Deformetrica 4: an open- source software for statistical shape analysisย ยท 2020-06-08ย ยท 2 =1 ๐...
Transcript of Deformetrica 4: an open- source software for statistical shape analysisย ยท 2020-06-08ย ยท 2 =1 ๐...
ShapeMI workshop
MICCAI conference
20 September 2018
Granada, Spain
Alexandre Bรดne, Maxime Louis, Benoรฎt Martin, Stanley Durrleman
Deformetrica 4: an open-source software for statistical shape analysis
I. Registration
II. Atlas
III.Regression
Deformetrica 4: an open-source software for statistical shape analysis
demo
Registration
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Registration
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Registration
cost
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cost
attachment
cost
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Registration
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Registration
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Registration
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Registration
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Registration
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Registration
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>> deformetrica estimate
model.xml data_set.xml โp
optimization_parameters.xml
Registration
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I. Registration
II. Atlas
III.Regression
Deformetrica 4: an open-source software for statistical shape analysis
demo
Deterministic atlas
Deterministic atlas
Deterministic atlas
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parametersoutputsinputs
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Deterministic atlas
Hyper-
parametersoutputsinputs
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Deterministic atlas
Hyper-
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Deterministic atlas
Hyper-
parametersoutputsinputs
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2+ ๐ (๐, ๐ผ๐)
Deterministic atlas
Hyper-
parametersoutputsinputs
>> deformetrica estimate
model.xml data_set.xml โp
optimization_parameters.xml
Deterministic atlas
Deterministic atlas
Deterministic atlas
I. Registration
II. Atlas
III.Regression
Deformetrica 4: an open-source software for statistical shape analysis
demo
Geodesic regression
๐ก1 = 5 ๐ก2 = 15 ๐ก3 = 25 ๐ก4 = 35Yin et al. 2008, โA High- Resolution 3D Dynamic Facial Expression Databaseโ
Geodesic regression
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parametersoutputsinputs
๐ก1 = 5 ๐ก2 = 15 ๐ก3 = 25 ๐ก4 = 35Yin et al. 2008, โA High- Resolution 3D Dynamic Facial Expression Databaseโ
๐ก1 = 5 ๐ก2 = 15 ๐ก3 = 25 ๐ก4 = 35Yin et al. 2008, โA High- Resolution 3D Dynamic Facial Expression Databaseโ
Geodesic regression
๐ก1 = 5 ๐ก2 = 15 ๐ก3 = 25 ๐ก4 = 35Yin et al. 2008, โA High- Resolution 3D Dynamic Facial Expression Databaseโ
Geodesic regression
Geodesic regression
>> deformetrica estimate
model.xml data_set.xml
๐ก1 = 5 ๐ก2 = 15 ๐ก3 = 25 ๐ก4 = 35Yin et al. 2008, โA High- Resolution 3D Dynamic Facial Expression Databaseโ
๐ก1 = 5 ๐ก2 = 15 ๐ก3 = 25 ๐ก4 = 35Yin et al. 2008, โA High- Resolution 3D Dynamic Facial Expression Databaseโ
Geodesic regression
Parallel transport
Transfer a reference temporal evolution towards a new target geometry
Data courtesy of Paolo Piras, Sapienza Universitร di Roma, Italy
MR image registration performance
Registration of full-resolution MR images (7 millions voxels) in 2-3 minutes, with low GPU memory usage
Teaser: graphical user interface alpha
Teaser: python API beta
PyTorch
โข Auto-differentiation, without memory
overflows
โข Seamless CUDA code
PyTorch + PyKeops
โข Auto-differentiation, without memory
overflows
โข Seamless CUDA code
Thanks to Benjamin Charlier, Jean Feydy & Joan Glaunรจs
Conclusion
Implements many statistical shape analysis tasks ...
โข Registration
โข Deterministic atlas
โข Bayesian atlas
โข Geodesic regression
โข Parallel transport
โข Longitudinal atlas
โข Principal geodesic
analysis
beta
alpha
Conclusion
Implements many statistical shape analysis tasks ...
โข Registration
โข Deterministic atlas
โข Bayesian atlas
โข Geodesic regression
โข Parallel transport
โข Longitudinal atlas
โข Principal geodesic
analysis
beta
alpha
... with very few requirements about the data
โข Image
โข Meshes
โข No required point
correspondence
โข Multi-object
โข Cross-sectional or
longitudinal datasets
โข Linux or Mac
โข Anaconda 3
Requirements
Thanks!
Install
conda install -c pytorch -c conda-
forge
-c anaconda -c aramislab deformetrica
www.deformetrica.org
Come see us at the lunch & demo session!
Future work
Grow the pool of users
โข Graphical user
interface (GUI)
โข Python API
โข Windows platform
Add functionalities
โข Longitudinal atlas
โข Principal geodesic
analysis
โข MCMC-SAEM
estimation algorithm
Improve performance
โข Achieve massive parallelization on large clusters
โข Emphasis on GPU-specific optimizations
A decade of development
Deformetrica 1 C++
Deformetrica 3 C++
Deformetrica 4 PythonDeformetrica 2
C++
2011 2013 2017 2018
Deterministic atlas: landmark/2d/skulls
Deterministic atlas: landmark/2d/skulls
Deterministic atlas: landmark/2d/skulls
A note on the Bayesian atlas
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1
๐๐2
๐=1
๐
ฮฆ๐๐ โ ๐ โ ๐๐ โฐ
2+๐ (๐๐ , ๐๐
2)
cost
functionregularization
cost
attachment
cost
A note on the Bayesian atlas
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1
๐๐2
๐=1
๐
ฮฆ๐๐ โ ๐ โ ๐๐ โฐ
2+๐ (๐๐ , ๐๐
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Gives a statistical interpretation of the regularization term, which arises from assumed underlying random
structures on the momenta and residuals
In practice, no need to specify ๐๐บ๐ anymore!
The optimal tradeoff between attachment and
regularity terms is estimated from the data
Bayesian atlas
๐ถ ๐, (๐๐)๐, ๐๐2 =
1
๐๐2
๐=1
๐
ฮฆ๐๐ โ ๐ โ ๐๐ โฐ
2+๐ (๐๐ , ๐๐
2)
cost
functionregularization
cost
attachment
cost
Statistical interpretation of the regularization term, which arises from assumed underlying random structures on
the momenta and residuals
In practice, no need to specify ๐๐บ๐ anymore!
Bayesian atlas
Registration
๐ ๐
Registration
๐ ๐
Registration
๐ ๐
Registration
๐ ๐
Registration
๐ ๐
>> deformetrica estimate model.xml
data_set.xml โp
optimization_parameters.xml