Local clustering
Local clustering - Published in JOSS (2018)
aesop
aesop: ARC Echelle Spectroscopic Observation Pipeline - Published in JOSS (2018)
sahi
Framework agnostic sliced/tiled inference + interactive ui + error analysis plots
Annotate-Lab
Annotate-Lab: Simplifying Image Annotation - Published in JOSS (2024)
ronswanson
ronswanson: Building Table Models for 3ML - Published in JOSS (2023)
partycls
partycls: A Python package for structural clustering - Published in JOSS (2021)
AstroPaint
AstroPaint: A Python Package for Painting Halo Catalogs into Celestial Maps - Published in JOSS (2020)
ampscan
ampscan: A lightweight Python package for shape analysis of prosthetics and orthotics - Published in JOSS (2020)
geocat-comp
GeoCAT-comp provides implementations of computational functions for operating on geosciences data. Many of these functions originated in NCL and were translated into Python.
LaMa
LaMa: a thematic labelling web application - Published in JOSS (2023)
easyaccess
easyaccess: Enhanced SQL command line interpreter for astronomical surveys - Published in JOSS (2019)
Syd
Syd: A package for making interactive data visualizations in python - Published in JOSS (2025)
PYroMat
PYroMat: A Python package for thermodynamic properties - Published in JOSS (2022)
PsiRESP
PsiRESP: calculating RESP charges with Psi4 - Published in JOSS (2022)
Scyland3D
Scyland3D: Processing 3D landmarks - Published in JOSS (2020)
tightbinder
tightbinder: A Python package for semi-empirical tight-binding models of crystalline and disordered solids - Published in JOSS (2024)
lintsampler
lintsampler: Easy random sampling via linear interpolation - Published in JOSS (2024)
Rainbow
Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow - Published in JOSS (2022)
pfsspy
pfsspy: A Python package for potential field source surface modelling - Published in JOSS (2020)
UnlockNN
UnlockNN: Uncertainty quantification for neural network models of chemical systems - Published in JOSS (2022)
h5preserve
h5preserve: Thin wrapper around h5py, inspired by camel - Published in JOSS (2018)
HostPhot
HostPhot: global and local photometry of galaxies hosting supernovae or other transients - Published in JOSS (2022)
hsi-wizard: A magical open-source Python package for medical hyperspectral imaging applications
hsi-wizard: A magical open-source Python package for medical hyperspectral imaging applications - Published in JOSS (2025)
MiSTree
MiSTree: a Python package for constructing and analysing Minimum Spanning Trees - Published in JOSS (2019)
Leafmap
Leafmap: A Python package for interactive mapping and geospatial analysis with minimal coding in a Jupyter environment - Published in JOSS (2021)
LDDS
LDDS: Python package for computing and visualizing Lagrangian Descriptors for Dynamical Systems - Published in JOSS (2021)
MSMetaEnhancer
MSMetaEnhancer: A Python package for mass spectra metadata annotation - Published in JOSS (2022)
pandas
Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
pyEQUIB Python Package, an addendum to proEQUIB
pyEQUIB Python Package, an addendum to proEQUIB: IDL Library for Plasma Diagnostics and Abundance Analysis - Published in JOSS (2020)
rtdpy
rtdpy: A python package for residence time distributions - Published in JOSS (2019)
pymeasure
Scientific measurement library for instruments, experiments, and live-plotting
PyArmadillo
PyArmadillo: a streamlined linear algebra library for Python - Published in JOSS (2021)
graphenv
graphenv: a Python library for reinforcement learning on graph search spaces - Published in JOSS (2022)
Recan
Recan: Python tool for analysis of recombination events in viral genomes - Published in JOSS (2020)
treemaker
treemaker: A Python tool for constructing a Newick formatted tree from a set of classifications. - Published in JOSS (2018)
seg1d
seg1d: A Python package for Automated segmentation of one-dimensional (1D) data - Published in JOSS (2020)
popkinmocks
popkinmocks: mock IFU datacubes for modelling stellar populations and kinematics - Published in JOSS (2023)
easyvvuq
Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.
