Publications

Braids of partitions for the hierarchical representation and segmentation of multimodal images

By Guillaume Tochon, Mauro Dalla Mura, Miguel Angel Veganzones, Thierry Géraud, Jocelyn Chanussot

2019-07-01

In Pattern Recognition

Abstract

Hierarchical data representations are powerful tools to analyze images and have found numerous applications in image processing. When it comes to multimodal images however, the fusion of multiple hierarchies remains an open question. Recently, the concept of braids of partitions has been proposed as a theoretical tool and possible solution to this issue. In this paper, we demonstrate the relevance of the braid structure for the hierarchical representation of multimodal images. We first propose a fully operable procedure to build a braid of partitions from two hierarchical representations. We then derive a framework for multimodal image segmentation, relying on an energetic minimization scheme conducted on the braid structure. The proposed approach is investigated on different multimodal images scenarios, and the obtained results confirm its ability to efficiently handle the multimodal information to produce more accurate segmentation outputs.

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One more step towards well-composedness of cell complexes over $n$-D pictures

By Nicolas Boutry, Rocio Gonzalez-Diaz, Maria-Jose Jimenez

2019-06-18

In Proceedings of the 21st international conference on discrete geometry for computer imagery (DGCI)

Abstract

An $n$-D pure regular cell complex $K$ is weakly well-composed (wWC) if, for each vertex $v$ of $K$, the set of $n$-cells incident to $v$ is face-connected. In previous work we proved that if an $n$-D picture $I$ is digitally well composed (DWC) then the cubical complex $Q(I)$ associated to $I$ is wWC. If $I$ is not DWC, we proposed a combinatorial algorithm to locally repair $Q(I)$ obtaining an $n$-D pure simplicial complex $P_S(I)$ homotopy equivalent to $Q(I)$ which is always wWC. In this paper we give a combinatorial procedure to compute a simplicial complex $P_S(\bar{I})$ which decomposes the complement space of $|P_S(I)|$ and prove that $P_S(\bar{I})$ is also wWC. This paper means one more step on the way to our ultimate goal: to prove that the $n$-D repaired complex is continuously well-composed (CWC), that is, the boundary of its continuous analog is an $(n-1)$-manifold.

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Estimation du niveau de bruit par arbre des formes et statistiques non paramétriques

By Baptiste Esteban, Guillaume Tochon, Thierry Géraud

2019-06-14

In Proceedings of the 27st symposium on signal and image processing (GRETSI)

Abstract

La connaissance du niveau de bruit dans une image est précieuse pour de nombreuses applications en traitement d’images. L’estimation de la fonction de niveau de bruit requiert l’identification des zones homogènes sur lesquelles les paramètres du bruit peuvent être calculés. Sutour et al. en 2015 ont proposé une méthode d’estimation de la fonction de niveau de bruit se basant sur la recherche de zones homogènes de forme carrée, donc inadaptées au contenu local de l’image. Nous généralisons cette méthode à la recherche de zones homogènes de forme quelconque en nous basant sur la représentation par arbre des formes de l’image étudiée, permettant ainsi une estimation plus robuste de la fonction de niveau de bruit.

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Filtres connexes multivariés par fusion d’arbres de composantes

By Edwin Carlinet, Thierry Géraud

2019-06-14

In Proceedings of the 27st symposium on signal and image processing (GRETSI)

Abstract

Les arbres de composantes fournissent une représentation d’images de haut niveau, hiérarchisée et invariante par contraste, adaptée à de nombreuses tâches de traitement d’image. Pourtant, ils sont mal définis sur des données multivariées, telle que celles des images couleur, des images multimodalités, des images multibande, etc. Les solutions courantes, telles que le traitement marginal, ou l’imposition d’un ordre total sur les données, ne sont pas satisfaisantes et génèrent de nombreux problèmes, tels que des artefacts visuels, la perte d’invariances, etc. Dans cet article, inspiré par la manière dont l’arbre des formes multivariés (MToS) a été défini, nous proposons une définition pour un Min-Tree ou un Max-Tree multivarié. Nous n’imposons pas un ordre total arbitraire aux valeurs; nous utilisons uniquement la relation d’inclusion entre les composantes. En conséquence, nous introduisons une nouvelle classe d’ouvertures et de fermetures connectées multivariées.

