Quand des processus administratifs limitent l’accès aux médicaments chez les étudiants

Étude de cas / Case study

Méthodes de génération et de validation de champs de déformation pour la recombinaison de distribution de dose à l’aide d’images 4DCT dans le cadre d’une planification de traitement de cancers pulmonaires

Des efforts de recherche considérables ont été déployés afin d'améliorer les résultats de traitement de cancers pulmonaires. L'étude de la déformation de l'anatomie du patient causée par la ventilation pulmonaire est au coeur du processus de planification de traitement radio-oncologique. À l'aide d'images de tomodensitométrie quadridimensionnelles (4DCT), une simulation dosimétrique peut être calculée sur les 10 ensembles d'images du 4DCT. Une méthode doit être employée afin de recombiner la dose de radiation calculée sur les 10 anatomies représentant une phase du cycle respiratoire. L'utilisation de recalage déformable d'images (DIR), une méthode de traitement d'images numériques, génère neuf champs vectoriels de déformation permettant de rapporter neuf ensembles d'images sur un ensemble de référence correspondant habituellement à la phase d'expiration profonde du cycle respiratoire. L'objectif de ce projet est d'établir une méthode de génération de champs de déformation à l'aide de la DIR conjointement à une méthode de validation de leur précision. Pour y parvenir, une méthode de segmentation automatique basée sur la déformation surfacique de surface à été créée. Cet algorithme permet d'obtenir un champ de déformation surfacique qui décrit le mouvement de l'enveloppe pulmonaire. Une interpolation volumétrique est ensuite appliquée dans le volume pulmonaire afin d'approximer la déformation interne des poumons. Finalement, une représentation en graphe de la vascularisation interne du poumon a été développée afin de permettre la validation du champ de déformation. Chez 15 patients, une erreur de recouvrement volumique de 7.6 ± 2.5[%] / 6.8 ± 2.1[%] et une différence relative des volumes de 6.8 ± 2.4 [%] / 5.9 ± 1.9 [%] ont été calculées pour le poumon gauche et droit respectivement. Une distance symétrique moyenne 0.8 ± 0.2 [mm] / 0.8 ± 0.2 [mm], une distance symétrique moyenne quadratique de 1.2 ± 0.2 [mm] / 1.3 ± 0.3 [mm] et une distance symétrique maximale 7.7 ± 2.4 [mm] / 10.2 ± 5.2 [mm] ont aussi été calculées pour le poumon gauche et droit respectivement. Finalement, 320 ± 51 bifurcations ont été détectées dans le poumons droit d'un patient, soit 92 ± 10 et 228 ± 45 bifurcations dans la portion supérieure et inférieure respectivement. Nous avons été en mesure d'obtenir des champs de déformation nécessaires pour la recombinaison de dose lors de la planification de traitement radio-oncologique à l'aide de la méthode de déformation hiérarchique des surfaces. Nous avons été en mesure de détecter les bifurcations de la vascularisation pour la validation de ces champs de déformation.

Patient-specific model of a scoliotic torso for surgical planning

A method for the construction of a patient-specific model of a scoliotic torso for surgical planning via inter- patient registration is presented. Magnetic Resonance Images (MRI) of a generic model are registered to surface topography (TP) and X-ray data of a test patient. A partial model is first obtained via thin-plate spline registration between TP and X-ray data of the test patient. The MRIs from the generic model are then fit into the test patient using articulated model registration between the vertebrae of the generic model’s MRIs in prone position and the test patient’s X-rays in standing position. A non-rigid deformation of the soft tissues is performed using a modified thin-plate spline constrained to maintain bone rigidity and to fit in the space between the vertebrae and the surface of the torso. Results show average Dice values of 0.975 ± 0.012 between the MRIs following inter-patient registration and the surface topography of the test patient, which is comparable to the average value of 0.976 ± 0.009 previously obtained following intra-patient registration. The results also show a significant improvement compared to rigid inter-patient registration. Future work includes validating the method on a larger cohort of patients and incorporating soft tissue stiffness constraints. The method developed can be used to obtain a geometric model of a patient including bone structures, soft tissues and the surface of the torso which can be incorporated in a surgical simulator in order to better predict the outcome of scoliosis surgery, even if MRI data cannot be acquired for the patient.

