Creating Open-Source software packages for Raman spectrum processing and analysis

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Développement d'un modèle géométrique 3D et analyse morphométrique des tendons de chevaux sains et lésés à partir de macrophotographies sériées

Les muscles et les articulations d'un cheval de sport de haut niveau sont très sollicités, ce qui peut entraîner de multiples tendinopathies telles que la déchirure ou la rupture d'un tendon. Plusieurs chercheurs s'intéressent à l'évaluation du pronostic fonctionnel des lésions tendineuses du cheval au moyen de l'échographie conventionnelle. La compréhension de l'information contenue dans les images échographiques est cependant très limitée. Cela est dû au manque de connaissance a priori sur l'architecture fasciculaire du tendon qui est responsable de la formation des images échographiques. Ce projet consistait à élaborer une technique de modélisation tridimensionnelle (3D) de l'architecture fasciculaire du tendon afin d'obtenir des mesures quantitatives sur celle-ci; variation et évolution longitudinale de l'architecture de même que les longueurs, volumes et rayons moyens des faisceaux la constituant. Pour ce faire, des photographies numériques provenant de coupes transversales sériées de tendons de chevaux (tendon fléchisseur superficiel du doigt) sains (8) ou lésés (2) ont été utilisées. À l'aide de méthodes de traitement numérique des images, les images ont été rehaussées, recalées, segmentées et fusionnéees pour obtenir un modèle 3D sur lequel les caractéristiques ont été calculées. Les rayons moyen des faisceaux analysés est de (moyenne ± écart-type)0,65±0,24 mm, leur longueur moyenne de 2,24±1,78 mm et seulement 34±6,5% des faisceaux ont été retrouvés dans plus d'une coupe (1,3 mm d'épaisseur). La variation et l'évolution longitudinale de l'architecture découvertes sont exactement les mêmes dans tous les tendons sains. À ce jour, à part celle-ci, aucune étude n'a fourni d'information précise et quantitative sur la distribution 3D des faisceaux tendineux. Les données recueillies, en plus d'enrichir la littérature et d'apporter une nouvelle compréhension de l'architecture fasciculaire, comble une partie des informations manquantes nécessaires à la compréhension de la formation des images échographiques du tendon

Postencephalitic epilepsy in dogs with meningoencephalitis of unknown origin: clinical features, risk factors, and long‐term outcome

Background: Although the presence of seizures in dogs with meningoencephalitis of unknown origin (MUO) has been associated with shorter survival times, data regarding the prevalence and risk factors for postencephalitic epilepsy (PEE) is lacking. Objectives: To describe the clinical features, prevalence, risk factors, and long‐term outcome of PEE in dogs with MUO. Animals: Sixty‐one dogs with presumptive diagnosis of MUO based on the clinicopathological and diagnostic imaging findings. Methods: Retrospective study. Cases were identified by search of hospital medical records for dogs with suspected or confirmed MUO. Medical records of dogs meeting inclusion criteria were reviewed. Signalment, seizure history, clinicopathologic, and magnetic resonance imaging (MRI) findings were recorded. Results: Among 61 dogs at risk of PEE, 14 (23%) dogs developed PEE. Three of 14 dogs with PEE (21%) developed drug‐resistant epilepsy. Dogs with PEE were younger (P = .03; ORadjusted = 0.75; 95% confidence interval [CI], 0.58‐0.98) and had significantly shorter survival times (log‐rank test P = .04) when compared to dogs that did not develop epilepsy. The risk factors associated with the development of PEE were the presence of acute symptomatic seizures (ASS; P = .04; ORadjusted = 4.76; 95% CI, 1.11‐20.4) and MRI lesions in the hippocampus (P = .04; ORadjusted = 4.75; 95% CI, 1.07‐21.0). Conclusions and Clinical Importance: Dogs with MUO and seizures at the early stage of the disease (ASS) seem to be at a higher risk of developing PEE

RESPE (French Network of Epidemiological surveillance for Equine diseases) : origin and sub-network for acute respiratory syndrome

