Nicolas Boutry

A new matching algorithm between trees of shapes and its application to brain tumor segmentation

By Nicolas Boutry, Thierry Géraud

2021-03-02

In Proceedings of the IAPR international conference on discrete geometry and mathematical morphology (DGMM)

Abstract

Many approaches exist to compute the distance between two trees in pattern recognition. These trees can be structures with or without values on their nodes or edges. However, none of these distances take into account the shapes possibly associated to the nodes of the tree. For this reason, we propose in this paper a new distance between two trees of shapes based on the Hausdorff distance. This distance allows us to make inexact tree matching and to compute what we call residual trees, representing where two trees differ. We will also see that thanks to these residual trees, we can obtain good results in matter of brain tumor segmentation. This segmentation does not provide only a segmentation but also the tree of shapes corresponding to the segmentation and its depth map.

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An equivalence relation between morphological dynamics and persistent homology in $n$-D

By Nicolas Boutry, Thierry Géraud, Laurent Najman

2021-03-02

In Proceedings of the IAPR international conference on discrete geometry and mathematical morphology (DGMM)

Abstract

In Mathematical Morphology (MM), dynamics are used to compute markers to proceed for example to watershed-based image decomposition. At the same time, persistence is a concept coming from Persistent Homology (PH) and Morse Theory (MT) and represents the stability of the extrema of a Morse function. Since these concepts are similar on Morse functions, we studied their relationship and we found, and proved, that they are equal on 1D Morse functions. Here, we propose to extend this proof to $n$-D, $n \geq 2$, showing that this equality can be applied to $n$-D images and not only to 1D functions. This is a step further to show how much MM and MT are related.

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Stability of the tree of shapes to additive noise

By Nicolas Boutry, Guillaume Tochon

2021-03-02

In Proceedings of the IAPR international conference on discrete geometry and mathematical morphology (DGMM)

Abstract

The tree of shapes (ToS) is a famous self-dual hierarchical structure in mathematical morphology, which represents the inclusion relationship of the shapes (i.e. the interior of the level lines with holes filled) in a grayscale image. The ToS has already found numerous applications in image processing tasks, such as grain filtering, contour extraction, image simplification, and so on. Its structure consistency is bound to the cleanliness of the level lines, which are themselves deeply affected by the presence of noise within the image. However, according to our knowledge, no one has measured before how resistant to (additive) noise this hierarchical structure is. In this paper, we propose and compare several measures to evaluate the stability of the ToS structure to noise.

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Deep learning for detection and segmentation of artefact and disease instances in gastrointestinal endoscopy

By Sharib Ali, Mariia Dmitrieva, Noha Ghatwary, Sophia Bano, Gorkem Polat, Alptekin Temizel, Adrian Krenzer, Amar Hekalo, Yun Bo Guo, Bogdan Matuszewski, Mourad Gridach, Irina Voiculescu, Vishnusai Yoganand, Arnav Chavan, Aryan Raj, Nhan T. Nguyen, Dat Q. Tran, Lê Duy Huỳnh, Nicolas Boutry, Shahadate Rezvy, Haijian Chen, Yoon Ho Choi, Anand Subramanian, Velmurugan Balasubramanian, Xiaohong W. Gao, Hongyu Hu, Yusheng Liao, Danail Stoyanov, Christian Daul, Stefano Realdon, Renato Cannizzaro, Dominique Lamarque, Terry Tran-Nguyen, Adam Bailey, Barbara Braden, James East, Jens Rittscher

2021-02-24

In Medical Image Analysis

Abstract

The Endoscopy Computer Vision Challenge (EndoCV) is a crowd-sourcing initiative to address eminent problems in developing reliable computer aided detection and diagnosis endoscopy systems and suggest a pathway for clinical translation of technologies. Whilst endoscopy is a widely used diagnostic and treatment tool for hollow-organs, there are several core challenges often faced by endoscopists, mainly: 1) presence of multi-class artefacts that hinder their visual interpretation, and 2) difficulty in identifying subtle precancerous precursors and cancer abnormalities. Artefacts often affect the robustness of deep learning methods applied to the gastrointestinal tract organs as they can be confused with tissue of interest. EndoCV2020 challenges are designed to address research questions in these remits. In this paper, we present a summary of methods developed by the top 17 teams and provide an objective comparison of state-of-the-art methods and methods designed by the participants for two sub-challenges: i) artefact detection and segmentation (EAD2020), and ii) disease detection and segmentation (EDD2020). Multi-center, multi-organ, multi-class, and multi-modal clinical endoscopy datasets were compiled for both EAD2020 and EDD2020 sub-challenges. The out-of-sample generalization ability of detection algorithms was also evaluated. Whilst most teams focused on accuracy improvements, only a few methods hold credibility for clinical usability. The best performing teams provided solutions to tackle class imbalance, and variabilities in size, origin, modality and occurrences by exploring data augmentation, data fusion, and optimal class thresholding techniques.

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Stacked and parallel U-nets with multi-output for myocardial pathology segmentation

By Zhou Zhao, Nicolas Boutry, Élodie Puybareau

2020-12-01

In Myocardial pathology segmentation combining multi-sequence CMR challenge

Abstract

In the field of medical imaging, many different image modalities contain different information, helping practitionners to make diagnostic, follow-up, etc. To better analyze images, mixing multi-modalities information has become a trend. This paper provides one cascaded UNet framework and uses three different modalities (the late gadolinium enhancement (LGE) CMR sequence, the balanced- Steady State Free Precession (bSSFP) cine sequence and the T2-weighted CMR) to complete the segmentation of the myocardium, scar and edema in the context of the MICCAI 2020 myocardial pathology segmentation combining multi-sequence CMR Challenge dataset (MyoPS 2020). We evaluate the proposed method with 5-fold-cross-validation on the MyoPS 2020 dataset.