Spechte als ökologische Indikatoren in Natur- und Wirtschaftswäldern im Bialowiera-Wald (Ostpolen)

Die vorliegende Untersuchung analysiert die Eignung der "Spechtgemeinschaft" als ökologische Indikatorengruppe und formuliert vor dem Hintergrund der Ergebnisse Forderungen und Empfehlungen für einen "spechtgerechten" Umgang mit Wäldern. Die Habitatnutzung von sieben Spechtarten beim Nahrungserwerb wurde über einen Zeitraum von zwei Jahren in urwaldartigen und forstlich genutzten Beständen verschiedener Waldgesellschaften systematisch beobachtet. Das Untersuchungsgebiet ist der Bialowieza-Wald im äußersten Osten Polens, wo in enger räumlicher Nachbarschaft Natur- und Wirtschaftswaldflächen bearbeitet werden konnten. Die Beobachtungen erfolgten zwischen Anfang März 1999 und Ende Februar 2001 und wurden zu allen Jahreszeiten durchgeführt. Vier der insgesamt sechs Probeflächen repräsentieren die wichtigste Laubwaldgesellschaft des Gebietes, das Tilio-Carpinetum, die übrigen zwei die wichtigste Nadelwaldgesellschaft, das Peucedano-Pinetum. Die Hälfte der zwischen 42 und 54 ha großen Probeflächen lag im streng geschützten Urwaldreservat des Bialowieza-Nationalparkes, die übrigen in forstlich genutzten Waldbeständen. Zusätzlich wurde ein 2,5 km langes Transekt durch bewirtschafteten Erlen-Eschen-Auenwald und sehr naturnahen Erlenbruch bearbeitet. Die Probeflächen wurden in ein Raster aus 50x50m großen Quadranten unterteilt. Zur Beobachtung der Spechte beim Nahrungserwerb erfolgten 21 Begehungen je Probefläche bzw. Transekt. Die Probeflächen wurden dazu auf parallelen Linien mit Abständen von je 100m begangen, Startpunkt und Startrichtung wurden variiert. Zur Charakterisierung der Vegetation und Bestandesstruktur erfolgten Erhebungen zur Baumartenzusammensetzung, Größenklassenverteilung der Bäume, Totholzanteil und Krautvegetation. 1332 Beobachtungen von Spechten beim Nahrungserwerb konnten ausgewertet werden. Der Buntspecht wurde in allen Flächen am häufigsten gesehen. Mittel-, Weißrücken- und Kleinspecht wurden überwiegend in den Tilio-Carpineten beobachtet, in den Naturwäldern häufiger als in den bewirtschafteten Beständen. Der Dreizehenspecht wurde im Nadelwald und stärker mit Fichten durchmischtem Laubwald angetroffen. Bei Schwarz- und Grauspecht konnte keine klare Vorliebe für bestimmte Waldgesellschaften ermittelt werden. Der Buntspecht ernährte sich vor allem im Herbst und Winter überwiegend von fetthaltigen Samen und wurde dann meist beim Bearbeiten von Fichten- oder Kiefernzapfen in Schmieden beobachtet. Der Mittelspecht suchte als "Sammelspecht" seine Nahrung vor allem an den Oberflächen der Stämme und Äste. Klein-, Weißrücken-, Dreizehen- und Schwarzspecht traten als Hackspechte in Erscheinung. Die wenigen Daten zum Grauspecht reichen nicht zur Ermittlung der bevorzugten Nahrungserwerbstechnik aus. Bei Bunt-, Mittel- und Weißrückenspecht konnte eine deutliche Vorliebe für die Stieleiche als Nahrungsbaum nachgewiesen werden. Der Dreizehenspecht ist jedoch die einzige der beobachteten Arten mit einer weitgehenden Spezialisierung auf eine bestimmte Baumart, er nutzte in allen Waldgesellschaften meist die Fichte. Insgesamt bevorzugten die Spechte Bäume mit großen Stammdurchmessern, beim Kleinspecht ist diese Vorliebe allerdings nur schwach ausgeprägt. Totholz wurde von Weißrücken-, Dreizehen- und Kleinspecht bei der Nahrungssuche bevorzugt, vom Mittelspecht jedoch nur gelegentlich genutzt. Beim Buntspecht zeigte der Totholz-Nutzungsanteil erhebliche Unterschiede zwischen verschiedenen Baumarten. Liegendes Totholz spielte in den Tilio-Carpineten im Vergleich zu stehendem Totholz und toten Teilen lebender Bäume nur eine geringe Rolle für Nahrung suchende Spechte.

