Reconstruction Toolkit (RTK) v2, an Insight Toolkit (ITK) module for tomographic reconstruction

International audienceSince its first presentation at ICCR 2013, the Reconstruction Toolkit (RTK) has become a reference software for tomographic reconstruction of computed tomography (CT) images. In this period, RTK has become a remote module of the Insight Toolkit (ITK), thus enabling improved continuous integration and Python wrapping. New functionalities have also been developed, including simulation of Forbild phantoms, handling of cylindrical detectors and new iterative reconstruction algorithms for conventional CT, single photon emission CT (SPECT), four-dimensional (4D) CT and spectral CT. This article summarizes these eleven years of developments to today's RTK v2

Description of the multi-dimensional environment at the territorial scale: A holistic framework using cluster analysis and open data in France

The impact of the environment on health is usually studied in a segmented manner, with a focus on a single source, pollutant, or exposure medium. To better understand spatial health inequalities, it is necessary to adopt multi-dimensional approaches to comprehensively describe the environment, especially at the territorial level. Clustering methods, which allow for the development of territorial typologies, are particularly interesting for this purpose. By simplifying complex datasets, these methods may reveal spatial patterns and geographical phenomena that would otherwise be difficult to observe. Based on the existing literature, there is a clear need for large-scale territorial typologies that comprehensively address the physical and outdoor environment.A robust and transposable framework was developed and applied to 3,041 municipalities in Northern France using open environmental data. It consists of five main steps: data collection, data selection, data preparation, cluster analysis, and cluster interpretation. This methodology allows for the development of an environmental classification of municipalities by identifying the primary environmental profiles represented in the study area. Cluster detection was performed based on 39 spatialized indicators that describe the level of environmental contamination (air, water, soil), the level of pollutant emissions, the proximity to emission sources, the land use, the agricultural practices, and the degree of naturalness in every municipality. As a result, municipalities were allocated into one of the seven following environmental profiles: (i) Dense urban centers; (ii) Peripheral urban municipalities; (iii) Intensive agricultural municipalities under urban influence; (iv) Intensive agricultural municipalities beyond urban influence; (v) More extensive and diversified agricultural municipalities; (vi) Municipalities with predominant livestock activities and significant natural areas; (vii) Municipalities with predominant natural areas: forests, wetlands, and water surfaces. The resulting typology goes far beyond a simple description of the urban–rural continuum. Five profiles of rural municipalities were identified, primarily distinguished by agricultural practices, degree of naturalness, and intensity of urban pressure.This approach enables researchers to identify the combination of environmental factors that shape a territory. It provides a more comprehensive and nuanced understanding of how environmental pressures and amenities are distributed in space and overlap with each other. By linking these typologies with health data, it could provide new insights into the etiology of complex diseases with unidentified environmental risk factors. Relying on open data, this framework is a valuable tool to assess etiological hypotheses at the territorial level

Unveiling the presence of endocrine disrupting chemicals in northern French soils: Land cover variability and implications

International audienceEndocrine disrupting chemicals (EDCs) are chemicals that can be found in the environment and have adverse effects on human health by mimicking, perturbing and blocking the function of hormones. They are commonly studied in water surfaces, rarely in soils, although it can be an important source of their presence in the environment. Their detection in soils is analytically challenging to quantify, hence the lack of known background concentrations found in the literature. This scientific research aimed to detect EDCs in soils by analyzing 240 soil samples using an optimized protocol of double extraction and analysis using liquid chromatography coupled to mass spectrometry. The optimized protocol allowed for very sensitive detection of the targeted compounds. The results showed a high concentration of 29.391 ng/g of 17β-estradiol in soils and 47.16 ng/g for 17α-ethinylestradiol. Testosterone and Progesterone were detected at a highest of 1.02 and 6.58 ng/g, respectively. The ∑EDCs which included estrogens, progesterone, testosterone and Bisphenol A was found at an average of 22.72 ± 35.46 ng/g in the study area. The results of this campaign showed a heterogeneous geographic distribution of the EDCs compounds in the different zones of study. Additionally, the study conducted a comparison of the concentration of EDCs in different land covers including urban areas, agricultural lands, grasslands and forests. We observed a significant difference between forests and other land covers (p < 0.0001) for 17α-ethinylestradiol, estriol, and progesterone. This presence of EDCs in forest lands is not yet understood and requires further studies concerning its origins, its fate and its effect on human health. This study is the first large-scale sampling campaign targeting EDCs in soils in Europe and the second in the world. It is also the first to assess the concentrations of these compounds based on different land covers

The Reconstruction Toolkit (RTK) : an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK)

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions

Anthropomorphic lung phantom based validation of in-room proton therapy 4D-CBCT image correction for dose calculation.

