Estimation de l'échelle des néoplasies en coloscopie par détection de la profondeur de défocalisation

National audienceLa coloscopie est l'examen médical privilégié dans le cadre du diagnostic et du traitement des maladies colorectales. Cette technique qualifiée de peu invasive permet aux gastro-entérologues d'explorer la cavité du côlon et d'ôter les néoplasies - proliférations cellulaires - telles que les polypes qui peuvent évoluer en tumeurs malignes. La taille, la texture ainsi que la forme des néoplasies constituent des critères essentiels à leurs diagnostics. L'estimation de la taille est cependant difficile à réaliser de part la perte de l'information de profondeur de la scène imagée par le gastro-entérologue. Nous proposons une amélioration de notre technique de détection de la Profondeur de Défocalisation (PD) permet- tant l'estimation de l'échelle des scènes endoscopiques par extraction de la PD au sein d'une séquence vidéo. L'estimation conjointe du suivi affine de la néoplasie au cours de la séquence vidéo et du flou de mise au point permet d'inférer avec une meilleure précision la taille des néoplasies. Par ailleurs, la méthode proposée est mieux adaptée aux conditions réelles de coloscopie pour lesquelles la manipulation du gastroscope peut être délicate

Estimation of gastrointestinal polyp size in video endoscopy

Abstract Worldwide the colorectal cancer is one of the most common public health problems, constituting in 2010 the seventh cause of death. This aggressive cancer is firstly identified during an endoscopy routine examination by characterizing a set of polyps that appear along the digestive tract, mainly in the colon and rectum. The polyp size is one of the most important features that determines the surgical endoscopy management and even can be used to predict the level of aggressiveness. For instance, the gastroenterologists only send a polyp sample to the pathology examination if the polyp diameter is larger than 10 mm, a measure that is achieved typically by examining the lesion with a calibrated endoscopy tool. However, the polyp size measure is very challenging because it must be performed during a procedure subjected to a complex mix of noise sources, such as: the distorted optical characteristics of the endoscopy, the exacerbated physiological conditions and abrupt motion. The main goal of this thesis was estimated the polyp size during an endoscopy video sequence using a spatio-temporal characterization. Firstly, the method estimated the region with more motion within which the polyp shape is approximated by those pixels with the largest temporal variance. On the above, an initial manual polyp delineation in the first frame captures the main features to be follow in posterior frames by a cross correlation procedure. Afterwards, a bayesian tracking strategy is used to refine the polyp segmentation. Finally a defocus strategy allows to estimate on the clear cut frame at a certain depth as a reference to determine the polyp size obtaining reliable results. In the segmentation task, the approach achieved a Dice Score of 0.7 in real endoscopy video-sequences, when comparing with an expert. In addition, the results polyp size estimation obtained a Root Mean Square Error (RMSE) of 0.87 mm with spheres of known size that simulated the polyps, and in real endoscopy sequences obtaining a RMSE of 4.7 mm compared with measures obtained by a group of four experts with similar experience.El cáncer colorectal es uno de los problemas de salud pública más comunes a nivel mundial, ocupando la séptima causa de muerte en el 2010. Este tipo de cáncer tan agresivo es identificado prematuramente por un conjunto de pólipos que crecen a lo largo del tracto digestivo, principalmente en el colon y el recto. El tamaño de los pólipos es una de las características mas importantes, con la cual se determina el manejo quirúrgico de la lesión e incluso puede ser usado para predecir el grado de malignidad. Acorde a esto, el experto solo envía una muestra del pólipo para un examen patológico, sí el diámetro del pólipo es más largo que 10 mm. típica mente, esta medida es tomada examinando la lesión con una herramienta endoscópica calibrada. Sin embargo, la medición del tamaño del pólipo es realmente difícil debido a que el procedimiento está sujeto a fuentes de ruido bastante complejas, tales como: la distorsión óptica que es característica del endoscopio, las condiciones fisiológicas del tracto digestivo y los movimientos abruptos con el dispositivo. La contribución principal de este trabajo fue la estimación del tamaño de los pólipos, sobre una secuencia de vídeo de un procedimiento de endoscopia usando una caracterización espacio-temporal. En primera parte, el método estima la región con mayor movimiento que corresponde aproximadamente a la región del pólipo, tomando aquellos pixeles con mayor varianza temporal. Sobre lo anterior, una delineación manual de la lesión es realizada en el primer cuadro para establecer las principales características, para ser seguidas en los cuadros posteriores usando un método de correlación cruzada. Después, se usó una estrategia de seguimiento bayesiana para refinar la segmentación del pólipo. Finalmente, una estrategia basada en la correspondencia del desenfoque de las imágenes de una secuencia a una profundidad o distancia determinada, se pudo obtener una referencia para determinar el tamaño de los pólipos, obteniendo resultados fiables. En la etapa de segmentación, la estrategia logra un Dice score de 0, 7 al comparar con un experto en secuencias de endoscopia reales. Y en la estimación del tamaño de los pólipo se obtuvo un error cuadrático medio (RMSE) de 0.87 mm, comparando con esferas de tamaño conocido que simulaban los pólipos, y en secuencias de endoscopia reales se obtuvo un RMSE de 4.7 mm comparando con las medidas obtenidas por un grupo de cuatro. expertos con experiencia similar.Maestrí

