Height growth curves from satellite images and national forest inventory measurements for various tree species

<p>Data corresponding to height growth curves from satellite images and national forest inventory measurements for various tree species. The heights are in meters and the ages in years.</p><p>Growth_curve_NFI corresponds to French National Forest Inventory data (IGN - National Forest Inventory of France Raw Data, Annual Campaigns from 2005 onwards, IGN – Inventaire forestier national français, Accessed 1 June 2023)</p><p>Growth_curve_EO gives the 5th, 25th, 50th, 75th, and 95th percentile of height per years. The tree height, age, and tree species information wee retried from satellite observations. </p><p>Schwartz M, Ciais P, De Truchis A, et al (2023) FORMS: Forest Multiple Source height, wood volume, and biomass maps in France at 10 to 30 m resolution based on Sentinel-1, Sentinel-2, and GEDI data with a deep learning approach. Earth Syst Sci Data Discuss 1–28. https://doi.org/10.5194/essd-2023-196, </p><p>Senf C, Seidl R (2021) Mapping the forest disturbance regimes of Europe. Nat Sustain 4:63–70. https://doi.org/10.1038/s41893-020-00609-y</p><p>IGN (2018b) BD Foret® version 2, Accessed 5 May 2023</p&gt

Discrimination cinétique de marqueurs fluorescents réversiblement photocommutables

Multiplexing, i.e. simultaneously imaging tens of chemical species in a cell, is a challenge for quantitative biology. To this aim, two imaging protocols, LIGHTNING and HIGHLIGHT, exploiting the kinetics of rich photocycles including photochemical and thermal steps are introduced and applied to reversibly photoswitchable fluorescent proteins (RSFPs). In LIGHTNING, four characteristic times defining the kinetic signature of an RSFP are extracted from fluorescence evolution in four constant illumination regimes granting access to four independent dynamics. Reduced chemical mechanisms derived for the four illumination regimes qualitatively account for fluorescence evolution. Two RSFPs can be distinguished provided that the distance between their 4-D kinetic signature is larger than a cutoff distance related to experimental accuracy. 20 RSFPs out of the 22 investigated RSFPs are discriminated. In HIGHLIGHT, reversibly photoactivatable fluorophores are submitted to sine-wave illumination. At each harmonics, either the in-phase or the quadrature Fourier amplitude of fluorescence oscillations exhibits a resonance in the space of control parameters formed by the excitation frequency and the mean light intensities. Resonance conditions relating the control parameters and parameters characterizing kinetics are made explicit. Tuning the control parameters to target a given fluorophore optimizes its fluorescence response and nearly eliminates the responses of fluorophores with different kinetic properties. Both protocols have complementary merits. LIGHTNING has a larger discriminatory power and HIGHLIGHT provides better quality images due to lock-inamplification.Le multiplexage ou imagerie simultanée de dizaines d’espèces dans une cellule, est un défi pour la biologie quantitative. Deux protocoles d’imagerie, LIGHTNING et HIGHLIGHT, exploitant la cinétique riche de photocycles comprenant des étapes photochimiques et thermiques, ont été conçus et appliqués à des protéines fluorescentes réversiblement photocommutables (RSFP). Dans LIGHTNING, 4 temps caractéristiques définissant la signature cinétique d’une RSFP sont extraits de l’évolution de la fluorescence pour 4 conditions d’illumination constante donnant accès à 4 dynamiques indépendantes. Des mécanismes chimiques réduits sont dérivés pour les 4 conditions d’illumination. Deux RSFP sont distinguées si la distance entre leurs signatures cinétiques est plus grande qu’une distance de coupure liée à la précision expérimentale. 20 RSFP parmi les 22 étudiées sont discriminées. Dans HIGHLIGHT, des fluorophores réversiblement photocommutables sont soumis à un éclairement sinusoı̈dal. A chaque harmonique, l’amplitude de Fourier en phase ou en quadrature des oscillations de fluorescence présente une résonance dans l’espace des paramètres de contrôle, fréquence d’excitation et intensités lumineuses moyennes. Des conditions de résonance reliant les paramètres de contrôle et les paramètres caractérisant la cinétique sont explicitées. Le choix des paramètres de contrôle permet d’optimiser la réponse d’un fluorophore tout en éliminant celle des fluorophores de cinétiques différentes. Les deux protocoles ont des mérites complémentaires. LIGHTNING a un pouvoir discriminant plus important et HIGHLIGHT fournit des images de meilleure qualité grâce à une détection synchrone

Teaching and Learning Materials on the Quasi-Steady-State Approximation and the Partial-Equilibrium Approximation

Starting from simple examples of chemical schemes for which a concentration or an extent of reaction can be eliminated, we highlight the common features of the quasi-steady-state approximation and the partial-equilibrium approximation. General conditions to apply either of these adiabatic eliminations are mentioned.<br /

Quasi-Steady-State and Partial-Equilibrium Approximations in Chemical Kinetics: One Stage Beyond the Elimination of a Fast Variable