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Estimating the noise level function with the tree of shapes and non-parametric statistics

By Baptiste Esteban, Guillaume Tochon, Thierry Géraud

2019-06-07

In Proceedings of the 18th international conference on computer analysis of images and patterns (CAIP)

Abstract

The knowledge of the noise level within an image is a valuableinformation for many image processing applications. Estimating the noise level function (NLF) requires the identification of homogeneous regions, upon which the noise parameters are computed. Sutour et al. have proposed a method to estimate this NLF based on the search for homogeneous regions of square shape. We generalize this method to the search for homogeneous regions with arbitrary shape thanks to the tree of shapes representation of the image under study, thus allowing a more robust and precise estimation of the noise level function.

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Benchmark on automatic 6-month-old infant brain segmentation algorithms: The iSeg-2017 challenge

By Li Wang, Dong Nie, Guannan Li, Élodie Puybareau, Jose Dolz, Qian Zhang, Fan Wang, Jing Xia, Zhengwang Wu, Jiawei Chen, Kim-Han Thung, Toan Duc Bui, Jitae Shin, Guodong Zeng, Guoyan Zheng, Vladimir S. Fonov, Andrew Doyle, Yongchao Xu, Pim Moeskops, Josien P. W. Pluim, Christian Desrosiers, Ismail Ben Ayed, Gerard Sanroma, Oualid M. Benkarim, Adrià Casamitjana, Verónica Vilaplana, Weili Lin, Gang Li, Dinggang Shen

2019-04-11

In IEEE Transactions on Medical Imaging

Abstract

Accurate segmentation of infant brain magnetic resonance (MR) images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is an indispensable foundation for early studying of brain growth patterns and morphological changes in neurodevelopmental disorders. Nevertheless, in the isointense phase (approximately 6-9 months of age), due to inherent myelination and maturation process, WM and GM exhibit similar levels of intensity in both T1-weighted (T1w) and T2-weighted (T2w) MR images, making tissue segmentation very challenging. Despite many efforts were devoted to brain segmentation, only few studies have focused on the segmentation of 6-month infant brain images. With the idea of boosting methodological development in the community, iSeg-2017 challenge (http://iseg2017.web.unc.edu) provides a set of 6-month infant subjects with manual labels for training and testing the participating methods. Among the 21 automatic segmentation methods participating in iSeg-2017, we review the 8 top-ranked teams, in terms of Dice ratio, modified Hausdorff distance and average surface distance, and introduce their pipelines, implementations, as well as source codes. We further discuss limitations and possible future directions. We hope the dataset in iSeg-2017 and this review article could provide insights into methodological development for the community.

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Standardized assessment of automatic segmentation of white matter hyperintensities: Results of the WMH segmentation challenge

By H. J. Kuijf, J. M. Biesbroek, J. de Bresser, R. Heinen, S. Andermatt, M. Bento, M. Berseth, M. Belyaev, M. J. Cardoso, A. Casamitjana, D. L. Collins, M. Dadar, A. Georgiou, M. Ghafoorian, D. Jin, A. Khademi, J. Knight, H. Li, X. Lladó, M. Luna, Q. Mahmood, R. McKinley, A. Mehrtash, S. Ourselin, B. Park, H. Park, S. H. Park, S. Pezold, Élodie Puybareau, L. Rittner, C. H. Sudre, S. Valverde, V. Vilaplana, R. Wiest, Yongchao Xu, Z. Xu, G. Zeng, J. Zhang, G. Zheng, C. Chen, W. van der Flier, F. Barkhof, M. A. Viergever, G. J. Biessels