Fast widefield techniques for fluorescence and phase endomicroscopy

Thesis (Ph.D.)--Boston UniversityEndomicroscopy is a recent development in biomedical optics which gives researchers and physicians microscope-resolution views of intact tissue to complement macroscopic visualization during endoscopy screening. This thesis presents HiLo endomicroscopy and oblique back-illumination endomicroscopy, fast widefield imaging techniques with fluorescence and phase contrast, respectively. Fluorescence imaging in thick tissue is often hampered by strong out-of-focus background signal. Laser scanning confocal endomicroscopy has been developed for optically-sectioned imaging free from background, but reliance on mechanical scanning fundamentally limits the frame rate and represents significant complexity and expense. HiLo is a fast, simple, widefield fluorescence imaging technique which rejects out-of-focus background signal without the need for scanning. It works by acquiring two images of the sample under uniform and structured illumination and synthesizing an optically sectioned result with real-time image processing. Oblique back-illumination microscopy (OBM) is a label-free technique which allows, for the first time, phase gradient imaging of sub-surface morphology in thick scattering tissue with a reflection geometry. OBM works by back-illuminating the sample with the oblique diffuse reflectance from light delivered via off-axis optical fibers. The use of two diametrically opposed illumination fibers allows simultaneous and independent measurement of phase gradients and absorption contrast. Video-rate single-exposure operation using wavelength multiplexing is demonstrated

Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions

Developing endoscopic instrumentation and techniques for in vivo fluorescence lifetime imaging and spectroscopy

Confocal fluorescence endomicroscopes employ fibre optics along with miniaturised scanning and focussing mechanisms to allow microscopic investigation of remote tissue samples with sub-cellular resolution. For this reason they are widely used in biomedical research, both in clinical studies and in small animal imaging experiments. Fluorescence lifetime imaging microscopy (FLIM) has been shown to provide contrast between normal and unhealthy tissue in several diseases including gastro-intestinal (GI) cancer. As such, there is significant interest in developing instrumentation that will allow endoscopic confocal FLIM as this would permit the in vivo investigation of human GI tissue. This thesis describes the development and use of several instruments and techniques aimed at clinically viable in vivo fluorescence lifetime spectroscopy and confocal endomicroscopy. This research has consisted of two broad branches: the study of the fluorescence signature of healthy and diseased tissue both ex vivo and in vivo; and the development of a novel method for achieving beam scanning in confocal endomicroscopy. Firstly the tissue studies are discussed. This begins with the application of a compact steady-state diffuse reflectance/fluorescence spectrometer and a fibre-optic-coupled time-resolved spectrofluorometer to an in vivo investigation of the spectral signatures of skin cancer. This study – which involved the interrogation of 27 clinically diagnosed lesions – was carried out in collaboration with researchers at Lund University in Sweden and revealed significant differences between healthy and diseased tissue both in terms of fluorescence lifetime and steady state reflectance and fluorescence spectra. Further to this study, work is presented charting the development of a clinically viable spectrometer, which measures time-resolved fluorescence spectra with two excitation wavelengths (375 nm and 435 nm) as well as diffuse reflectance spectra. The entire system is contained within a compact trolley (120 x 70 x 55 cm) for easy transportation and safe use in a clinic. It utilises a fibre optic probe to deliver/collect light that can be inserted into the working channel of a medical endoscope meaning that the system can be used to measure diffuse reflectance and time-resolved fluorescence spectra in the GI tract in vivo. The development and testing of this system are discussed and data are presented from both ex vivo and in vivo studies of GI cancer. The second broad section of this thesis focuses more closely on confocal endomicroscopy. Firstly current methods used in this field are discussed and the sources of several drawbacks are explained. A novel approach to laser scanning endomicroscopy is then presented, which requires no moving parts and can be implemented without the need for any distal scanners or optics. This technique is similar in concept to the use of adaptive optics to focus through turbid media: it utilises a proximal spatial light modulator to correct for phase variations across a fibre imaging bundle and then to encode for arbitrary wavefronts at the distal end of that fibre bundle. Thus, it is possible to realise both focussing and beam scanning at the output of the fibre bundle with no distal components, permitting extremely compact endoscopic probes to be developed. Proof-of-principle results are presented illustrating the imaging capabilities of this novel system as well as simulations showing the achievable resolution and field of view in several feasible endoscopic configurations. Overall, this thesis contains work from two quite different projects both aimed at developing novel optical techniques for clinical diagnostic use in endoscopic procedures. The first is aimed at investigating the temporal and spectral properties of the fluorescence and reflectance signatures of cancer, while the goal of the second is to develop improved confocal endomicroscopes

