Nicolas Passat

A non-local fuzzy segmentation method: Application to brain MRI

The Fuzzy C-Means (FCM) algorithm is a widely used and flexible approach to automated image segmentation, especially in the field of brain tissue segmentation from 3D MRI, where it addresses the problem of partial volume effects. In order to improve its robustness to classical image deterioration, namely noise and bias field artifacts, which arise in the MRI acquisition process, we propose to integrate into the FCM segmentation methodology concepts inspired by the non-local (NL) framework, initially defined and considered in the context of image restoration. The key algorithmic contributions of this article are the definition of an NL data term and an NL regularisation term to efficiently handle intensity inhomogeneities and noise in the data. The resulting new energy formulation is then built into an NL-FCM brain tissue segmentation algorithm. Experiments performed on both synthetic and real MRI data, leading to the classification of brain tissues into grey matter, white matter and cerebrospinal fluid, indicate a significant improvement in performance in the case of higher noise levels, when compared to a range of standard algorithms.

Magnetic resonance angiography: From anatomical knowledge modeling to vessel segmentation

Magnetic resonance angiography (MRA) has become a common way to study cerebral vascular structures. Indeed, it enables to obtain information on flowing blood in a totally non-invasive and non-irradiant fashion. MRA exams are generally performed for three main applications: detection of vascular pathologies, neurosurgery planning, and vascular landmark detection for brain functional analysis. This large field of applications justifies the necessity to provide efficient vessel segmentation tools. Several methods have been proposed during the last fifteen years. However, the obtained results are still not fully satisfying. A solution to improve brain vessel segmentation from MRA data could consist in integrating high-level a priori knowledge in the segmentation process. A preliminary attempt to integrate such knowledge is proposed here. It is composed of two methods devoted to phase contrast MRA (PC MRA) data. The first method is a cerebral vascular atlas creation process, composed of three steps: knowledge extraction, registration, and data fusion. Knowledge extraction is performed using a vessel size determination algorithm based on skeletonization, while a topology preserving non-rigid registration method is used to fuse the information into the atlas. The second method is a segmentation process involving adaptive sets of gray-level hit-or-miss operators. It uses anatomical knowledge modeled by the cerebral vascular atlas to adapt the parameters of these operators (number, size, and orientation) to the searched vascular structures. These two methods have been tested by creating an atlas from a 18 MRA database, and by using it to segment 30 MRA images, comparing the results to those obtained from a region-growing segmentation method.

Extraction of complex patterns from multiresolution remote sensing images: A hierarchical top-down methodology

The extraction of urban patterns from very high spatial resolution (VHSR) optical images presents several challenges related to the size, the accuracy and the complexity of the considered data. Based on the availability of several optical images of a same scene at various resolutions (medium, high, and very high spatial resolution), a hierarchical approach is proposed to progressively extract segments of interest from the lowest to the highest resolution data, and then finally determine urban patterns from VHSR images. This approach, inspired by the principle of photo-interpretation, has for purpose to use as much as possible the users skills while minimising his/her interaction. In order to do so, at each resolution, an interactive segmentation of one sample region is required for each semantic class of the image. Then, the users behaviour is automatically reproduced in the remainder of the image. This process is mainly based on tree-cuts in binary partition trees. Since it strongly relies on user-defined segmentation examples, it can involve only low level-spatial and radiometric-criteria, then enabling fast computation of comprehensive results. Experiments performed on urban images datasets provide satisfactory results which may be further used for classification purpose.

Region-growing segmentation of brain vessels: An atlas-based automatic approach

To propose an atlas‐based method that uses both phase and magnitude images to integrate anatomical information in order to improve the segmentation of blood vessels in cerebral phase‐contrast magnetic resonance angiography (PC‐MRA).

Filtering and segmentation of 3D angiographic data: Advances based on mathematical morphology

In the last 20 years, 3D angiographic imaging has proven its usefulness in the context of various clinical applications. However, angiographic images are generally difficult to analyse due to their size and the complexity of the data that they represent, as well as the fact that useful information is easily corrupted by noise and artifacts. Therefore, there is an ongoing necessity to provide tools facilitating their visualisation and analysis, while vessel segmentation from such images remains a challenging task. This article presents new vessel segmentation and filtering techniques, relying on recent advances in mathematical morphology. In particular, methodological results related to spatially variant mathematical morphology and connected filtering are stated, and included in an angiographic data processing framework. These filtering and segmentation methods are evaluated on real and synthetic 3D angiographic data.