Enhanced Reality Visualization in a Surgical Environment

Enhanced reality visualization is the process of enhancing an image by adding to it information which is not present in the original image. A wide variety of information can be added to an image ranging from hidden lines or surfaces to textual or iconic data about a particular part of the image. Enhanced reality visualization is particularly well suited to neurosurgery. By rendering brain structures which are not visible, at the correct location in an image of a patient's head, the surgeon is essentially provided with X-ray vision. He can visualize the spatial relationship between brain structures before he performs a craniotomy and during the surgery he can see what's under the next layer before he cuts through. Given a video image of the patient and a three dimensional model of the patient's brain the problem enhanced reality visualization faces is to render the model from the correct viewpoint and overlay it on the original image. The relationship between the coordinate frames of the patient, the patient's internal anatomy scans and the image plane of the camera observing the patient must be established. This problem is closely related to the camera calibration problem. This report presents a new approach to finding this relationship and develops a system for performing enhanced reality visualization in a surgical environment. Immediately prior to surgery a few circular fiducials are placed near the surgical site. An initial registration of video and internal data is performed using a laser scanner. Following this, our method is fully automatic, runs in nearly real-time, is accurate to within a pixel, allows both patient and camera motion, automatically corrects for changes to the internal camera parameters (focal length, focus, aperture, etc.) and requires only a single image.

From Genetic Algorithms to Efficient Organization

The work described in this thesis began as an inquiry into the nature and use of optimization programs based on "genetic algorithms." That inquiry led, eventually, to three powerful heuristics that are broadly applicable in gradient-ascent programs: First, remember the locations of local maxima and restart the optimization program at a place distant from previously located local maxima. Second, adjust the size of probing steps to suit the local nature of the terrain, shrinking when probes do poorly and growing when probes do well. And third, keep track of the directions of recent successes, so as to probe preferentially in the direction of most rapid ascent. These algorithms lie at the core of a novel optimization program that illustrates the power to be had from deploying them together. The efficacy of this program is demonstrated on several test problems selected from a variety of fields, including De Jong's famous test-problem suite, the traveling salesman problem, the problem of coordinate registration for image guided surgery, the energy minimization problem for determining the shape of organic molecules, and the problem of assessing the structure of sedimentary deposits using seismic data.

