Software

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NEST is a simulator for spiking neural network models that focuses on the dynamics, size and structure of neural systems rather than on the exact morphology of individual neurons. For further information, visit https://www.nest-simulator.org [...]

Tools to calibrate a (scanning) transmission electron microscope from data, with a focus on 4D STEM. Recovers the geometric calibration of a 4D STEM experiment, including scan and detector rotation, handedness, camera length, scan pixel pitch, overfocus and descan error, using a differentiable digital twin of the microscope built on TemGymCore and JAX..

A differentiable ray tracing package for transmission electron microscopy built on JAX. Optical systems are described through the Jacobian (ABCD ray transfer matrices) or Taylor-expansion coefficients of the ray coordinates through the system, enabling, for example, the verification of coordinate systems and descan error in 4D STEM shadow-image experiments..

NESTML 9.0.1 contains several fixes and documentation updates. For further information, please visit https://github.com/nest/nestml/releases/tag/v9.0.1..

The SensorThings API (STA) from the Open Geospatial Consortium has become a quasi-standard for publishing time-series data from sensor systems on the web. Due to its lightweight and generic data model, STA is being adopted across a wide range of domains. [...]

This file contains the code to derive the simulation results supporting the paper: 'Continuum multiscale model of root water and nutrient uptake from soil with explicit consideration of the 3D root architecture and the rhizosphere gradients'. DOI: https://doi.org/10.1007/s11104-018-3890-4

This file contains the code used to produce the simulation results supporting the paper: “From hydraulic root architecture models to efficient macroscopic sink terms including perirhizal resistance: quantifying accuracy and computational speed”. DOI: https://doi.org/10.5194/hess-29-1759-2025

This file contains the code and simulation results supporting the paper:  “3D U-Net Segmentation Improves Root System Reconstruction from 3D MRI Images in Automated and Manual Virtual Reality Work Flows”. DOI: https://doi.org/10.34133/plantphenomics.0076

This is a collection of Python plot script used to generate the plots in the paper manuscript 'Advancing data assimilation with the renewed Parallel Data Assimilation Framework (PDAF V3.1)' by L. Nerger, Y. [...]