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

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

Interstitial imaging with multiple diffusive reflectance spectroscopy projections for in vivo blood vessels detection during brain needle biopsy procedures

Blood vessel injury during image-guided brain biopsy poses a risk of hemorrhage. Approaches that reduce this risk may minimize related patient morbidity. We present here an intraoperative imaging device that has the potential to detect the brain vasculature in situ. The device uses multiple diffuse reflectance spectra acquired in an outward-viewing geometry to detect intravascular hemoglobin, enabling the construction of an optical image in the vicinity of the biopsy needle revealing the proximity to blood vessels. This optical detection system seamlessly integrates into a commercial biopsy system without disrupting the neurosurgical clinical workflow. Using diffusive brain tissue phantoms, we show that this device can detect 0.5-mm diameter absorptive carbon rods up to approximately 2 mm from the biopsy window. We also demonstrate feasibility and practicality of the technique in a clinical environment to detect brain vasculature in an in vivo model system. In situ brain vascular detection may add a layer of safety to image-guided biopsies and minimize patient morbidity

Towards comprehensive observing and modeling systems for monitoring and predicting regional to coastal sea level

A major challenge for managing impacts and implementing effective mitigation measures and adaptation strategies for coastal zones affected by future sea level (SL) rise is our limited capacity to predict SL change at the coast on relevant spatial and temporal scales. Predicting coastal SL requires the ability to monitor and simulate a multitude of physical processes affecting SL, from local effects of wind waves and river runoff to remote influences of the large-scale ocean circulation on the coast. Here we assess our current understanding of the causes of coastal SL variability on monthly to multi-decadal timescales, including geodetic, oceanographic and atmospheric aspects of the problem, and review available observing systems informing on coastal SL. We also review the ability of existing models and data assimilation systems to estimate coastal SL variations and of atmosphere-ocean global coupled models and related regional downscaling efforts to project future SL changes. We discuss (1) observational gaps and uncertainties, and priorities for the development of an optimal and integrated coastal SL observing system, (2) strategies for advancing model capabilities in forecasting short-term processes and projecting long-term changes affecting coastal SL, and (3) possible future developments of sea level services enabling better connection of scientists and user communities and facilitating assessment and decision making for adaptation to future coastal SL change.RP was funded by NASA grant NNH16CT00C. CD was supported by the Australian Research Council (FT130101532 and DP 160103130), the Scientific Committee on Oceanic Research (SCOR) Working Group 148, funded by national SCOR committees and a grant to SCOR from the U.S. National Science Foundation (Grant OCE-1546580), and the Intergovernmental Oceanographic Commission of UNESCO/International Oceanographic Data and Information Exchange (IOC/IODE) IQuOD Steering Group. SJ was supported by the Natural Environmental Research Council under Grant Agreement No. NE/P01517/1 and by the EPSRC NEWTON Fund Sustainable Deltas Programme, Grant Number EP/R024537/1. RvdW received funding from NWO, Grant 866.13.001. WH was supported by NASA (NNX17AI63G and NNX17AH25G). CL was supported by NASA Grant NNH16CT01C. This work is a contribution to the PIRATE project funded by CNES (to TP). PT was supported by the NOAA Research Global Ocean Monitoring and Observing Program through its sponsorship of UHSLC (NA16NMF4320058). JS was supported by EU contract 730030 (call H2020-EO-2016, “CEASELESS”). JW was supported by EU Horizon 2020 Grant 633211, Atlantos

Altimetry for the future: Building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the ‘‘Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Altimetry for the future: building on 25 years of progress