Towards Detecting Changes in Underwater Image Sequences

Detecting changes between images of the same scene taken at different times is of great interest for monitoring and understanding the environment. It is widely used for on-land application but suffers from different constraints. Unfortunately, Change detection algorithms require highly accurate geometric and photometric registration. This requirement has precluded their use in underwater imagery in the past. In this paper, the change detection techniques available nowadays for on-land application were analyzed and a method to automatically detect the changes in sequences of underwater images is proposed. Target application scenarios are habitat restoration sites, or area monitoring after sudden impacts from hurricanes or ship groundings. The method is based on the creation of a 3D terrain model from one image sequence over an area of interest. This model allows for synthesizing textured views that correspond to the same viewpoints of a second image sequence. The generated views are photometrically matched and corrected against the corresponding frames from the second sequence. Standard change detection techniques are then applied to find areas of difference. Additionally, the paper shows that it is possible to detect false positives, resulting from non-rigid objects, by applying the same change detection method to the first sequence exclusively. The developed method was able to correctly find the changes between two challenging sequences of images from a coral reef taken one year apart and acquired with two different cameras

Perspectives of auto-correcting lens distortions in mosaic-based underwater navigation

When unmanned underwater vehicles (UUVs) perform missions near the ocean floor, optical sensors can be used to improve local navigation. Video mosaics allow to efficiently process the images acquired by the vehicle, and also to obtain position estimates. We discuss in this paper the role of lens distortions in this context, proving that degenerate mosaics have their origin not only in the selected motion model or in registration errors, but also in the cumulative effect of radial distortion residuals. Additionally, we present results on the accuracy of different feature-based approaches for self-correction of lens distortions that may guide the choice of appropriate techniques for correcting distortions

Large-Area Photo-Mosaics Using Global Alignment and Navigation Data

Seafloor imagery is a rich source of data for the study of biological and geological processes. Among several applications, still images of the ocean floor can be used to build image composites referred to as photo-mosaics. Photo-mosaics provide a wide-area visual representation of the benthos, and enable applications as diverse as geological surveys, mapping and detection of temporal changes in the morphology of biodiversity. We present an approach for creating globally aligned photo-mosaics using 3D position estimates provided by navigation sensors available in deep water surveys. Without image registration, such navigation data does not provide enough accuracy to produce useful composite images. Results from a challenging data set of the Lucky Strike vent field at the Mid Atlantic Ridge are reported

A system to evaluate the accuracy of a visual mosaicking methodology

When underwater vehicles navigate close to the ocean floor, computer vision techniques can be applied to obtain motion estimates. A complete system to create visual mosaics of the seabed is described in this paper. Unfortunately, the accuracy of the constructed mosaic is difficult to evaluate. The use of a laboratory setup to obtain an accurate error measurement is proposed. The system consists on a robot arm carrying a downward looking camera. A pattern formed by a white background and a matrix of black dots uniformly distributed along the surveyed scene is used to find the exact image registration parameters. When the robot executes a trajectory (simulating the motion of a submersible), an image sequence is acquired by the camera. The estimated motion computed from the encoders of the robot is refined by detecting, to subpixel accuracy, the black dots of the image sequence, and computing the 2D projective transform which relates two consecutive images. The pattern is then substituted by a poster of the sea floor and the trajectory is executed again, acquiring the image sequence used to test the accuracy of the mosaicking system

A Motion compensated filtering approach to remove sunlight flicker in shallow water images

A common problem in video surveys in very shallow waters is the presence of strong light fluctuations, due to sun light refraction. Refracted sunlight casts fast moving patterns, which can significantly degrade the quality of the acquired data. Motivated by the growing need to improve the quality of shallow water imagery, we propose a method to remove sunlight patterns in video sequences. The method exploits the fact that video sequences allow several observations of the same area of the sea floor, over time. It is based on computing the image difference between a given reference frame and the temporal median of a registered set of neighboring images. A key observation is that this difference will have two components with separable spectral content. One is related to the illumination field (lower spatial frequencies) and the other to the registration error (higher frequencies). The illumination field, recovered by lowpass filtering, is used to correct the reference image. In addition to removing the sunflickering patterns, an important advantage of the approach is the ability to preserve the sharpness in corrected image, even in the presence of registration inaccuracies. The effectiveness of the method is illustrated in image sets acquired under strong camera motion containing non-rigid benthic structures. The results testify the good performance and generality of the approach