RESPE is the first European network of epidemiological surveillance for equine diseases, based on a group of sentinel veterinary practitioners. RESPE has three objectives: the surveillance of specific syndromes or diseases, the creation of a centre of veterinary expertise to collect epidemiological data rapidly and manage health crises not associated with notifiable diseases. The results of the sub-network for equine acute respiratory syndrome demonstrated the effectiveness and relevance of RESPE. Although they do not give an exhaustive evaluation of equine acute respiratory syndromes in France, these results provided general data on the incidence of influenza, equine herpes, and equine arteritis viruses. The isolation and typing data of viral strains are used to ensure that vaccines are suited to the viruses circulating in the field, and to improve our understanding of the origin of the various foci. The capacity for rapid reaction of the veterinary practitioners and laboratories involved in this network plays a key role in the detection of emerging or re-emerging diseases. The management of the equine arteritis outbreak in the summer of 2007 demonstrated its efficacy.Le réseau d'épidémiosurveillance en pathologie équine (RESPE) est le premier réseau européen de ce type, fondé sur un groupe de vétérinaires sentinelles. Il a un triple objectif: assurer la veille sanitaire de certaines affections ou syndromes, développer un réseau de compétences vétérinaires permettant une collecte rapide d'informations épidémiologiques, et gérer les crises sanitaires hors maladies réglementées, grâce à un système d'alerte et à la constitution d'une cellule de crise. Le bilan du sous-réseau «Syndrome respiratoire aigu» (SRA) démontre l'intérêt et la pertinence du RESPE. Si les résultats ne constituent pas un bilan exhaustif des syndromes respiratoires aigus chez les équidés en France, ils permettent d'évaluer globalement, pour ce syndrome, l'incidence des virus de la grippe, de la rhinopneumonie et de l'artérite virale. L'isolement des souches et leur caractérisation génomique permettent de s'assurer de l'adéquation entre les souches circulantes et les souches vaccinales et de mieux comprendre l'origine des différents foyers. Enfin grâce à la réactivité des vétérinaires sentinelles et des laboratoires impliqués dans ce réseau, il permet la détection des maladies émergentes ou ré-émergentes: l'épisode d'artérite virale lors de l'été 2007 a démontré son efficacité

Wide-field optical spectroscopy system integrating reflectance and spatial frequency domain imaging to measure attenuation-corrected intrinsic tissue fluorescence in radical prostatectomy specimens

The development of a multimodal optical imaging system is presented that integrates endogenous fluorescence and diffuse reflectance spectroscopy with single-wavelength spatial frequency domain imaging (SFDI) and surface profilometry. The system images specimens at visible wavelengths with a spatial resolution of 70 microm, a field of view of 25 cm(2) and a depth of field of approximately 1.5 cm. The results of phantom experiments are presented demonstrating the system retrieves absorption and reduced scattering coefficient maps using SFDI with <6% reconstruction errors. A phase-shifting profilometry technique is implemented and the resulting 3-D surface used to compute a geometric correction ensuring optical properties reconstruction errors are maintained to <6% in curved media with height variations <20 mm. Combining SFDI-computed optical properties with data from diffuse reflectance spectra is shown to correct fluorescence using a model based on light transport in tissue theory. The system is used to image a human prostate, demonstrating its ability to distinguish prostatic tissue (anterior stroma, hyperplasia, peripheral zone) from extra-prostatic tissue (urethra, ejaculatory ducts, peri-prostatic tissue). These techniques could be integrated in robotic-assisted surgical systems to enhance information provided to surgeons and improve procedural accuracy by minimizing the risk of damage to extra-prostatic tissue during radical prostatectomy procedures and eventually detect residual cancer

Quantitative spectral quality assessment technique validated using intraoperative in vivo Raman spectroscopy measurements

Significance: Ensuring spectral quality is prerequisite to Raman spectroscopy applied to surgery. This is because the inclusion of poor-quality spectra in the training phase of Raman-based pathology detection models can compromise prediction robustness and generalizability to new data. Currently, there exists no quantitative spectral quality assessment technique that can be used to either reject low-quality data points in existing Raman datasets based on spectral morphology or, perhaps more importantly, to optimize the in vivo data acquisition process to ensure minimal spectral quality standards are met. Aim: To develop a quantitative method evaluating Raman signal quality based on the variance associated with stochastic noise in important tissue bands, including C─C stretch, CH2  /  CH3 deformation, and the amide bands. Approach: A single-point hand-held Raman spectroscopy probe system was used to acquire 315 spectra from 44 brain cancer patients. All measurements were classified as either high or low quality based on visual assessment (qualitative) and using a quantitative quality factor (QF) metric. Receiver-operator-characteristic (ROC) analyses were performed to evaluate the performance of the quantitative metric to assess spectral quality and improve cancer detection accuracy. Results: The method can separate high- and low-quality spectra with a sensitivity of 89% and a specificity of 90% which is shown to increase cancer detection sensitivity and specificity by up to 20% and 12%, respectively. Conclusions: The QF threshold is effective in stratifying spectra in terms of spectral quality and the observed false negatives and false positives can be linked to limitations of qualitative spectral quality assessment

Macroscopic-Imaging Technique for Subsurface Quantification of Near-Infrared Markers During Surgery

