Sébastien Martin

Automated segmentation of the prostate in 3D MR images using a probabilistic atlas and a spatially constrained deformable model.

PURPOSEnThe authors present a fully automatic algorithm for the segmentation of the prostate in three-dimensional magnetic resonance (MR) images.nnnMETHODSnThe approach requires the use of an anatomical atlas which is built by computing transformation fields mapping a set of manually segmented images to a common reference. These transformation fields are then applied to the manually segmented structures of the training set in order to get a probabilistic map on the atlas. The segmentation is then realized through a two stage procedure. In the first stage, the processed image is registered to the probabilistic atlas. Subsequently, a probabilistic segmentation is obtained by mapping the probabilistic map of the atlas to the patients anatomy. In the second stage, a deformable surface evolves toward the prostate boundaries by merging information coming from the probabilistic segmentation, an image feature model and a statistical shape model. During the evolution of the surface, the probabilistic segmentation allows the introduction of a spatial constraint that prevents the deformable surface from leaking in an unlikely configuration.nnnRESULTSnThe proposed method is evaluated on 36 exams that were manually segmented by a single expert. A median Dice similarity coefficient of 0.86 and an average surface error of 2.41 mm are achieved.nnnCONCLUSIONSnBy merging prior knowledge, the presented method achieves a robust and completely automatic segmentation of the prostate in MR images. Results show that the use of a spatial constraint is useful to increase the robustness of the deformable model comparatively to a deformable surface that is only driven by an image appearance model.

Atlas-Based Prostate Segmentation Using an Hybrid Registration

PurposeThis paper presents the preliminary results of a semi-automatic method for prostate segmentation of magnetic resonance images (MRI) which aims to be incorporated in a navigation system for prostate brachytherapy.MethodsThe method is based on the registration of an anatomical atlas computed from a population of 18 MRI exams onto a patient image. An hybrid registration framework which couples an intensity-based registration with a robust point-matching algorithm is used for both atlas building and atlas registration.ResultsThe method has been validated on the same dataset that the one used to construct the atlas using the leave-one-out method. Results gives a mean error of 3.39xa0mm and a standard deviation of 1.95xa0mm with respect to expert segmentations.ConclusionsWe think that this segmentation tool may be a very valuable help to the clinician for routine quantitative image exploitation.

MR prior based automatic segmentation of the prostate in TRUS images for MR/TRUS data fusion

The poor signal-to-noise ratio in transrectal ultrasound (TRUS) images makes the fully automatic segmentation of the prostate challenging and most approaches proposed in the literature still lack robustness and accuracy. However, it is relatively straightforward to obtain high quality segmentations in magnetic resonance (MR) images. In the context of MR to TRUS data fusion the information gathered in the MR images can hence provide a strong prior for US segmentation. In this paper, we describe a method to non-linearly register a patient specific mesh of the prostate build from MR images to TRUS volume. The MR prior provides shape and volume constraints that are used to guide the MR-to-TRUS surface deformation, in collaboration with a US image contour appearance model. The anatomical point correspondences between the MR and TRUS surfaces are obtained implicitly. The method was validated on 30 pairs of MR/TRUS patient exams and achieves a mean Dice value 0.85 and a mean surface error of 2.0 mm.

Kinetics and Mechanisms of Ciprofloxacin Oxidation on Hematite Surfaces

Adsorption of antibiotics at mineral surfaces has been extensively studied over the past 20 years, yet much remains to be learned on their interfacial properties and transformation mechanisms. In this study, interactions of Ciprofloxacin (CIP), a fluoroquinolone antibiotic with two sets of synthetic nanosized hematite particles, with relatively smooth (H10, 10-20 nm in diameter) and roughened (H80, 80-90 nm in diameter) surfaces, were studied by means of liquid chromatography (LC), mass spectrometry (MS), and spectroscopy (vibration and X-ray photoelectron). Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy provides evidence for inner-sphere bidentate complex formation of CIP at hematite surfaces in 0.01 M NaCl, irrespective of pH and particle size. ATR-FTIR spectroscopy also revealed that the sorbed mother CIP molecule decayed to other surface species over a period of at least 65 h. This was supported by the detection of three daughter products in the aqueous phase by LC/MS. The appearance of NH3(+) groups during the course of these experiments, revealed by cryogenic XPS, provides further evidence that CIP oxidation proceeds through an opening of piperazine ring via N-dealkylation. Additional in vacuo FTIR experiments under temperature-programmed desorption also showed that oxidation of sorbed byproducts were effectively degraded beyond 450 °C, a result denoting considerably strong (inter)molecular bonds of both mother and daughter products. This work also showed that rougher, possibly multidomainic particles (H80) generated slower rates of CIP decomposition but occurring through more complex schemes than at smoother particle surfaces (H10). This work thus uncovered key aspects of the binding of an important antibiotic at iron oxide surfaces, and therefore provided additional constraints to our growing understanding of the fate of emerging contaminants in the environment.