PURPOSE: Ventilation-induced tumour motion remains a challenge for the accuracy of proton therapy treatments in lung patients. We investigated the feasibility of using a 4D virtual CT (4D-vCT) approach based on deformable image registration (DIR) and motion-aware 4D CBCT reconstruction (MA-ROOSTER) to enable accurate daily proton dose calculation using a gantry-mounted CBCT scanner tailored to proton therapy. METHODS: Ventilation correlated data of 10 breathing phases were acquired from a porcine ex-vivo functional lung phantom using CT and CBCT. 4D-vCTs were generated by (1) DIR of the mid-position 4D-CT to the mid-position 4D-CBCT (reconstructed with the MA-ROOSTER) using a diffeomorphic Morphons algorithm and (2) subsequent propagation of the obtained mid-position vCT to the individual 4D-CBCT phases. Proton therapy treatment planning was performed to evaluate dose calculation accuracy of the 4D-vCTs. A robust treatment plan delivering a nominal dose of 60Gy was generated on the average intensity image of the 4D-CT for an approximated internal target volume (ITV). Dose distributions were then recalculated on individual phases of the 4D-CT and the 4D-vCT based on the optimized plan. Dose accumulation was performed for 4D-vCT and 4D-CT using DIR of each phase to the mid position, which was chosen as reference. Dose based on the 4D-vCT was then evaluated against the dose calculated on 4D-CT both, phase-by-phase as well as accumulated, by comparing dose volume histogram (DVH) values (Dmean, D2%, D98%, D95%) for the ITV, and by a 3D-gamma index analysis (global, 3%/3mm, 5Gy, 20Gy and 30Gy dose thresholds). RESULTS: Good agreement was found between the 4D-CT and 4D-vCT-based ITV-DVH curves. The relative differences ((CT-vCT)/CT) between accumulated values of ITV Dmean, D2%, D95% and D98% for the 4D-CT and 4D-vCT-based dose distributions were -0.2%, 0.0%, -0.1% and -0.1%, respectively. Phase specific values varied between -0.5% and 0.2%, -0.2% and 0.5%, -3.5% and 1.5%, and -5.7% and 2.3%. The relative difference of accumulated Dmean over the lungs was 2.3% and Dmean for the phases varied between -5.4% and 5.8%. The gamma pass-rates with 5Gy, 20Gy and 30Gy thresholds for the accumulated doses were 96.7%, 99.6% and 99.9%, respectively. Phase-by-phase comparison yielded pass-rates between 86% and 97%, 88% and 98%, and 94% and 100%. CONCLUSIONS: Feasibility of the suggested 4D-vCT workflow using proton therapy specific imaging equipment was shown. Results indicate the potential of the method to be applied for daily 4D proton dose estimation

Aircraft Wake Vortex Study and Characterization with 1.5 µm Fiber Doppler Lidar

International audienceFor ten years now, Onera has been developing lidar tools for wake vortex detection and studies. Since 2003, new developments based on 1.5 µM fibered laser sources have been achieved in parallel with extensive research work on the laser sources themselves.Three innovative lidars have been developed and are presented in this paper:1) A mini-lidar, based on a CW (continuous-wave) 2 W / 1.5 µM laser source, for aircraft model wake vortex characterization in a catapult facility. A self-triangulation technique allows the vortex core position to be found with 10 cm error, and the circulation error is 10 %.2) A pulsed 1.5 µM lidar, based on a 50 µJ / 15 kHz MOPA (Master Oscillator Power Amplifier) source, for lateral wake vortex monitoring at airports. The range is 400 m, the core position error is about ± 2 m and the circulation error is about 10 %.3) A pulsed 1.5 µM lidar, based on a 120 µJ / 12 kHz MOPA source, for onboard axial wake vortex detection. Ground based lidar tests at Orly airport have demonstrated wake vortex detection up to 1.2 km