Virtual Biophysical Lab · Vegetation Remote Sensing

Sandbox, not a full framework

The lab is not a full processing chain. It is a lightweight place to try ideas before moving them into larger tools or pipelines (e.g. project-specific repositories or operational code).

Leaf → canopy → scene

Examples focus on radiative transfer, trait sensitivity and scaling. Scripts can simulate reflectance, fluorescence and thermal signals for simple scenarios and compare them across stress conditions.

Support for exercises

The repository can host short exercises for students: parameter sweeps, index experiments, quick plots for slides and small notebooks illustrating model behaviour.

ToolsRTM

ToolsRTM is an R package designed to perform detailed simulations of leaf and canopy reflectance using a wide suite of radiative transfer (RT) models. It operates across multiple satellite spectral configurations and enables high-fidelity analysis of vegetation biophysical and biochemical traits.

At the canopy level, ToolsRTM includes models such as INFORM, fourSAIL, and fourSAIL2, enabling the simulation of BRDF-sensitive canopy reflectance under variable structural and illumination conditions.

At the leaf level, the package integrates several established models: PROSPECT (D and PRO versions), Liberty, and FLUSPECT (B–Cx), allowing users to simulate biochemical effects on reflectance and transmittance, including pigment composition, water content, and dry matter.

ToolsRTM also incorporates the SPART model (Soil–Plant–Atmosphere Radiative Transfer), a framework specifically developed to simulate top-of-atmosphere (TOA) directional reflectance across the solar spectrum. SPART couples three efficient RT components:

• BSM – a soil reflectance model;
• PROSAIL – vegetation canopy reflectance;
• SMAC – atmospheric correction / transmittance.

These modules are combined through the four-stream theory and the adding method, enabling realistic simulations that account for sun–sensor geometry, soil anisotropy, and non-Lambertian surface behaviour.

The package also integrates the MARMIT model (Multilayer rAdiative tRansfer Model of soIl reflecTance), which predicts bare-soil reflectance from 400–2500 nm at 1 nm resolution as a function of soil water content. MARMIT simulations can be executed via the get.marmit1 and get.marmit2 functions.

ToolsRTM provides links to eight reference soil and vegetation spectral databases (Bablet-2016, Dupiau-2020, Humper-2015, Lesaignoux-2008, Liu-2002, Lobell-2002, Marcq-2012, Philpot-2014), which support validation and parameterisation of the included models.

GitLab repository:
ToolsRTM package
Tutoriales and more

SCOPEinR

SCOPEinR is an R package designed to implement the Soil Canopy Observation, Photochemistry and Energy Fluxes (SCOPE) model, originally developed in MATLAB by Van der Tol et al. (2009) and extended by Yang et al. (2020). SCOPEinR enables users to simulate the interactions between radiation, vegetation canopies, soil, and the atmosphere within a single, coupled radiative transfer and energy balance framework.

The package powers the online RT-Simulator, offering a Shiny interface that allows users to simulate top-of-canopy (TOC) reflectance, canopy temperature, and chlorophyll fluorescence emissions under variable meteorological and structural conditions. This makes SCOPEinR particularly useful for studying vegetation stress, energy partitioning, and photochemical efficiency.

For full intercomparison with other radiative transfer (RT) models, SCOPEinR can be used together with the ToolsRTM package, enabling parallel simulations across different RT formulations (leaf-level, canopy-level, and RTM-based flux retrievals).

SCOPEinR can be used in the Virtual Biophysical Lab to:

• Simulate canopy fluxes, temperature, TOC reflectance, fluorescence (SIF), and energy balance.
• Compare environmental scenarios such as drought, heat stress, stomatal closure, or nutrient limitations.
• Generate synthetic diurnal cycles for benchmarking against flux tower observations (e.g., GPP, LE, Rn).
• Drive forward simulations for evaluating radiative transfer parameterizations and machine learning inversion pipelines.

The SCOPEinR and ToolsRTM packages have been integrated into an online RT-platform (currently in testing) that provides real-time simulations and visualizations through an interactive interface.

GitLab repositories:
SCOPEinR package
Online RT-platform (Shiny RT-Simulator)

Note: These modules are currently in the testing phase before public release.

rtm/

Basic radiative transfer examples using ToolsRTM and SCOPEinR: single-run scripts, parameter sweeps and small lookup table generators.

traits/

Scripts that link biochemical and structural traits to simulated spectra, indices or SIF, including simple stress scenarios.

time-series/

Toy diurnal or seasonal simulations driven by changing radiation, soil moisture or photosynthetic capacity.

notebooks/

R or Python notebooks used for exploration, teaching or quick checks of model behaviour.

figures/

Plots and diagrams generated by the lab that can later be reused in slides or papers.

docs/

Short notes for students, mini-tutorials and descriptions of example scripts or exercises.

Simple exercises

Use short scripts for exercises on LAI and chlorophyll effects, stress vs. control scenarios, or comparison between simulated spectra and satellite bands.

Idea testing

Implement quick tests of new indices, sensitivity analyses or inversion strategies before they are integrated in bigger project repositories or pipelines.

Figures & mini-demos

Generate figures or tiny demos that illustrate model behaviour for presentations, meetings or internal documentation.