Oxolinic Acid Binding at Goethite and Akaganéite Surfaces: Experimental Study and Modeling

Oxolinic acid (OA) is a widely used quinolone antibiotic in aquaculture. In this study, its interactions with synthetic goethite (α-FeOOH) and akaganéite (β-FeOOH) particle surfaces were monitored to understand the potential fate of OA in marine sediments where these phases occur. Batch sorption experiments, liquid chromatography (LC) analyses of supernatants, attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and multisite complexation (MUSIC) modeling were used to monitor OA binding at these particle surfaces. Both LC and ATR-FTIR showed that adsorption did not degrade OA, and that OA adsorption was largely unaffected by NaCl concentrations (10-1000 mM). This was explained further by ATR-FTIR suggesting the formation of metal-bonded complexes at circumneutral to low pHc = -log [H(+)] and with a strongly hydrogen-bonded complex at high pHc. The stronger OA binding to akaganéite can be explained both by the higher isoelectric point/point-of-zero charge (9.6-10) of this mineral than of goethite (9.1-9.4), and an additional OA surface complexation mechanism at the (010) plane. Geminal sites (≡Fe(OH2)2(+)) at this plane could be especially reactive for metal-bonded complexes, as they facilitate a mononuclear six-membered chelate complex via the displacement of two hydroxo/aquo groups at the equatorial plane of a single Fe octahedron. Collectively, these findings revealed that Fe-oxyhydroxides may strongly contribute to the fate and transport of OA-type antibacterial agents in marine sediments and waters.

Sorption of Phthalic Acid at Goethite Surfaces under Flow-Through Conditions

The objectives of this investigation were to improve our understanding of organic acid transport in porous media by focusing on a model system involving phthalic acid and goethite-coated sand (GCS). This was specifically made by first recalibrating a molecularly sound phthalate surface complexation model to GCS and then applying this model to describe breakthrough curves (BTC) in a GCS packed column. ATR-FTIR spectra of phthalic acid adsorbed at goethite surfaces at pH 3.0 and 6.0 and at loadings from 2.0 to 40.8 μmol/m(2) confirmed the coexistence of metal-bonded (MB) and hydrogen-bonded (HB) complexes at low pH and the predominance of HB complexes at high pH. This concept was incorporated into a surface complexation model used to describe BTC at influent pH (pH(in)) values of 3.0, 6.0, and 7.8. The BTC revealed strongly pH-dependent behaviors. At pH(in) 3.0, the BTC revealed one front/plateau behavior while at pH(in) 6.0 two fronts/plateaus occurred. The existence of a second front/plateau led to an overestimation of the sorbed amount compared to that observed in the batch and caused a failure in the prediction of BTC. Additional column investigations suggested that surface loadings of nonspecifically adsorbed complexes could vary with pH and ionic strength and that the two-step breakthrough behavior may have emerged as a result of the formation of surface species of different natures than those during the first step, with the latter even serving as attachment sites corresponding to the second step. These findings call for refinements in current day modeling approaches used in reactive transport studies.

Fast segmentation of the mitral valve leaflet in echocardiography

This paper presents a semi-automatic method for tracking the mitral valve leaflet in transesophageal echocardiography. The algorithm requires a manual initialization and then segments an image sequence. The use of two constrained active contours and curve fitting techniques results in a fast segmentation algorithm. The active contours successfully track the inner cardiac muscle and the mitral valve leaflet axis. Three sequences have been processed and the generated muscle outline and leaflet axis have been visually assessed by an expert. This work is a part of a more general project which aims at providing real-time detection of the mitral valve leaflet in transesophageal echocardiography images.

Tracking of the mitral valve leaflet in echocardiography images

This paper presents a semi-automatic method for the segmentation and the tracking of the mitral valve leaflet in transesophageal echocardiography. We use two connected active contours in order to track efficiently the mitral leaflet. Segmentation of very fast and non rigid motions involved are realized in two steps. In the first step we use transformation fitting to provide a rough segmentation that will be refined in a second step using snakes with dynamic programming minimization. The method successfully tracks the inner cardiac muscle and the mitral valve leaflet axis