In 2018 we celebrated 25 years of development of radar altimetry, and the progress achieved by this methodology in the fields of global and coastal oceanography, hydrology, geodesy and cryospheric sciences. Many symbolic major events have celebrated these developments, e.g., in Venice, Italy, the 15th (2006) and 20th (2012) years of progress and more recently, in 2018, in Ponta Delgada, Portugal, 25 Years of Progress in Radar Altimetry. On this latter occasion it was decided to collect contributions of scientists, engineers and managers involved in the worldwide altimetry community to depict the state of altimetry and propose recommendations for the altimetry of the future. This paper summarizes contributions and recommendations that were collected and provides guidance for future mission design, research activities, and sustainable operational radar altimetry data exploitation. Recommendations provided are fundamental for optimizing further scientific and operational advances of oceanographic observations by altimetry, including requirements for spatial and temporal resolution of altimetric measurements, their accuracy and continuity. There are also new challenges and new openings mentioned in the paper that are particularly crucial for observations at higher latitudes, for coastal oceanography, for cryospheric studies and for hydrology. The paper starts with a general introduction followed by a section on Earth System Science including Ocean Dynamics, Sea Level, the Coastal Ocean, Hydrology, the Cryosphere and Polar Oceans and the “Green” Ocean, extending the frontier from biogeochemistry to marine ecology. Applications are described in a subsequent section, which covers Operational Oceanography, Weather, Hurricane Wave and Wind Forecasting, Climate projection. Instruments’ development and satellite missions’ evolutions are described in a fourth section. A fifth section covers the key observations that altimeters provide and their potential complements, from other Earth observation measurements to in situ data. Section 6 identifies the data and methods and provides some accuracy and resolution requirements for the wet tropospheric correction, the orbit and other geodetic requirements, the Mean Sea Surface, Geoid and Mean Dynamic Topography, Calibration and Validation, data accuracy, data access and handling (including the DUACS system). Section 7 brings a transversal view on scales, integration, artificial intelligence, and capacity building (education and training). Section 8 reviews the programmatic issues followed by a conclusion

Sonde Raman multimodale intégrée à une plateforme d'imagerie TRUS-IRM à l'aide d'un capteur électromagnétique pour améliorer le guidage des biopsies de la prostate

RÉSUMÉ: La substitution des chirurgies ouvertes par des procédures minimalement invasives constitue une évolution majeure de la médecine moderne. Ce progrès est rendu possible par le développement des systèmes d'imagerie servant à guider en temps réel la navigation des instruments chirurgicaux. Toutefois ces technologies, basées essentiellement sur un contraste anatomique, souffrent de limites de précision dues à la taille ou à l'hétérogénéité des lésions ciblées. Cette thèse vise à répondre à ce problème clinique, dans le cas particulier du guidage des procédures de biopsie de la prostate, grâce au contraste moléculaire que procure la spectroscopie Raman. Le premier objectif est la validation d'une preuve de concept du guidage d'une aiguille de biopsie optique, lors de son insertion dans un modèle animal in vivo. Les résultats ont montré la capacité de la sonde tomographique, basée sur la spectroscopie de réflectance diffuse, à retrouver la signature de l'hémoglobine permettant de localiser spatialement les vaisseaux sanguins. Le deuxième objectif vise à concevoir et manufacturer le nouveau prototype de sonde multimodale optimisé pour le guidage de la procédure de biopsie de la prostate. Les contraintes techniques sont majeures car elles imposent de miniaturiser, dans un diamètre inférieur à 1.3 mm, un système de spectroscopie Raman combinant les régions fingerprint (FP) et high wavenumber (HWN). Un aspect critique est également l'intégration d'un capteur Électromagnétique (EM) sur le nouveau prototype permettant son insertion dans une plateforme de guidage standard TRUS-IRM. Finalement le troisième objectif est de valider la capacité de la spectroscopie Raman à discriminer entre les tissus sains et cancéreux de la prostate. Nous démontrons pour la première fois l'utilisation et le diagnostic in situ de tissus cancéreux prostatiques sur 18 patients, avec une précision de 79%, à l'aide d'un système de spectroscopie Raman intégré à une plateforme de navigation TRUS-IRM-EM. Les résultats de cette thèse valident expérimentalement la capacité de la spectroscopie Raman à améliorer le guidage des procédures de biopsie de la prostate en détectant in situ les échantillons cancéreux. ABSTRACT: The transition from open to minimally invasive surgeries represents a major evolution of modern medicine. This improvement is possible thanks to the development of imaging systems, used in real time, for the surgical instruments guidance. However, these technologies, mostly based on anatomical contrast, suffer from accuracy limitations due to the size and heterogeneity of the targeted lesions. This thesis aims to answer the specific clinical problem of the prostate biopsy procedure guidance, by using the molecular contrast provided by Raman spectroscopy. The first objective is to provide a proof of concept for the guidance of an optical biopsy needle, during its insertion in an animal model experiment. The results showed the ability of the tomographic probe, based on diffuse reflectance spectroscopy, to retrieve the hemoglobin signature allowing to spatially locate blood vessels. The second objective is to design and manufacture a new multimodal prototype probe optimized for the prostate procedure biopsy guidance. The technical constraints are significant due to the requirement of miniaturizing, in a 1.3 mm diameter, a Raman spectroscopy system combining fingerprint and high wavenumber spectral regions. A critical aspect is also the Electromagnetic tracker integration on this new prototype to ensure its clean insertion in a standard TRUS-MRI navigation platform. Finally, the third objective is the validation of Raman spectroscopy to discriminate between normal and cancerous prostate tissue. We show for the first time the in situ acquisition and diagnosis of cancerous prostate tissue performed on 18 patients, with a 79% accuracy, using our Raman spectroscopy system integrated to a TRUS-MRI-EM navigation platform. The results of this thesis experimentally validate the ability of Raman spectroscopy to enhance the prostate procedure biopsy guidance thanks to an in situ detection of cancerous samples

