MuSE Lab Software
Exploring forests, biodiversity, and open-source innovation at the Leiden Institute of Environmental Sciences
Software developed at the lab
Based at the Institute of Environmental Sciences (Leiden University), we at the MuSE Lab publish and maintain multiple software packages for high-performance computing, automated tracking, and radiative transfer modeling. Collectively, these tools have surpassed 100,000 downloads worldwide, highlighting our commitment to empowering researchers and practitioners to use state-of-the-art code to advance ecological insights.
ccrtm: Coupled Chain Radiative Transfer Models
ccrtm combines multiple radiative transfer models (e.g., PROSPECT, 4SAIL, INFORM) to predict how vegetation reflects and transmits solar energy from the leaf to the canopy scale. It supports both forward simulations (generate spectra from known traits) and backward “inversion” (estimate traits from measured spectra). This enables advanced remote sensing and ecological research on plant optical properties, canopy structure, and atmosphere–vegetation interactions. (CRAN link)
trackdem: Automated Tracking and Population Estimates
trackdem automates the tracking of moving objects—like Daphnia or fish—from videos or image sequences. It offers background detection, particle identification & linking, and a neural network–based noise filter. The result? Unbiased, automated estimates of population densities, size distributions, and individual movement. Perfect for evolutionary and ecological studies requiring precise organism tracking and behavior analysis. (CRAN link)
aprof: Amdahl’s Profiler for R
aprof helps R users identify and optimize code bottlenecks using Amdahl’s Law. It expands on R’s standard profilers by organizing execution and memory profiling data into intuitive plots—showing precisely which lines of code deliver the greatest performance gains if optimized. Ideal for data scientists, researchers, and HPC teams who want to spend development time efficiently. (Official site & release notes)