scikit-image: Image processing in Python

Abstract

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal "Modified BSD" open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image.

Distributed under Creative Commons CC-BY 4.0. Published in PeerJ

References in corpus (3)

• Scikit-learn: Machine Learning in Python
• The NumPy array: a structure for efficient numerical computation
• Mahotas: Open source software for scriptable computer vision

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• High-contrast spectroscopy with the new VLT/ERIS instrument: Molecular maps and radial velocity of the gas giant AF Lep b
• Toyz: A Framework for Scientific Analysis of Large Datasets and Astronomical Images
• Shape As Points: A Differentiable Poisson Solver
• Portable learning environments for hands-on computational instruction: Using container- and cloud-based technology to teach data science
• Mesoscale microscopy for micromammals: image analysis tools for understanding the rodent brain
• Determination of optimal experimental conditions for accurate 3D reconstruction of the magnetization vector via XMCD-PEEM
• Reflected Light Observations of the Galilean Satellites from Cassini: a testbed for cold terrestrial exoplanets
• Mapping the multiphase structure of H I in the Low-Latitude Intermediate-Velocity Arch 1
• Spatial Variations and Breaks in the Optical-NIR spectra of the Pulsar and PWN in SNR 0540-69.3
• Average solar active region: I. Intensities, velocities, and the photospheric magnetic field
• Robust Multiple-Path Orienteering Problem: Securing Against Adversarial Attacks
• Parallel mode differential phase contrast in transmission electron microscopy, II: K${}_2$CuF${}_4$ phase transition
• Circumplanetary Disk Candidate in the Disk of HD 163296 Traced by Localized Emission from Simple Organics
• Meshless Monte Carlo Radiation Transfer Method for Curved Geometries using Signed Distance Functions
• Deep learning approach for identification of HII regions during reionization in 21-cm observations -- III. image recovery
• Modeling Strong Lenses from Wide-Field Ground-Based Observations in KiDS and GAMA
• Optical dispersions through intracellular inhomogeneities
• Self-calibration technique for characterization of integrated THz waveguides
• Cosmic Ray Rejection with Attention Augmented Deep Learning
• Fully Adaptive Bayesian Algorithm for Data Analysis, FABADA
• A forward-modelling method to infer the dark matter particle mass from strong gravitational lenses
• WISDOM project -- XVIII. Molecular gas distributions and kinematics of three megamaser galaxies
• OAH-Net: A Deep Neural Network for Hologram Reconstruction of Off-axis Digital Holographic Microscope
• DriveGuard: Robustification of Automated Driving Systems with Deep Spatio-Temporal Convolutional Autoencoder
• Interpreting Angle Dependent Magnetoresistance in Layered Materials: Application to Cuprates
• Calibrated simplex-mapping classification
• Speeding up Python-based Lagrangian Fluid-Flow Particle Simulations via Dynamic Collection Data Structures
• Fast TILs -- A Pipeline for Efficient TILs Estimation in Non-Small Cell Lung Cancer
• AMEP: The Active Matter Evaluation Package for Python
• Predicting trajectory behaviour via machine-learned invariant manifolds
• Rotation-Invariant Rapid TRISO-Fueled Pebble Identification Based on Feature Matching and Point Cloud Registration
• Non-utopian optical properties computed of a tomographically reconstructed real photonic nanostructure
• A Morphological Study on AGN-host Dwarf Galaxies
• Noise2Void for Denoising Atomic Resolution Scanning Transmission Electron Microscopy Images
• Angle-resolved photoelectron spectroscopy in a low energy electron microscope
• Mask-RCNN and U-net Ensembled for Nuclei Segmentation
• An Imaging Search for Post-Main-Sequence Planets of Sirius B
• An evaluation of the LLC4320 global ocean simulation based on the submesoscale structure of modeled sea surface temperature fields
• VISIONS: The VISTA Star Formation Atlas -- II. The data processing pipeline
• The STATiX pipeline for the detection of X-ray transients in three dimensions
• Exoplanet Analog Observations of Earth from Galileo Disk-integrated Photometry
• Deep Learning Based Event Reconstruction for Cyclotron Radiation Emission Spectroscopy
• Formation of Substructure in Luminous Submillimeter Galaxies (FOSSILS): Evidence of Multiple Pathways to Trigger Starbursts in Luminous Submillimeter Galaxies
• Calibrating a Finite-strain Phase-field Model of Fracture for Bonded Granular Materials with Uncertainty Quantification
• Flux-trapping characterization for superconducting electronics using a cryogenic widefield N-$V$ diamond microscope