STARRED
STARRED: a two-channel deconvolution method with Starlet regularization - Published in JOSS (2023)
Learning Simulator
Learning Simulator: A simulation software for animal and human learning - Published in JOSS (2021)
MetObs - a Python toolkit for using non-traditional meteorological observations
MetObs - a Python toolkit for using non-traditional meteorological observations - Published in JOSS (2024)
dtaidistance
Time series distances: Dynamic Time Warping (fast DTW implementation in C)
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
cosasi
cosasi: Graph Diffusion Source Inference in Python - Published in JOSS (2022)
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.
FEniCS-arclength
FEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanics - Published in JOSS (2024)
napari-clusters-plotter
A napari plugin for clustering objects according to their properties.
pypsa
PyPSA: Python for Power System Analysis
VlaPy
VlaPy: A Python package for Eulerian Vlasov-Poisson-Fokker-Planck Simulations - Published in JOSS (2020)
MyPTV
MyPTV: A Python Package for 3D Particle Tracking - Published in JOSS (2022)
Surjectors
Surjectors: surjection layers for density estimation with normalizing flows - Published in JOSS (2024)
pytransform3d
pytransform3d: 3D Transformations for Python - Published in JOSS (2019)
plotastic
plotastic: Bridging Plotting and Statistics in Python - Published in JOSS (2024)
pykeen
🤖 A Python library for learning and evaluating knowledge graph embeddings
gdess
gdess: A framework for evaluating simulated atmospheric CO₂ in Earth System Models - Published in JOSS (2022)
PyCVI
PyCVI: A Python package for internal Cluster Validity Indices, compatible with time-series data - Published in JOSS (2024)
tissueloc
tissueloc: Whole slide digital pathology image tissue localization - Published in JOSS (2019)
CheSweet
CheSweet: An application to predict glycan’s chemicals shifts - Published in JOSS (2018)
tesliper
tesliper: a theoretical spectroscopist's little helper - Published in JOSS (2022)
DeBEIR
DeBEIR: A Python Package for Dense Bi-Encoder Information Retrieval - Published in JOSS (2023)
BATMAN
BATMAN: Statistical analysis for expensive computer codes made easy - Published in JOSS (2018)
pySRURGS - a python package for symbolic regression by uniform random global search
pySRURGS - a python package for symbolic regression by uniform random global search - Published in JOSS (2019)
Text detection in screen images with a Convolutional Neural Network
Text detection in screen images with a Convolutional Neural Network - Published in JOSS (2017)
pymsis
Python interface to the NRLMSIS codes for calculating atmospheric densities and constituents at satellite altitudes
AstronomicAL
AstronomicAL: an interactive dashboard for visualisation, integration and classification of data with Active Learning - Published in JOSS (2021)
Mantik
Mantik: A Workflow Platform for the Development of Artificial Intelligence on High-Performance Computing Infrastructures - Published in JOSS (2024)
connected-components-3d
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)
lightkurve
A friendly package for Kepler & TESS time series analysis in Python.
bmi-topography
Fetch and cache land elevation data from OpenTopography through an API, BMI, or CLI
SHGYield
SHGYield - Published in JOSS (2017)
qsim
Fast C++ and Python library for state-vector simulation of quantum circuits.
Foam
Foam: A Python package for forward asteroseismic modelling of gravity modes - Published in JOSS (2024)
herbie-data
Download numerical weather prediction datasets (HRRR, RAP, GFS, IFS, etc.) from NOMADS, NODD partners (Amazon, Google, Microsoft), ECMWF open data, and the University of Utah Pando Archive System.
skpro
A unified framework for tabular probabilistic regression, time-to-event prediction, and probability distributions in python
Minimalist And Customisable Optimisation Package
Minimalist And Customisable Optimisation Package - Published in JOSS (2021)
qcelemental
Periodic table, physical constants, and molecule parsing for quantum chemistry.
igneous-pipeline
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
kimimaro
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