Classical approximations in chemical kinetics, the quasi-steady-state approximation (QSSA) and the partial-equilibrium approximation (PEA), are used to reduce rate equations for the concentrations and the extents of the reaction steps, respectively. We make precise two conditions on the rate constants necessary and sufficient to eliminate a well-chosen variable in the vicinity of a steady state. The first condition expresses that dynamics admits a small characteristic time associated with a fast variable. The second condition ensures that the fast variable is a concentration for QSSA and an extent for PEA. Both approximations exploit the zeroth order of a singular perturbation method. Eliminating a fast variable does not mean that it has reached a steady state. The fast evolution is considered over and the slow evolution of the eliminated variable is governed by the slow variables. The evolution of the slow variables occurs on a slow manifold in the space of the concentrations or the extents. In some cases the dynamics of the slow variables can be associated with a reduced chemical scheme. QSSA and PEA are applied to three chemical schemes associated with linear and nonlinear dynamics. We find that QSSA cannot be identified with the elimination of a reactive intermediate. The nonlinearities of the rate equations induce a more complex behavior.</pre

Correlation of fluorescence evolution for quantitative analysis of labels and sensors

International audienceTitration without separation, e.g. quantification of a target species in living cells, is a challenge of analytical chemistry. We perform the selective detection of a target using the kinetics involved in a photochemical process and develop a correlation method that we illustrate by the titration of a fluorescent photoswitcher and the target of a photoswitching sensor. Correlating an input time series and a well-chosen weighting function associated with a variable characteristic time yields a spectrum of characteristic times. The upper integration limit of the correlation output can be chosen to match the argument of an extremum of the spectrum with a characteristic time of the input time series in order to quantify the target. A similar procedure is followed to optimize the signal-to-noise ratio. Selectivity and signal-tonoise ratio associated with 15 weighting functions are theoretically predicted. The results are applied to the titration of the reversibly photoswitchable fluorescent protein Dronpa-2 and the titration of calcium using a reversibly photoswitchable fluorescent sensor. The performance of the correlation method is favorably compared to the one of other dynamic contrast protocols

Dynamic contrast for overcoming spectral interferences in fluorescence imaging

International audienc

Dynamic contrast with reversibly photoswitchable fluorescent labels for imaging living cells

International audienc

Combining satellite images with national forest inventory measurements for monitoring post-disturbance forest height growth

International audienceIntroduction: The knowledge about forest growth, influenced by factors such as tree species, tree age, and environmental conditions, is a key for future forest preservation. Height and age data can be combined to describe forest growth and used to infer known environmental effects. Methods: In this study, we built 14 height growth curves for stands composed of monospecific or mixed species using ground measurements and satellite data. We built a random forest height model from tree species, age, area of disturbance, and 125 environmental parameters (climate, altitude, soil composition, geology, stand ownership, and proximity to road and urban areas). Using feature elimination and SHapley Additive exPlanations (SHAP) analysis, we identified six key features explaining the forest growth and investigated how they affect the height. Results: The agreement between satellite and ground data justifies their simultaneous exploitation. Age and tree species are the main predictors of tree height (49% and 10%, respectively). The disturbed patch area, revealing the regeneration method, impacts post-disturbance growth at 19%. The soil pH, altitude, and climatic water budget in summer impact tree height differently depending on the age and tree species. Discussion: Methods integrating satellite and field data show promise for analyzing future forest evolution

Open-Canopy: A Country-Scale Benchmark for Canopy Height Estimation at Very High Resolution

22 pages, 8 figures, Submitted to NeurIPS 2024 Datasets and Benchmarks TrackInternational audienceEstimating canopy height and canopy height change at meter resolution from satellite imagery has numerous applications, such as monitoring forest health, logging activities, wood resources, and carbon stocks. However, many existing forest datasets are based on commercial or closed data sources, restricting the reproducibility and evaluation of new approaches. To address this gap, we introduce Open-Canopy, the first open-access and country-scale benchmark for very high resolution (1.5 m) canopy height estimation. Covering more than 87,000 km$^2$ across France, Open-Canopy combines SPOT satellite imagery with high resolution aerial LiDAR data. We also propose Open-Canopy-$\Delta$, the first benchmark for canopy height change detection between two images taken at different years, a particularly challenging task even for recent models. To establish a robust foundation for these benchmarks, we evaluate a comprehensive list of state-of-the-art computer vision models for canopy height estimation. The dataset and associated codes can be accessed at https://github.com/fajwel/Open-Canopy

Open-Canopy: A Country-Scale Benchmark for Canopy Height Estimation at Very High Resolution

22 pages, 8 figures, Submitted to NeurIPS 2024 Datasets and Benchmarks TrackInternational audienceEstimating canopy height and canopy height change at meter resolution from satellite imagery has numerous applications, such as monitoring forest health, logging activities, wood resources, and carbon stocks. However, many existing forest datasets are based on commercial or closed data sources, restricting the reproducibility and evaluation of new approaches. To address this gap, we introduce Open-Canopy, the first open-access and country-scale benchmark for very high resolution (1.5 m) canopy height estimation. Covering more than 87,000 km$^2$ across France, Open-Canopy combines SPOT satellite imagery with high resolution aerial LiDAR data. We also propose Open-Canopy-$\Delta$, the first benchmark for canopy height change detection between two images taken at different years, a particularly challenging task even for recent models. To establish a robust foundation for these benchmarks, we evaluate a comprehensive list of state-of-the-art computer vision models for canopy height estimation. The dataset and associated codes can be accessed at https://github.com/fajwel/Open-Canopy