• Inverse-Designed Metasurfaces for Wavefront Restoration in Under-Display Camera Systems
• Andromeda XXXV: The Faintest Dwarf Satellite of the Andromeda Galaxy
• Magnetic Field-Constrained Ensemble Image Segmentation of Coronal Holes in Chromospheric Observations
• Financial Table Extraction in Image Documents
• Deterministic preparation of a dual-species two-ion crystal
• Differencing and Coadding JWST Images with Matched Point Spread Function
• Stellar clustering and the kinematics of stars around Collinder 121 using Gaia DR3
• PhagoStat a scalable and interpretable end to end framework for efficient quantification of cell phagocytosis in neurodegenerative disease studies
• The Sun at millimeter wavelengths IV. Magnetohydrodynamic waves in small-scale bright features
• Molecules with ALMA at Planet-forming Scales (MAPS) XIX. Spiral Arms, a Tail, and Diffuse Structures Traced by CO around the GM Aur Disk
• Compressed Sensing for STM imaging of defects and disorder
• Persistent fluid flows defined by active matter boundaries
• Simulation of live-cell imaging system reveals hidden uncertainties in cooperative binding measurements
• Sensitivity analysis on imaging the calcaneus using microwaves
• Implicit LOD using points ordering for processing and visualisation in Point Cloud Servers
• Keck Near-Infrared Detections of Mab and Perdita
• Investigations of MWISP Filaments. I. Filament Identification and Analysis Algorithms, and Source Catalogue
• Dynamic Atomic Column Detection in Transmission Electron Microscopy Videos via Ridge Estimation
• Statistical Image Reconstruction for High-Throughput Thermal Neutron Computed Tomography
• Amoeba: An AGN Model of Optical Emissions Beyond steady-state Accretion discs
• Scaling Up Collaborative Filtering Data Sets through Randomized Fractal Expansions
• Model-Based Iterative Reconstruction of Three-Dimensional Magnetisation in a Nanowire Structure Using Electron Holographic Vector Field Tomography
• Restoring Spatially-Heterogeneous Distortions using Mixture of Experts Network
• Acoustofluidic phase microscopy in a tilted segmentation-free configuration
• On (Emergent) Systematic Generalisation and Compositionality in Visual Referential Games with Straight-Through Gumbel-Softmax Estimator
• Fast, accurate, and predictive method for atom detection in site-resolved images of microtrap arrays
• Cosmic rays, gas and dust in the Central Molecular Zone I -- $X_{CO}$ factors, cosmic-ray densities and dust opacities
• Utilizing 3D Fast Spin Echo Anatomical Imaging to Reduce the Number of Contrast Preparations in $T_{1\rho }$ Quantification of Knee Cartilage Using Learning-Based Methods
• Immersed Cantilever Apparatus for Mechanics and Microscopy
• Transport-Related Surface Detection with Machine Learning: Analyzing Temporal Trends in Madrid and Vienna
• Developing a Bubble Chamber Particle Discriminator Using Semi-Supervised Learning
• Taking control of compressible modes: bulk viscosity and the turbulent dynamo
• Understanding Training-Data Leakage from Gradients in Neural Networks for Image Classification
• Towards Online Steering of Flame Spray Pyrolysis Nanoparticle Synthesis
• Label merge-and-split: A graph-colouring approach for memory-efficient brain parcellation
• MeanShift++: Extremely Fast Mode-Seeking With Applications to Segmentation and Object Tracking
• Radiative Cooling Effects on Plasmoid Formation in Black Hole Accretion Flows with Multiple Magnetic Loops
• All-optical photoacoustic tomography via beam deflection
• OmniPrint: A Configurable Printed Character Synthesizer
• Clumpiness of galaxies revealed in the near-infrared with COSMOS-Web
• Towards Tumour Graph Learning for Survival Prediction in Head & Neck Cancer Patients
• Design and Commissioning of an LWA Swarm Station: The Long Wavelength Array -- North Arm
• The superclouds of the local Milky Way
• End-to-end Surface Optimization for Light Control
• A WISPR of the Venus Surface: Analysis of the Venus Nightside Thermal Emission at Optical Wavelengths
• Optimizations of Autoencoders for Analysis and Classification of Microscopic In Situ Hybridization Images
• Lenses In VoicE (LIVE): Searching for strong gravitational lenses in the VOICE@VST survey using Convolutional Neural Networks
• NucMM Dataset: 3D Neuronal Nuclei Instance Segmentation at Sub-Cubic Millimeter Scale
• Semi-supervised Cardiac Image Segmentation via Label Propagation and Style Transfer
• Probing inner and outer disk misalignments in transition disks
• Quantifying yeast colony morphologies with feature engineering from time-lapse photography