3D segmentation of coronary arteries based on advanced mathematical morphology techniques

In this article, we propose an automatic algorithm for coronary artery segmentation from 3D X-ray data sequences of a cardiac cycle (3D-CT scan, 64 detectors, 10 phases). This method is based on recent mathematical morphology techniques (some of them being extended in this article). It is also guided by anatomical knowledge, using discrete geometric tools to fit on the artery shape independently from any perturbation of the data. The application of the method on a validation dataset (60 images: 20 patients in 3 phases) led to 90% correct (and automatically obtained) segmentations, the 10% remaining cases corresponding to images where the SNR was very low.

Grey-level hit-or-miss transforms-Part I: Unified theory

The hit-or-miss transform (HMT) is a fundamental operation on binary images, widely used since 40 years. As it is not increasing, its extension to grey-level images is not straightforward, and very few authors have considered it. Moreover, despite its potential usefulness, very few applications of the grey-level HMT have been proposed until now. Part I of this paper, developed hereafter, is devoted to the description of a theory leading to a unification of the main definitions of the grey-level HMT, mainly proposed by Ronse and Soille, respectively (part II will deal with the applicative potential of the grey-level HMT, which will be illustrated by its use for vessel segmentation from 3D angiographic data). In this first part, we review the previous approaches to the grey-level HMT, especially the supremal one of Ronse, and the integral one of Soille; the latter was defined only for flat structuring elements (SEs), but it can be generalized to non-flat ones. We present a unified theory of the grey-level HMT, which is decomposed into two steps. First a fitting associates to each point the set of grey-levels for which the SEs can be fitted to the image; as in Soilles approach, this fitting step can be constrained. Next, a valuation associates a final grey-level value to each point; we propose three valuations: supremal (as in Ronse), integral (as in Soille) and binary.

Grey-level hit-or-miss transforms-part II: Application to angiographic image processing

The hit-or-miss transform (HMT) is a fundamental operation on binary images, widely used since 40 years. As it is not increasing, its extension to grey-level images is not straightforward, and very few authors have considered it. Moreover, despite its potential usefulness, very few applications of the grey-level HMT have been proposed until now. Part I of this paper [B. Naegel, N. Passat, C. Ronse, Grey-level hit-or-miss transforms-part I: unified theory. Pattern Recogn., in press doi:10.1016/j.patcog.2006.06.004] was devoted to the description of a theory enabling to unify the main definitions of the grey-level HMT, mainly proposed by Ronse and Soille, respectively. Part II of this paper, developed hereafter, deals with the applicative potential of the grey-level HMT, illustrated by its use for vessel segmentation from 3D angiographic data. Different HMT-based segmentation methods are then described and analysed, leading to concrete analysis techniques for brain and liver vessels, but also providing algorithmic strategies which could further be used for many other kinds of image processing applications.

A Non-Local Fuzzy Segmentation Method: Application to Brain MRI

The Fuzzy C-Means algorithm is a widely used and flexible approach for brain tissue segmentation from 3D MRI. Despite its recent enrichment by addition of a spatial dependency to its formulation, it remains quite sensitive to noise. In order to improve its reliability in noisy contexts, we propose a way to select the most suitable example regions for regularisation. This approach inspired by the Non-Local Mean strategy used in image restoration is based on the computation of weights modelling the grey-level similarity between the neighbourhoods being compared. Experiments were performed on MRI data and results illustrate the usefulness of the approach in the context of brain tissue classification.

Fully automatic 3D segmentation of coronary arteries based on mathematical morphology

In this paper we propose a fully automatic algorithm for coronary artery extraction from X-ray data (3D-CT scan, 64 detectors) based on the mathematical morphology techniques and guided by anatomical knowledge. Growing and thresholding methods, in their most general form, are not sufficient to extract only the whole coronary arteries, because of the properties of these images. Finding appropriate methods is known to be a challenging problem because of the data imperfections such as noise, heterogeneous intensity and contrasts of similar tissues. We deal with these challenges by employing discrete geometric tools to fit on the arteries form independently from any perturbation of the data.