Characterization and modelling of complex motion patterns

Movement analysis is the principle of any interaction with the world and the survival of living beings completely depends on the effciency of such analysis. Visual systems have remarkably developed eficient mechanisms that analyze motion at different levels, allowing to recognize objects in dynamical and cluttered environments. In artificial vision, there exist a wide spectrum of applications for which the study of complex movements is crucial to recover salient information. Yet each domain may be different in terms of scenarios, complexity and relationships, a common denominator is that all of them require a dynamic understanding that captures the relevant information. Overall, current strategies are highly dependent on the appearance characterization and usually they are restricted to controlled scenarios. This thesis proposes a computational framework that is inspired in known motion perception mechanisms and structured as a set of modules. Each module is in due turn composed of a set of computational strategies that provide qualitative and quantitative descriptions of the dynamic associated to a particular movement. Diverse applications were herein considered and an extensive validation was performed for each of them. Each of the proposed strategies has shown to be reliable at capturing the dynamic patterns of different tasks, identifying, recognizing, tracking and even segmenting objects in sequences of video.Resumen. El análisis del movimiento es el principio de cualquier interacción con el mundo y la supervivencia de los seres vivos depende completamente de la eficiencia de este tipo de análisis. Los sistemas visuales notablemente han desarrollado mecanismos eficientes que analizan el movimiento en diferentes niveles, lo cual permite reconocer objetos en entornos dinámicos y saturados. En visión artificial existe un amplio espectro de aplicaciones para las cuales el estudio de los movimientos complejos es crucial para recuperar información saliente. A pesar de que cada dominio puede ser diferente en términos de los escenarios, la complejidad y las relaciones de los objetos en movimiento, un común denominador es que todos ellos requieren una comprensión dinámica para capturar información relevante. En general, las estrategias actuales son altamente dependientes de la caracterización de la apariencia y por lo general están restringidos a escenarios controlados. Esta tesis propone un marco computacional que se inspira en los mecanismos de percepción de movimiento conocidas y esta estructurado como un conjunto de módulos. Cada módulo esta a su vez compuesto por un conjunto de estrategias computacionales que proporcionan descripciones cualitativas y cuantitativas de la dinámica asociada a un movimiento particular. Diversas aplicaciones fueron consideradas en este trabajo y una extensa validación se llevó a cabo para cada uno de ellas. Cada una de las estrategias propuestas ha demostrado ser fiable en la captura de los patrones dinámicos de diferentes tareas identificando, reconociendo, siguiendo e incluso segmentando objetos en secuencias de video.Doctorad