• Correlating Visual Characteristics and Cryogenic Performance of Superconducting Detectors
• Fantômas: Understanding Face Anonymization Reversibility
• Simulating volume-controlled invasion of a non-wetting fluid in volumetric images using basic image processing tools
• On the use of a consumer-grade 360-degree camera as a radiometer for scientific applications
• VoDEx: a Python library for time annotation and management of volumetric functional imaging data
• ComPACT: ACT+Planck galaxy cluster catalogue
• Minimal Sufficient Views: A DNN model making predictions with more evidence has higher accuracy
• Instance Segmentation XXL-CT Challenge of a Historic Airplane
• Multibranch Generative Models for Multichannel Imaging with an Application to PET/CT Synergistic Reconstruction
• Compact [OIII] emission-line regions ("Green Seeds") in $\mathrm{H}\alpha$ emitters at Cosmic Noon from JWST Observations
• Modeling of optical scattering from topographic surface measurements of high-quality mirrors
• SPACE-SUIT: An Artificial Intelligence Based Chromospheric Feature Extractor and Classifier for SUIT
• On volume density and star formation in nearby molecular clouds
• A Lightweight and Extensible Cell Segmentation and Classification Model for Whole Slide Images
• Superpixel Segmentation via Convolutional Neural Networks with Regularized Information Maximization
• Fast Sphericity and Roundness approximation in 2D and 3D using Local Thickness
• Inferring activity from the flow field around active colloidal particles using deep learning
• SurveilEdge: Real-time Video Query based on Collaborative Cloud-Edge Deep Learning
• Mapping neutral islands during end stages of reionization with photometric intergalactic medium tomography
• Robust and compact single-lens crossed-beam optical dipole trap for Bose-Einstein condensation in microgravity
• Experimental demonstration of a tomographic 5D phase-space reconstruction
• Coarse-to-fine Kidney Segmentation Framework Incorporating with Abnormal Detection and Correction
• evoxels: A differentiable physics framework for voxel-based microstructure simulations
• Early Stages of Dusty Tori: The First Infrared Spectra from a Highly Multiscale Quasar Simulation
• Quantitative Stain Mapping in X-ray Virtual Histology
• PorousGen: An Efficient Algorithm for Generating Porous Structures with Accurate Porosity and Uniform Density Distribution
• RIGEL: Feedback-regulated cloud-scale star formation efficiency in a simulated dwarf galaxy merger
• Constraints on gravitational waves from the 2024 Vela pulsar glitch
• JWST imaging of the Pleiades: anisotropy of turbulence in the cold neutral medium
• Evaluating Graphical Perception Capabilities of Vision Transformers
• Points as Tori: Fast Pointwise Signed Distance for Point Clouds
• exoALMA XX: Tomographic Detection of Embedded Planets in Protoplanetary Disks
• Incrementally Building Topology Graphs via Distance Maps
• Fusion of JWST data: Demonstrating practical feasibility
• Maritime Activities Observed Through Open-Access Positioning Data: Moving and Stationary Vessels in the Baltic Sea
• Meta-learners for few-shot weakly-supervised optic disc and cup segmentation on fundus images
• High-Resolution Mapping of Port Dynamics from Open-Access AIS Data in Tokyo Bay
• Sex-based Bias Inherent in the Dice Similarity Coefficient: A Model Independent Analysis for Multiple Anatomical Structures
• Diffusion-Shock Filtering on the Space of Positions and Orientations
• ALEXIS: Recreating the X-Ray Emission from the Full Solar Disk as a Linear Combination of Discrete Regions in the Extreme Ultraviolet and Soft X-Rays
• Uncertainty Quantification for Linear Inverse Problems with Besov Prior: A Randomize-Then-Optimize Method
• The SARAO MeerKAT Galactic Plane Survey filamentary source catalogue
• Towards the second H.E.S.S. Galactic plane catalogue
• Counting Molecules: Python based scheme for automated enumeration and categorization of molecules in scanning tunneling microscopy images
• k-Means Aperture Optimization Applied to Kepler K2 Time Series Photometry of Titan
• A New Semi-Automated Algorithm for Volumetric Segmentation of the Left Ventricle in Temporal 3D Echocardiography Sequences
• DeepTEGINN: Deep Learning Based Tools to Extract Graphs from Images of Neural Networks
• Parallel-beam X-ray CT datasets of apples with internal defects and label balancing for machine learning
• Histogram Matching Augmentation for Domain Adaptation with Application to Multi-Centre, Multi-Vendor and Multi-Disease Cardiac Image Segmentation
• AI-driven Bayesian inference of statistical microstructure descriptors from finite-frequency waves