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Do not treat boundaries and regions differently: An example on heart left atrial segmentation

By Zhou Zhao, Nicolas Boutry, Élodie Puybareau, Thierry Géraud

2020-11-02

In Proceedings of the 25th international conference on pattern recognition (ICPR)

Abstract

Atrial fibrillation is the most common heart rhythm disease. Due to a lack of understanding in matter of underlying atrial structures, current treatments are still not satisfying. Recently, with the popularity of deep learning, many segmentation methods based on fully convolutional networks have been proposed to analyze atrial structures, especially from late gadolinium-enhanced magnetic resonance imaging. However, two problems still occur: 1) segmentation results include the atrial- like background; 2) boundaries are very hard to segment. Most segmentation approaches design a specific network that mainly focuses on the regions, to the detriment of the boundaries. Therefore, this paper proposes an attention full convolutional network framework based on the ResNet-101 architecture, which focuses on boundaries as much as on regions. The additional attention module is added to have the network pay more attention on regions and then to reduce the impact of the misleading similarity of neighboring tissues. We also use a hybrid loss composed of a region loss and a boundary loss to treat boundaries and regions at the same time. We demonstrate the efficiency of the proposed approach on the MICCAI 2018 Atrial Segmentation Challenge public dataset.

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FOANet: A focus of attention network with application to myocardium segmentation

By Zhou Zhao, Nicolas Boutry, Élodie Puybareau, Thierry Géraud

2020-11-02

In Proceedings of the 25th international conference on pattern recognition (ICPR)

Abstract

In myocardium segmentation of cardiac magnetic resonance images, ambiguities often appear near the boundaries of the target domains due to tissue similarities. To address this issue, we propose a new architecture, called FOANet, which can be decomposed in three main steps: a localization step, a Gaussian-based contrast enhancement step, and a segmentation step. This architecture is supplied with a hybrid loss function that guides the FOANet to study the transformation relationship between the input image and the corresponding label in a three-level hierarchy (pixel-, patch- and map-level), which is helpful to improve segmentation and recovery of the boundaries. We demonstrate the efficiency of our approach on two public datasets in terms of regional and boundary segmentations.

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Equivalence between digital well-composedness and well-composedness in the sense of Alexandrov on $n$-D cubical grids

By Nicolas Boutry, Laurent Najman, Thierry Géraud

2020-09-03

In Journal of Mathematical Imaging and Vision

Abstract

Among the different flavors of well-composednesses on cubical grids, two of them, called respectively Digital Well-Composedness (DWCness) and Well-Composedness in the sens of Alexandrov (AWCness), are known to be equivalent in 2D and in 3D. The former means that a cubical set does not contain critical configurations when the latter means that the boundary of a cubical set is made of a disjoint union of discrete surfaces. In this paper, we prove that this equivalence holds in $n$-D, which is of interest because today images are not only 2D or 3D but also 4D and beyond. The main benefit of this proof is that the topological properties available for AWC sets, mainly their separation properties, are also true for DWC sets, and the properties of DWC sets are also true for AWC sets: an Euler number locally computable, equivalent connectivities from a local or global point of view… This result is also true for gray-level images thanks to cross-section topology, which means that the sets of shapes of DWC gray-level images make a tree like the ones of AWC gray-level images.

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Topological properties of the first non-local digitally well-composed interpolation on $n$-D cubical grids

By Nicolas Boutry, Laurent Najman, Thierry Géraud

2020-09-03

In Journal of Mathematical Imaging and Vision

Abstract

In discrete topology, we like digitally well-composed (shortly DWC) interpolations because they remove pinches in cubical images. Usual well-composed interpolations are local and sometimes self-dual (they treat in a same way dark and bright components in the image). In our case, we are particularly interested in $n$-D self-dual DWC interpolations to obtain a purely self-dual tree of shapes. However, it has been proved that we cannot have an $n$-D interpolation which is at the same time local, self-dual, and well-composed. By removing the locality constraint, we have obtained an $n$-D interpolation with many properties in practice: it is self-dual, DWC, and in-between (this last property means that it preserves the contours). Since we did not published the proofs of these results before, we propose to provide in a first time the proofs of the two last properties here (DWCness and in-betweeness) and a sketch of the proof of self-duality (the complete proof of self-duality requires more material and will come later). Some theoretical and practical results are given.

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A 4D counter-example showing that DWCness does not imply CWCness in $n$-D

By Nicolas Boutry, Rocio Gonzalez-Diaz, Laurent Najman, Thierry Géraud

2020-07-21

In Combinatorial image analysis: Proceedings of the 20th international workshop (IWCIA 2020)

Abstract

In this paper, we prove that the two flavours of well-composedness called Continuous Well-Composedness (shortly CWCness), stating that the boundary of the continuous analog of a discrete set is a manifold, and Digital Well-Composedness (shortly DWCness), stating that a discrete set does not contain any critical configuration, are not equivalent in dimension 4. To prove this, we exhibit the example of a configuration of 8 tesseracts (4D cubes) sharing a common corner (vertex), which is DWC but not CWC. This result is surprising since we know that CWCness and DWCness are equivalent in 2D and 3D. To reach our goal, we use local homology.

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