2019-04-10

In IEEE Transactions on Medical Imaging

Abstract

Quantification of cerebral white matter hyperintensities (WMH) of presumed vascular origin is of key importance in many neurological research studies. Currently, measurements are often still obtained from manual segmentations on brain MR images, which is a laborious procedure. Automatic WMH segmentation methods exist, but a standardized comparison of the performance of such methods is lacking. We organized a scientific challenge, in which developers could evaluate their method on a standardized multi-center/-scanner image dataset, giving an objective comparison: the WMH Segmentation Challenge (https://wmh.isi.uu.nl/). Sixty T1+FLAIR images from three MR scanners were released with manual WMH segmentations for training. A test set of 110 images from five MR scanners was used for evaluation. Segmentation methods had to be containerized and submitted to the challenge organizers. Five evaluation metrics were used to rank the methods: (1) Dice similarity coefficient, (2) modified Hausdorff distance (95th percentile), (3) absolute log-transformed volume difference, (4) sensitivity for detecting individual lesions, and (5) F1-score for individual lesions. Additionally, methods were ranked on their inter-scanner robustness. Twenty participants submitted their method for evaluation. This paper provides a detailed analysis of the results. In brief, there is a cluster of four methods that rank significantly better than the other methods, with one clear winner. The inter-scanner robustness ranking shows that not all methods generalize to unseen scanners. The challenge remains open for future submissions and provides a public platform for method evaluation.

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Implementing baker’s SUBTYPEP decision procedure

By Léo Valais, Jim Newton, Didier Verna

2019-04-01

In ELS 2019, the 12th european lisp symposium

Abstract

We present here our partial implementation of Baker’s decision procedure for SUBTYPEP. In his article “A Decision Procedure for Common Lisp’s SUBTYPEP Predicate”, he claims to provide implementation guidelines to obtain a SUBTYPEP more accurate and as efficient as the average implementation. However, he did not provide any serious implementation and his description is sometimes obscure. In this paper we present our implementation of part of his procedure, only supporting primitive types, CLOS classes, member, range and logical type specifiers. We explain in our words our understanding of his procedure, with much more detail and examples than in Baker’s article. We therefore clarify many parts of his description and fill in some of its gaps or omissions. We also argue in favor and against some of his choices and present our alternative solutions. We further provide some proofs that might be missing in his article and some early efficiency results. We have not released any code yet but we plan to open source it as soon as it is presentable.

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Model checking with generalized Rabin and Fin-less automata

By Vincent Bloemen, Alexandre Duret-Lutz, Jaco van de Pol

2019-04-01

In International Journal on Software Tools for Technology Transfer

Abstract

In the automata theoretic approach to explicit state LTL model checking, the synchronized product of the model and an automaton that represents the negated formula is checked for emptiness. In practice, a (transition-based generalized) Büchi automaton (TGBA) is used for this procedure.This paper investigates whether using a more general form of acceptance, namely a transition-based generalized Rabin automaton (TGRA), improves the model checking procedure. TGRAs can have significantly fewer states than TGBAs, however the corresponding emptiness checking procedure is more involved. With recent advances in probabilistic model checking and LTL to TGRA translators, it is only natural to ask whether checking a TGRA directly is more advantageous in practice.We designed a multi-core TGRA checking algorithm and performed experiments on a subset of the models and formulas from the 2015 Model Checking Contest and generated LTL formulas for models from the BEEM database. While we found little to no improvement by checking TGRAs directly, we show how various aspects of a TGRA’s structure influences the model checking performance.In this paper, we also introduce a Fin-less acceptance condition, which is a disjunction of TGBAs. We show how to convert TGRAs into automata with Fin-less acceptance and show how a TGBA emptiness procedure can be extended to check Fin-less automata.

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Parallelizing quickref

By Didier Verna

2019-04-01

In ELS 2019, the 12th european lisp symposium

Abstract

Quickref is a global documentation project for Common Lisp software. It builds a website containing reference manuals for Quicklisp libraries. Each library is first compiled, loaded, and introspected. From the collected information, a Texinfo file is generated, which is then processed into an HTML one. Because of the large number of libraries in Quicklisp, doing this sequentially may require several hours of processing. We report on our experiments in parallelizing Quickref. Experimental data on the morphology of Quicklisp libraries has been collected. Based on this data, we are able to propose a number of parallelization schemes that reduce the total processing time by a factor of 3.8 to 4.5, depending on the exact situation.

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