La vinciennite, Cu10Fe4Sn(As,Sb)S16, une nouvelle espèce minérale. Etude paragénétique du gîte type de Chizeuil, Saône-et-Loire

Vinciennite Cu10Fe4Sn(As0.8Sb0.2)S16 was discovered in the pyrite deposit in Chizeuil, Saône-et-Loire, France. It is associated with pyrite, chalcopyrite, colusite, stannite, bornite, enargite, tetrahedrite, tennantite and other minerals in a gangue of quartz and/or barite. Other minerals include : hessite, altaite, tetradymite, cassiterite, stannoidite, kesterite, mawsonite, aikinite, cosalite, bismuthinite, wittichenite, bismuth, molybdenite, rutile, chalcocite and covellite. Vinciennite also has been found at Huaron, Peru. As small opaque grains up to 1 mm, with a metallic lustre and an orange colour ; VHN25 = 280, calculated density 4.29 g.cm-3. Very brittle with a conchoidal fracture. In polarized light, the anisotropism is weak with colours ranging from purplish-blue to greenish brown-yellow ; simple or weakly polysynthetic twins are occasionally observed. The reflectance values are (SiC standard) : 420 nm : 19.4-19.4 ; 460 nm : 21.8-20.6 ; 500 nm : 23.9-22.8 ; 540 nm : 27.7-26.5 ; 580 nm : 30.7-29.5 ; 620 nm : 33.6-32.1 ; 660 nm : 35.9-34.3 ; 700 nm : 37.8-36.0 ; 740 nm : 38.8-36.8 ; 780 nm : 39.5-36.6. Pseudo-cubic, vinciennite is in fact tetragonal P4122 (or possibly P4/mmm, P422 or P4mm) with a = b = c = 10.697(6) Å and Z = 2. Strongest lines of the X-ray powder diagram are : 4.37 (3) 211 ; 3.088 (10) 222 ; 2.676 (5) 400-004 ; 1.895 (9) 440-404 ; 1.614 (7) 622-226 ; 1.227 (4) 626-662 ; 1.091 (5) 844-448. Analytical results (mean of 6 analyses) with a cameca electron microprobe using Sb2S3, SnO2, As, Cu and Fe as standards are : Cu 40.90 ; Fe 14.63 ; Sn 7.33 ; As 3.43 ; Sb 1.60 ; S 31.85 ; total 99.74 %. The name is for Prof. Henri Vincienne (1898-1965) who first called attention to the mineral. Type material is preserved in the mineralogical collection of the Ecole Nationale Supérieure des Mines de Paris. Its description was approved by I. M. A.La vinciennite Cu10Fe4Sn(As0.8Sb0.2)S16 a été découverte dans le gisement pyriteux de Chizeuil (Saône-et-Loire) associée à : pyrite, chalcopyrite, colusite, stannite, bornite, énargite, tétraédrite-tennantite, etc., dans une gangue de quartz et/ou barytine. La minéralisation complète inclut hessite, altaïte, tétradymite, cassitérite, stannoïdite, kesterite, mawsonite, aïkinite, cosalite, bismuthinite, wittichenite, bismuth, molybdénite, rutile, chalcopyrite et covellite. La vinciennite a également été observée à Huaron, Pérou. Elle se présente en grains opaques atteignant 1 à 2 mm avec un éclat métallique et une couleur orangée ; dureté Vickers 280 kg. mm-2 (P = 25 g), densité calculée 4,29. Très fragile avec une cassure conchoïdale. Entre polariseurs croisés, l'anisotropie est faible avec des couleurs allant du bleu violacé au brun-jaune verdâtre ; les macles, simples ou polysynthétiques, sont rares. Les pouvoirs réflecteurs sont (étalon SiC) : 420 nm : 19,4-19,4 ; 460 nm : 21,8-20,6 ; 500 nm : 23,9-22,8 ; 540 nm : 27,7-26,5 ; 580 nm : 30,7-29,5 ; 620 nm : 33,6-32,1 ; 660 nm : 35,9-34,3 ; 700 nm : 37,8-36,0 ; 740 nm : 38,8-36,8 ; 780 nm : 39,5-36,6. Quadratique pseudo-cubique apparemment P4122 (ou P4/mmm, P422, P4/mm) avec a = b = c = 10,697(6) Å et Z = 2. Les raies principales du diagramme de poudre sont 4,37 (3) 211 ; 3,088 (10) 222 ; 2,676 (5) 400-004 ; 1,895 (9) 440-404 ; 1,614 (7) 622-226 ; 1,227 (4) 626-662 ; 1,091 (5) 844-448. L'analyse à la microsonde électronique (étalons : Sb2S3, SnO2, As, Cu, Fe) a donné (moyenne de 6 analyses) : Cu 40,90 ; Fe 14,63 ; Sn 7,33 ; As 3,43 ; Sb 1,60 ; S 31,85 ; total 99,74 %. Nommée en l'honneur du Prof. Henri Vincienne (1898-1965) qui le premier attira l'attention sur ce minéral dont les échantillons originaux sont conservés dans la collection de minéralogie de l'Ecole Nationale Supérieure des Mines de Paris. Sa description a été approuvée par l'I.M.A.Cesbron Fabien, Giraud Roger, Picot Paul, Pillard François. La vinciennite, Cu10Fe4Sn(As,Sb)S16, une nouvelle espèce minérale. Etude paragénétique du gîte type de Chizeuil, Saône-et-Loire. In: Bulletin de Minéralogie, volume 108, 3-4, 1985. Minéralogie dans les Sciences de la Terre et l'Industrie - Hommage à François Permingeat

