Synaptus
Synaptus: A Matlab/Octave toolbox for synthetic aperture ultrasound imaging - Published in JOSS (2022)
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images - Published in JOSS (2022)
MSMExplorer
MSMExplorer: Data Visualizations for Biomolecular Dynamics - Published in JOSS (2017)
AliasFinder
AliasFinder: A Python script to search for the true planetary frequency within radial velocity data - Published in JOSS (2020)
TSE
TSE: A triple stellar evolution code - Published in JOSS (2024)
Bayesian model reconstruction based on spectral line observations with pomme
Bayesian model reconstruction based on spectral line observations with pomme - Published in JOSS (2024)
Excimontec v1.0
Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices - Published in JOSS (2020)
geocat-viz
GeoCAT-viz contains tools to help plot geoscience data, including convenience and plotting functions that are used to facilitate plotting geosciences data with Matplotlib, Cartopy, and other visualization packages.
GENRE (GPU Elastic-Net REgression)
GENRE (GPU Elastic-Net REgression): A CUDA-Accelerated Package for Massively Parallel Linear Regression with Elastic-Net Regularization - Published in JOSS (2020)
ShUShER
ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees - Published in JOSS (2021)
pollucheck v1.0
pollucheck v1.0: A package to explore open-source air pollution data - Published in JOSS (2021)
FEniCS-arclength
FEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanics - Published in JOSS (2024)
SeqIKPy: a Python package for inverse kinematics in insects
SeqIKPy: a Python package for inverse kinematics in insects - Published in JOSS (2026)
Taxonomy Resolver
Taxonomy Resolver: A Python package for building and filtering taxonomy trees - Published in JOSS (2025)
napari-clusters-plotter
A napari plugin for clustering objects according to their properties.
UPOsHam
UPOsHam: A Python package for computing unstable periodic orbits in two-degree-of-freedom Hamiltonian systems - Published in JOSS (2020)
papaya2
papaya2: 2D Irreducible Minkowski Tensor computation - Published in JOSS (2020)
MSG
MSG: A software package for interpolating stellar spectra in pre-calculated grids - Published in JOSS (2023)
TransiFlow: A Python package for performing bifurcation analysis on fluid flow problems
TransiFlow: A Python package for performing bifurcation analysis on fluid flow problems - Published in JOSS (2026)
Virtual Engineering: Python framework for engineering process design
Virtual Engineering: Python framework for engineering process design - Published in JOSS (2025)