Recovering Euclidean deformable models from stereo-motion

In this paper we present a novel structure from motion (SfM) approach able to infer 3D deformable models from uncalibrated stereo images. Using a stereo setup dramatically improves the 3D model estimation when the observed 3D shape is mostly deforming without undergoing strong rigid motion. Our approach first calibrates the stereo system automatically and then computes a single metric rigid structure for each frame. Afterwards, these 3D shapes are aligned to a reference view using a RANSAC method in order to compute the mean shape of the object and to select the subset of points on the object which have remained rigid throughout the sequence without deforming. The selected rigid points are then used to compute frame-wise shape registration and to extract the motion parameters robustly from frame to frame. Finally, all this information is used in a global optimization stage with bundle adjustment which allows to refine the frame-wise initial solution and also to recover the non-rigid 3D model. We show results on synthetic and real data that prove the performance of the proposed method even when there is no rigid motion in the original sequence

Planar homography: accuracy analysis and applications

Projective homography sits at the heart of many problems in image registration. In addition to many methods for estimating the homography parameters (R.I. Hartley and A. Zisserman, 2000), analytical expressions to assess the accuracy of the transformation parameters have been proposed (A. Criminisi et al., 1999). We show that these expressions provide less accurate bounds than those based on the earlier results of Weng et al. (1989). The discrepancy becomes more critical in applications involving the integration of frame-to-frame homographies and their uncertainties, as in the reconstruction of terrain mosaics and the camera trajectory from flyover imagery. We demonstrate these issues through selected examples

Physiotherapy cervicothoracic PPIVMs

A script for a streaming video clip modelling the movements of thoracic PPIVMs as performed by a physiotherapist. Access to this clip requires an ISS username and password. Please enter in the format soton\username when prompted. Creation date: 08.02.2008 Academic year: 2007/08 Produced by: School of Health Professions and Rehabilitation Sciences Length of clip: 4 min Level: Level 2 pre-registration neuromusculoskeletal manipulation of the cervicothorax Distribution: Can be viewed by all staff and students at the University of Southampton. Requires an ISS username and password.

Factores asociados al desarrollo de eventos adversos con transfusión de plasma fresco congelado en la Fundación Cardioinfantil-Instituto de Cardiología

Objetivo: Determinar los factores asociados con reacciones adversas transfusionales al Plasma Fresco Congelado en la FCI-IC durante los años 2008-2010. Metodología: Estudio de Casos y Controles, en relación 1:3. Pacientes mayores de 18 años transfundidos con plasma fresco congelado en la FCI-IC durante los años 2008-2010. Se definieron como casos pacientes identificados a partir del registro de eventos adversos transfusionales de la FCI que presentaron una reacción adversa transfusional a Plasma Fresco Congelado de los siguientes tipos: alérgica, febril, edema pulmonar no cardiogénico, sobrecarga volumen, CID o PTT. Los controles se definieron como personas que recibieron transfusión de plasma fresco congelado y cumpliendo los criterios de selección, no presentaron reacción adversa transfusional. Resultados: La edad de los casos fue significativamente menor (52,4 vs. 60,5 p=0,001). Para las reacciones alérgicas, el número de unidades de plasma provenientes de una unidad externa (0,7 vs. 0,0 p=0,003), de una donante de sexo femenino (2,5 vs. 1,4 p=0,11) y la paridad de dichas donantes (4,0 vs. 2,6 p=0,04), fueron en promedio mayor que para los controles. La presencia de sépsis (OR:0.01, IC95%:0,01-0,87, p=0,015) y de diabetes (OR:0.9, IC95%:0,01-0,54, p=0,003) se comportaron como factores protectores para el desarrollo de una reacción alérgica. Discusión y Conclusiones: Los resultados de este trabajo son compatibles con el hecho de que las reacciones adversas transfusionales están relacionadas con plasma provenientes de un banco de sangre externo, de donantes mujeres y de mujeres con un mayor número de gestaciones.