Applications and Experiences of Quality Control

The rich palette of topics set out in this book provides a sufficiently broad overview of the developments in the field of quality control. By providing detailed information on various aspects of quality control, this book can serve as a basis for starting interdisciplinary cooperation, which has increasingly become an integral part of scientific and applied research

Comparing Gaussian and Bessel-Gauss beams for translating ultrafast laser ablation towards soft tissue surgery

The goal of this research was to further improve existing ultrafast laser surgery techniques. To do so, different beam shapes (Bessel-Gauss and Gaussian) were compared for performing ultrashort picosecond pulsed surgery on various soft biological tissues, with the goal of minimising collateral thermal damage. Initially, theoretical modelling was performed using OpticStudio to test axicons of various conical angles. A 20° axicon was selected, but unfortunately early tests on murine intestinal tissue indicated a lack of sufficient intensity to achieve plasma-mediated ablation of the tissue with the 6ps input pulses of 85 µJ energy. Subsequently, a reimaged setup was designed in OpticStudio to demagnify the beam by a factor of 1.4x. The ability of this demagnified Bessel-Gauss beam to perform plasma-mediated ablation of murine intestinal tissue was confirmed through histological analysis. Another setup was also designed to produce a Gaussian beam of equivalent spot size. These beams were then tested on porcine intestinal tissue using lower pulse repetition rates of 1, 2 and 3 kHz, with optimal ablation and thermal damage margins of less than 20 µm (confirmed through histological analysis) being achieved with the Bessel-Gauss beam for spatial pulse overlaps of 70%, while for the Gaussian beam the prominence of cavitation bubble formation at both 2 and 3 kHz inhibited the respective ablation processes at this same spatial pulse overlap. As the numbers of passes were increased, the Bessel-Gauss beam also showed a trend of increased ablation depths. This was attributed to its large depth of focus of over 1 mm, compared to the theoretical 48 µm depth of focus for the Gaussian beam. After characterisation of fixated, non-ablated porcine intestine sample surfaces to quantify the inhomogeneity, another set of ablation trials was performed at higher pulse repetition rates (5, 10 and 20 kHz) to test more clinically viable processes. For the Bessel-Gauss beam, spatial pulse overlaps of up to around 50% at 5, 10 and 20 kHz offered excellent thermal confinement (with damage margins of < 30 µm, < 50 µm and < 25 µm respectively) and shape control, but at 70% and greater pulse overlaps the ablated feature became hard to control despite good thermal confinement (< 40 µm). The Gaussian beam, while having the advantage of achieving plasma formation at lower input pulse energies, was again found to be more prone to undesirable cavitation effects. Cavitation bubbles were observed in the histology images for spatial pulse overlaps as low as 15% for 5 kHz and 30% for both 10 and 20 kHz. From the histology images it is clear to see that these effects became more pronounced as the pulse repetition rate was increased. Conversely, the more consistent spot size of the Bessel-Gauss beam across its longer focal depth resulted in a higher tolerance to cavitation bubble formation. This was also demonstrated by high-speed videos of the beams being scanned across porcine skin samples. This could be significant as it may allow for higher ablation rates. In addition, it could ease the design constraint of the maximum speed at which the beam can be scanned at the distal end of an endoscopic device. Despite this, both beams were able to achieve distinct ablation with high thermal confinement for certain parameters. This work further highlights fibre-delivered ultrashort laser pulses as a promising alternative to existing endoscopic tumour resection techniques, which carry a higher risk of bowel perforation.James Watt Scholarshi

Konzeption und Entwicklung eines trinokularen Endoskops zur robusten Oberflächenerfassung in der minimalinvasiven Chirurgie