Envisat Ocean Altimetry Performance Assessment and Cross-calibration

Nearly three years of Envisat altimetric observations over ocean are available inGeophysical Data Record (GDR) products. The quality assessment of these data is routinelyperformed at the CLS Space Oceanography Division in the frame of the CNES Segment SolAltimétrie et Orbitographie (SSALTO) and ESA French Processing and Archiving Center(F-PAC) activities. This paper presents the main results in terms of Envisat data quality:verification of data availability and validity, monitoring of the most relevant altimeter(ocean1 retracking) and radiometer parameters, assessment of the Envisat altimeter systemperformances. This includes a cross-calibration analysis of Envisat data with Jason-1, ERS-2 and T/P. Envisat data show good general quality. A good orbit quality and a low level ofnoise allow Envisat to reach the high level of accuracy of other precise missions such as T/Pand Jason-1. Some issues raised in this paper, as the gravity induced orbit errors, will besolved in the next version of GDR products. Some others, as the Envisat Mean Sea Level inthe first year, still need further investigation

Sensitivity analysis aimed at blood vessels detection using interstitial optical tomography during brain needle biopsy procedures

A brain needle biopsy procedure is performed for suspected brain lesions in order to sample tissue that is subsequently analysed using standard histopathology techniques. A common complication resulting from this procedure is brain hemorrhaging from blood vessels clipped off during tissue extraction. Interstitial optical tomography (iOT) has recently been introduced by our group as a mean to assess the presence of blood vessels in the vicinity of the needle. The clinical need to improve safety requires the detection of blood vessels within 2 mm from the outer surface of the needle, since this distance is representative of the volume of tissue that is aspirated durirng tissue extraction. Here, a sensitivity analysis is presented to establish the intrinsic detection limits of iOT based on simulations and experiments using brain tissue phantoms. It is demonstrated that absorbers can be detected with diameters >300 μm located up to >2 mm from the biopsy needle core for bulk optical properties consistent with brain tissue