• Upscaling the porosity-permeability relationship of a microporous carbonate to the Darcy scale with machine learning
• Equivariant neural networks for inverse problems
• Improving reproducibility in synchrotron tomography using implementation-adapted filters
• Automatic detection of impact craters on Al foils from the Stardust interstellar dust collector using convolutional neural networks
• Direct Visualisation of Out-of-Equilibrium Structural Transformations in Atomically-Thin Chalcogenides
• Similarity-Based Assessment of Computational Reproducibility in Jupyter Notebooks
• Ram-pressure stripping caught in action in a young cluster at $z=2.51$
• CRISP: A Framework for Cryo-EM Image Segmentation and Processing with Conditional Random Field
• WAYLA - Generating Images from Eye Movements
• Modeling Heavy-Gas Dispersion in Air with Two-Layer Shallow Water Equations
• Learning Mechanically Driven Emergent Behavior with Message Passing Neural Networks
• Deep Learning generated observations of galaxy clusters from dark-matter-only simulations
• Localized Perturbations For Weakly-Supervised Segmentation of Glioma Brain Tumours
• CLOWN: The PASO cloud detection for optimization of automatic optical surveys
• Contour Analysis Tool: an interactive tool for background and morphology analysis
• Segmentation and Smoothing Affect Explanation Quality More Than the Choice of Perturbation-based XAI Method for Image Explanations
• Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes
• Decoding the human brain tissue response to radiofrequency excitation using a biophysical-model-free deep MRI on a chip framework
• Fragmentation and aggregation of cyanobacterial colonies
• Image warp preserving content intensity
• Estimating Free Parameters in Stochastic Oscillatory Models Using a Weighted Cost Function
• MicroBundlePillarTrack: A Python package for automated segmentation, tracking, and analysis of pillar deflection in cardiac microbundles
• A new Surrogate Microstructure Generator for Porous Materials with Applications to the Buffer Layer of TRISO Nuclear Fuel Particles
• How to design cell-mediated self-assembled colloidal scaffolds
• LC-SLab -- An object-based deep learning framework for large-scale land cover classification from satellite imagery and sparse in-situ labels
• Fidelity-preserving enhancement of ptychography with foundational text-to-image models
• An Information-Theoretic Approach to Persistent Environment Monitoring Through Low Rank Model Based Planning and Prediction
• Identification of Coronal Holes on AIA/SDO images using unsupervised Machine Learning
• Brought to Light III: Colors of Disk and Clump Substructures in Dwarf Early-Type Galaxies of the Fornax Cluster
• Score-based diffusion models for accurate crystal-structure inpainting and reconstruction of hydrogen positions
• A joint voxel flow-phase field framework for ultra-long microstructure evolution prediction with physical regularization
• Assessment of normalizing flows for parameter estimation on time-frequency representations of gravitational-wave data
• AnomalyMatch: Discovering Rare Objects of Interest with Semi-supervised and Active Learning
• TESS Data for Asteroseismology: Photometry
• Morphological variations of solar granules in the presence of magnetic fields
• Clustered Star Formation in the center of NGC 253 Contributes to Driving the Ionized Nuclear Wind
• Methods of interpreting error estimates for grayscale image reconstructions
• Searching for and characterizing halo substructures with the GALAH DR4 survey
• Investigating the Relationship Between Physical Properties and Spatial Irregularities at Coronal Hole Boundaries
• DEM Super-Resolution with EfficientNetV2
• Investigations of MWISP Bubbles: Identification and Analysis of Enclosed Molecular Bubbles by Weight Fields
• Computational Microstructure Analysis of Sintered Ceramics
• Semi-Supervised Learning for Lensed Quasar Detection
• Spatially resolved spectral properties of M87* on event horizon scales
• Parallel mode differential phase contrast in transmission electron microscopy, I: Theory and analysis
• TopoTEM: A Python Package for Quantifying and Visualising Scanning Transmission Electron Microscopy Data of Polar Topologies
• A 5kHz modulator for pyramid wavefront sensors
• Interpretable liquid crystal phase classification via two-by-two ordinal patterns
• The Application of Ridgelines in Extended Radio Source Cross-Identification
• Method for tilt correction of calibration lines in high resolution spectra
• Reducing Textural Bias Improves Robustness of Deep Segmentation Models
• Bayesian learning of adatom interactions from atomically-resolved imaging data