents
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 2
• Motivation• Background• Firstexperiments• Methodformulation• Conclusion
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Motivation
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Marching-cubes(Siggraph,1987)
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 4
Findthe0-surface(oranyiso-surface)ofadiscrete3Dfield
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Progressofhigh-resolutionimagingtechnology
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 5
WilliamE.Lorensen&HarveyE.Cline,"MarchingCubes:aHighResolution3DSurfaceConstructionAlgorithm",Siggraph,1987
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Progressofhigh-resolutionimagingtechnology
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 6
NobelPrizeinChemistry2014awardedtoBetzig,Moerner&Hellfor"developmentofsuper-resolvedfluorescencemicroscopy,"whichbrings"opticalmicroscopyintothenanodimension"
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Progressofhigh-resolutionimagingtechnology
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 7
Source:FeiChen,PaulW.Tillberg,EdwardS.Boyden.Expansionmicroscopy.Science,January152015;DOI:10.1126/science.1260088
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Progressofhigh-resolutionimagingtechnology
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 8
TheViSUSsoftwareframeworkwasdesignedtoallowtheinteractiveexplorationofmassivescientificmodelsonavarietyofhardware,evengeographicallydistributed
NeuroscientistAlessandraMichelucci(Utah)withViSUSpowerwallandneuronesimage
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“Houston:We’vehadaproblem”
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 9
Searchfordetailedgeometricmodelsfromhi-resimaging
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“Apollo13:Wehaveasolution”
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 10
Lookforgeometricmodelsusingextremehi-resimaging
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Andcontinuingthetravel...
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 11
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Background
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LAR:noveltopologicalrepresentationscheme
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 13
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LinearAlgebraicRepresentation:
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 14
fromcellularmodelstosparsebinarymatrices
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Sparsematrices:COO,CSRandCSCformats
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 15
aaaaaa
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LARexamples(1/2)
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 16
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LARexamples(2/2)
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 17
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Algorithm:matrixof∂2operator
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 18
Forasurface(topologicalspace)madeofallquads(2-cells)
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Topologicalincidenceoperators
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 19
BinarytopologicalrelationsbetweenLARcells
andcorrespondingtopologicaloperatorson∂◦chains
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Goal:integratingLARwithViSUS
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 20
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Firstexperiments
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Firstexperiments
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 22
STEP1:surfaceextraction(512×512×128)
TestDataSet:B-repofthechainofvoxelsabovealuminancethreshold
B-repmodel,includingnoise
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Firstexperiments
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 23
STEP1:surfaceextraction(512×512×128)
TestDataSet:B-repofthechainofvoxelsabovealuminancethreshold
modelafternoisefiltering
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Firstexperiments
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 24
STEP1:surfaceextraction(512×512×128)
TestDataSet:B-repofthechainofvoxelsabovealuminancethreshold
modelafterclosingandopeningmathematicalmorphologyoperators
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Surfaceextraction(512×512×128)
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 25
interiorviewofaclosedshell(portionofdatachain)
TestDataSet:B-repofthechainofvoxelsabovealuminancethreshold
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Methodformulation
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IDEA:computeafamilyofintrinsiccurves
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 27
ForeachVolinablock-partitionofa3-image:
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Somethingwronghere?
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 28
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Algorithm:map_image_2_b-rep
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 29
Extractboundarymodelsfrom3D"bricks"ofvoxels
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Algorithm:simplify-B-Rep
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 30
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Algorithm:example1
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 31
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Algorithm:example1
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 32
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Algorithm:example2
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 33
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Algorithm:example2
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 34
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Algorithm:example3
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 35
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Algorithm:example3
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 36
Extract"intrinsic"curvesandGeneratehomologicallyequivalent&stronglyreducedmodels
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Nextsteps
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 37
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Conclusion
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(Partial)resultsobtainedandfurtheradvances
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 39
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Thanksforyourattention
CAD'16Vancouver,Canada GiuliaClementi;DaniloSalvati;GiorgioScorzelli;AlbertoPaoluzzi;ValerioPascucci 40
QUESTIONS?