Computational anatomy in Theano

Line Kühnel; Stefan Horst Sommer

doi:10.1007/978-3-319-67675-3_15

Computational anatomy in Theano

Line Kühnel, Stefan Horst Sommer

Department of Computer Science

5 Citations (Scopus)

Abstract

To model deformation of anatomical shapes, non-linear statistics are required to take into account the non-linear structure of the data space. Computer implementations of non-linear statistics and differential geometry algorithms often lead to long and complex code sequences. The aim of the paper is to show how the Theano framework can be used for simple and concise implementation of complex differential geometry algorithms while being able to handle complex and high-dimensional data structures. We show how the Theano framework meets both of these requirements. The framework provides a symbolic language that allows mathematical equations to be directly translated into Theano code, and it is able to perform both fast CPU and GPU computations on high-dimensional data. We show how different concepts from non-linear statistics and differential geometry can be implemented in Theano, and give examples of the implemented theory visualized on landmark representations of Corpus Callosum shapes.

Original language	English
Title of host publication	Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics : First International Workshop, GRAIL 2017, 6th International Workshop, MFCA 2017, and Third International Workshop, MICGen 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10–14, 2017, Proceedings
Editors	J. Cardoso, T. Arbel, E. Ferrante, X. Pennec, A. Dalca, S. Parisot, S. Joshi, N. K. Batmanghelich, A. Sotiras, M. Nielsen, M. R. Sabuncu, T. Fletcher, L. Shen, S. Durrleman, S. Sommer
Number of pages	13
Publisher	Springer
Publication date	2017
Pages	164-176
ISBN (Print)	978-3-319-67674-6
ISBN (Electronic)	978-3-319-67675-3
DOIs	https://doi.org/10.1007/978-3-319-67675-3_15
Publication status	Published - 2017
Event	6th International Workshop on Mathematical Foundations of Computational Anatomy - Québec City, Canada Duration: 10 Sept 2017 → 14 Sept 2017 Conference number: 6

Conference

Conference	6th International Workshop on Mathematical Foundations of Computational Anatomy
Number	6
Country/Territory	Canada
City	Québec City
Period	10/09/2017 → 14/09/2017

Series	Lecture notes in computer science
Volume	10551
ISSN	0302-9743

Access to Document

10.1007/978-3-319-67675-3_15

https://arxiv.org/pdf/1706.07690.pdf

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Kühnel, L., & Sommer, S. H. (2017). Computational anatomy in Theano. In J. Cardoso, T. Arbel, E. Ferrante, X. Pennec, A. Dalca, S. Parisot, S. Joshi, N. K. Batmanghelich, A. Sotiras, M. Nielsen, M. R. Sabuncu, T. Fletcher, L. Shen, S. Durrleman, & S. Sommer (Eds.), Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics: First International Workshop, GRAIL 2017, 6th International Workshop, MFCA 2017, and Third International Workshop, MICGen 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10–14, 2017, Proceedings (pp. 164-176). Springer. https://doi.org/10.1007/978-3-319-67675-3_15

Computational anatomy in Theano. / Kühnel, Line; Sommer, Stefan Horst.
Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics: First International Workshop, GRAIL 2017, 6th International Workshop, MFCA 2017, and Third International Workshop, MICGen 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10–14, 2017, Proceedings. ed. / J. Cardoso; T. Arbel; E. Ferrante; X. Pennec; A. Dalca; S. Parisot; S. Joshi; N. K. Batmanghelich; A. Sotiras; M. Nielsen; M. R. Sabuncu; T. Fletcher; L. Shen; S. Durrleman; S. Sommer. Springer, 2017. p. 164-176 (Lecture notes in computer science, Vol. 10551).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Kühnel, L & Sommer, SH 2017, Computational anatomy in Theano. in J Cardoso, T Arbel, E Ferrante, X Pennec, A Dalca, S Parisot, S Joshi, NK Batmanghelich, A Sotiras, M Nielsen, MR Sabuncu, T Fletcher, L Shen, S Durrleman & S Sommer (eds), Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics: First International Workshop, GRAIL 2017, 6th International Workshop, MFCA 2017, and Third International Workshop, MICGen 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10–14, 2017, Proceedings. Springer, Lecture notes in computer science, vol. 10551, pp. 164-176, 6th International Workshop on Mathematical Foundations of Computational Anatomy, Québec City, Canada, 10/09/2017. https://doi.org/10.1007/978-3-319-67675-3_15

Kühnel L, Sommer SH. Computational anatomy in Theano. In Cardoso J, Arbel T, Ferrante E, Pennec X, Dalca A, Parisot S, Joshi S, Batmanghelich NK, Sotiras A, Nielsen M, Sabuncu MR, Fletcher T, Shen L, Durrleman S, Sommer S, editors, Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics: First International Workshop, GRAIL 2017, 6th International Workshop, MFCA 2017, and Third International Workshop, MICGen 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10–14, 2017, Proceedings. Springer. 2017. p. 164-176. (Lecture notes in computer science, Vol. 10551). doi: 10.1007/978-3-319-67675-3_15

Kühnel, Line ; Sommer, Stefan Horst. / Computational anatomy in Theano. Graphs in Biomedical Image Analysis, Computational Anatomy and Imaging Genetics: First International Workshop, GRAIL 2017, 6th International Workshop, MFCA 2017, and Third International Workshop, MICGen 2017, Held in Conjunction with MICCAI 2017, Québec City, QC, Canada, September 10–14, 2017, Proceedings. editor / J. Cardoso ; T. Arbel ; E. Ferrante ; X. Pennec ; A. Dalca ; S. Parisot ; S. Joshi ; N. K. Batmanghelich ; A. Sotiras ; M. Nielsen ; M. R. Sabuncu ; T. Fletcher ; L. Shen ; S. Durrleman ; S. Sommer. Springer, 2017. pp. 164-176 (Lecture notes in computer science, Vol. 10551).

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Computational anatomy in Theano

Abstract

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