Obtaining accurate quantitative information on the concentration and distribution of fluorescent markers lying at a depth below the surface of optically turbid media, such as tissue, is a significant challenge. Here, we introduce a fluorescence reconstruction technique based on a diffusion light transport model that can be used during surgery, including guiding resection of brain tumors, for depth-resolved quantitative imaging of near-infrared fluorescent markers. Hyperspectral fluorescence images are used to compute a topographic map of the fluorophore distribution, which yields structural and optical constraints for a three-dimensional subsequent hyperspectral diffuse fluorescence reconstruction algorithm. Using the model fluorophore Alexa Fluor 647 and brain-like tissue phantoms, the technique yielded estimates of fluorophore concentration within ±25% of the true value to depths of 5 to 9 mm, depending on the concentration. The approach is practical for integration into a neurosurgical fluorescence microscope and has potential to further extend fluorescence-guided resection using objective and quantified metrics of the presence of residual tumor tissue

Experimental validation of a spectroscopic Monte Carlo light transport simulation technique and Raman scattering depth sensing analysis in biological tissue

ABSTRACT: Significance: Raman spectroscopy (RS) applied to surgical guidance is attracting attention among scientists in biomedical optics. Offering a computational platform for studying depthresolved RS and probing molecular specificity of different tissue layers is of crucial importance to increase the precision of these techniques and facilitate their clinical adoption. Aim: The aim of this work was to present a rigorous analysis of inelastic scattering depth sampling and elucidate the relationship between sensing depth of the Raman effect and optical properties of the tissue under interrogation. Approach: A new Monte Carlo (MC) package was developed to simulate absorption, fluorescence, elastic, and inelastic scattering of light in tissue. The validity of the MC algorithm was demonstrated by comparison with experimental Raman spectra in phantoms of known optical properties using nylon and polydimethylsiloxane as Raman-active compounds. A series of MC simulations were performed to study the effects of optical properties on Raman sensing depth for an imaging geometry consistent with single-point detection using a handheld fiber optics probe system. Results: The MC code was used to estimate the Raman sensing depth of a handheld fiber optics system. For absorption and reduced scattering coefficients of 0.001 and 1 mm−1, the sensing depth varied from 105 to 225 μm for a range of Raman probabilities from 10−6 to 10−3. Further, for a realistic Raman probability of 10−6, the sensing depth ranged between 10 and 600 μm for the range of absorption coefficients 0.001 to 1.4 mm−1 and reduced scattering coefficients of 0.5 to 30 mm−1. Conclusions: A spectroscopic MC light transport simulation platform was developed and validated against experimental measurements in tissue phantoms and used to predict depth sensing in tissue. It is hoped that the current package and reported results provide the research community with an effective simulating tool to improve the development of clinical applications of RS

Chemins de vie. Dix-neuf visages et paroles de migrant-e-s, 1956-2012

Dix-neuf entretiens avec des migrant-e-s ont été réalisés et analysés par des étudiant-e-s du Master d’histoire moderne et contemporaine des Universités Lyon 2 et Lyon 3.Ces migrant-e-s appartiennent à diverses générations (le plus âgé, Ferdinand Gonzalez, est née en 1935 et la plus jeune, Anaïs Quenette, en 1995) et sont d’origines géographiques variées (Europe, Afrique du Nord et subsaharienne, Amérique latine…). Ce sont des femmes et hommes qui ont émigré en France pour des raisons de travail, mais aussi pour suivre leurs parents, rejoindre un-e conjoint-e ou simplement pour faire des études supérieures. Certain-e-s ont demandé leur naturalisation, d’autres pas.Le fil rouge qui a été choisi pour structurer les entretiens est celui de « l’insertion » envisagée sous diverses facettes : le départ et les réactions de l’entourage, les représentations liées à la France, mais aussi les réactions des Françaises face à l’Autre, l’insertion sur le marché du travail, l’apprentissage de la langue, le logement comme les différents réseaux tissés dans l’exil, les différentes identités induites et bousculées par la migration.Le volume est organisé en deux parties. La première est l’analyse des entretiens en six grandes thématiques. La deuxième partie regroupe la retranscription intégrale des entretiens menés, qui sont classés par ordre alphabétique des noms de famille, qui peuvent être des pseudonymes. Les retranscriptions sont précédées de quelques lignes méthodologiques sur les conditions de l’entretien

Data consistency and classification model transferability across biomedical Raman spectroscopy systems

Surgical guidance applications using Raman spectroscopy are being developed at a rapid pace in oncology to ensure safe and complete tumor resection during surgery. Clinical translation of these approaches relies on the acquisition of large spectral and histopathological data sets to train classification models. Data calibration must ensure compatibility across Raman systems and predictive model transferability to allow multi-centric studies to be conducted. This paper addresses issues relating to Raman measurement standardization by first comparing Raman spectral measurements made on an optical phantom and acquired with nine distinct point probe systems and one wide-field imaging instrument. Data standardization method led to normalized root-mean-square deviations between instruments of 2%. A classification model discriminating between white and gray matter was trained with one point probe system. When used to classify independent data sets acquired with the other systems, model predictions led to >95% accuracy, preliminarily demonstrating model transferability across different biomedical Raman spectroscopy instruments