Publications

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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An equivalence relation between morphological dynamics and persistent homology in 1D

By Nicolas Boutry, Thierry Géraud, Laurent Najman

2019-03-13

In Mathematical morphology and its application to signal and image processing – proceedings of the 14th international symposium on mathematical morphology (ISMM)

Abstract

We state in this paper a strong relation existing between Mathematical Morphology and Discrete Morse Theory when we work with 1D Morse functions. Specifically, in Mathematical Morphology, a classic way to extract robust markers for segmentation purposes, is to use the dynamics. On the other hand, in Discrete Morse Theory, a well-known tool to simplify the Morse-Smale complexes representing the topological information of a Morse function is the persistence. We show that pairing by persistence is equivalent to pairing by dynamics. Furthermore, self-duality and injectivity of these pairings are proved.

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Constructing a braid of partitions from hierarchies of partitions

By Guillaume Tochon, Mauro Dalla Mura, Jocelyn Chanussot

2019-03-13

In Mathematical morphology and its application to signal and image processing – proceedings of the 14th international symposium on mathematical morphology (ISMM)

Abstract

Braids of partitions have been introduced in a theoretical framework as a generalization of hierarchies of partitions, but practical guidelines to derive such structures remained an open question. In a previous work, we proposed a methodology to build a braid of partitions by experimentally composing cuts extracted from two hierarchies of partitions, notably paving the way for the hierarchical representation of multimodal images. However, we did not provide the formal proof that our proposed methodology was yielding a braid structure. We remedy to this point in the present paper and give a brief insight on the structural properties of the resulting braid of partitions.

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Introducing multivariate connected openings and closings

By Edwin Carlinet, Thierry Géraud

2019-03-13

In Mathematical morphology and its application to signal and image processing – proceedings of the 14th international symposium on mathematical morphology (ISMM)

Abstract

The component trees provide a high-level, hierarchical, and contrast invariant representations of images, suitable for many image processing tasks. Yet their definition is ill-formed on multivariate data, e.g., color images, multi-modality images, multi-band images, and so on. Common workarounds such as marginal processing, or imposing a total order on data are not satisfactory and yield many problems, such as artifacts, loss of invariances, etc. In this paper, inspired by the way the Multivariate Tree of Shapes (MToS) has been defined, we propose a definition for a Multivariate min-tree or max-tree. We do not impose an arbitrary total ordering on values; we use only the inclusion relationship between components. As a straightforward consequence, we thus have a new class of multivariate connected openings and closings.

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Spherical fluorescent particle segmentation and tracking in 3D confocal microscopy

By Élodie Puybareau, Edwin Carlinet, Alessandro Benfenati, Hugues Talbot

2019-03-13

In Mathematical morphology and its application to signal and image processing – proceedings of the 14th international symposium on mathematical morphology (ISMM)

Abstract

Spherical fluorescent particle are micrometer-scale spherical beads used in various areas of physics, chemistry or biology as markers associated with local physical media. They are useful for example in fluid dynamics to characterize flows, diffusion coefficients, viscosity or temperature; they are used in cells dynamics to estimate mechanical strain and stress at the micrometer scale. In order to estimate these physical measurements, tracking these particles is necessary. Numerous approaches and existing packages, both open-source and proprietary are available to achieve tracking with a high degree of precision in 2D. However, little such software is available to achieve tracking in 3D. One major difficulty is that 3D confocal microscopy acquisition is not typically fast enough to assume that the beads are stationary during the whole 3D scan. As a result, beads may move between planar scans. Classical approaches to 3D segmentation may yield objects are not spherical. In this article, we propose a 3D bead segmentation that deals with this situation.

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