Die minimalinvasive Chirurgie ist eine besonders anspruchsvolle Aufgabe für den Chirurgen, da die Operation ausschließlich über Endoskope und stangenartige, filigrane Instrumente erfolgt. Computerassistierte Stereo-Endoskopiesysteme erleichtern die Tiefenwahrnehmung und unterstützen bei verschiedensten Anwendungen wie z.B. der Resektion eines Nierentumors durch Augmented Reality. Eine wesentliche Aufgabe ist die robuste dreidimensionale Erfassung der beobachteten Oberfläche der Organe. Aufgrund starker Reflexionen durch die endoskopische Lichtquelle, homogener Texturen und weicher, sich bewegender Geometrien ist eine zuverlässige Oberflächenerfassung sehr herausfordernd und stellt noch ein ungelöstes Problem dar. In dieser Arbeit wird deshalb ein neuartiges miniaturisiertes Dreikamerasystem als Demonstrator für ein trinokulares Endoskop sowie ein Algorithmus zur Dreibildauswertung mit semi-globaler Optimierung entwickelt. Durch synthetische und reale Messdaten werden theoretische Überlegungen anhand von drei Hypothesen geprüft. Im Vergleich zu einer stereoskopischen Auswertung wird untersucht, ob eine Dreibildauswertung robustere Ergebnisse liefert, kleinere Referenz- und Suchfenster ermöglicht und eine rechenzeitaufwendige semi-globale Optimierung ersetzt. Es stellt sich heraus, dass die ersten beiden Annahmen grundsätzlich zutreffen, eine semi-globale Optimierung aber nur bedingt ersetzt werden kann. Weiterhin werden die Fehlereinflüsse durch Reflexionen näher spezifiziert und durch gekreuzte Polarisationsfilter sehr effektiv unterdrückt. Das vorgestellte Dreikamera-Endoskop und angepasste Auswerteverfahren tragen wesentlich zur Verbesserung der computerassistierten Endoskopie bei und bringen die Forschungen in diesem Gebiet einen Schritt voran.Minimally invasive surgery is a quite challenging task to the surgeon due to operation through an endoscope and sensitive telescopic instruments exclusively. Computer assisted stereo endoscopic systems eases depth perception and supports several tasks such as dissection of a renal tumour by augmented reality. An essential procedure is robust surface reconstruction of the observed organs. Due to strong reflections from the endoscopic light source, homogeneous textures and weak deforming geometries robust surface reconstruction becomes quite challenging and is not solved successfully yet. Therefore, in this work a novel miniaturised three camera endoscope is introduced and an algorithm for three image analysis and semi-global optimisation is implemented. Synthetic and real experimental measurements are conducted to evaluate theoretical assumptions and review three hypotheses. In contrast to stereo analysis, it is examined whether three image analysis leads to more robust results, allows for smaller matching window sizes and replaces a time-consuming semiglobal matching algorithm. The investigations show that the first two assumptions can generally be confirmed, but the semi-global matching is necessary in some cases. Additionally, errors by reflections are examined in more detail and are suppressed efficiently by crossed polarising filters. The novel three camera endoscope and customized image analysis algorithm gives a great benefit to computer assisted endoscopy and brings research a step closer to more reliable assistant systems

Development and clinical translation of optical and software methods for endomicroscopic imaging

Endomicroscopy is an emerging technology that aims to improve clinical diagnostics by allowing for in vivo microscopy in difficult to reach areas of the body. This is most commonly achieved by using coherent fibre bundles to relay light for illumination and imaging to and from the area under investigation. Endomicroscopy’s attraction for researchers and clinicians is two-fold: on the one hand, its use can reduce the invasiveness of a diagnostic procedure by removing the need for biopsies; On the other hand, it allows for structural and functional in vivo imaging. Endomicroscopic images acquired through optical fibre bundles exhibit artefacts that deteriorate image quality and contrast. This thesis aims to improve an existing endomicroscopy imaging system by exploring two methods that mitigate these artefacts. The first, software-based method takes several processing steps from literature and implements them in an existing endomicroscopy device with a focus on real-time application to enable clinical use, after image quality was found to be inadequate without further processing. A contribution to the field is that two different approaches are implemented and compared in quantitative and qualitative means that have not been compared directly in this manner before. This first attempt at improving endomicroscopy image quality relies solely on digital image processing methods and is developed with a strong focus on real-time applicability in clinical use. Both approaches are compared on pre-clinical and clinical human imaging data. The second method targets the effect of inter-core coupling, which reduces contrast in fibre images. A parallelised confocal imaging method is developed in which a sequence of images is acquired while selectively illuminating groups of fibre cores through the use of a spatial light modulator. A bespoke algorithm creates a composite image in a final processing step. In doing so, unwanted light is detected and removed from the final image. This method is shown to reduce the negative impact of inter-core coupling on image contrast on small imaging targets, while no benefit was found in large, scattering samples