Reproducible Research in Computational Science
http://www.csee.wvu.edu/~xinl/source.html
“It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong” - Richard Feynman
"As a method for finding things out, science lives by its disdain for authority and its reliance on experimentation." - Chris Quigg
Welcome to this site about reproducible research in computational science (including signal processing, computer vision, machine learning and neural computation). This site is intended to share the source codes of the latest advances in various technical fields to the best of my knowledge. Only throughReproducible Research (RR), can we live up to the standard that hard-core science has established since Bacon and Newton. If you know of any release of the source codes that is missing from the list or any broken link, please kindly let me know.
Image denoising
Image coding
- JPEG-LS standardLOCO-I
- Context-Based, Adaptive, Lossless Image Coding CALIC
- Edge directed prediction for lossless image compression EDP
- TMW lossless image compression Download Code (lost in cyberspace)
- Minimum rate prediction with DP-based optimization Code
- Embedded Predictive Wavelet Image Coder Code
- SPIHT image codec SPIHTMATLAB codes (third-party implementation)
- Estimation Quantization lossy image codec EQ
- Least-Square Estionation Quantization Codec LS-EQ
- EBCOT codec for JPEG2000 EBCOT
- Multiple description coding with prediction compensationcode
- Multiple description image coding based on lagrangian rate allocation code
Image demosaicing
- Primary-consistent soft-decision (PCSD)-based schemeexecutable
- Alternate projection (AP)-based scheme AP
- Adaptive Homogeneity-Directed (AHD) demosaicing AHD
- DLMMSE demosaicing DLMMSE
- Demosaicing by successive approximation SA
- Demosaicing by directional filtering and a posteriori decision dfapd
- LPA-ICI demosaicing LPA-ICI
- A Model of Retinal Local Adaptation for the Tone Mapping of Color Filter Array Images
- Leaning simultaneous sparsity coding (LSSC) code (only runs on 64-bit Linux machine with MATLAB)
- PCA-based Spatially Adaptive Denoising of CFA Images for Single-Sensor Digital Cameras code
- Self-similarity driven image dmosaicing
- Color Demosaicking by Local Directional Interpolation and Non-local Adaptive Thresholding code
- Residual Interpolation for color image demosaicking
Image interpolation and Superresolution
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Super-resolution code
- Linear interpolation revitalized
- New edge directed interpolation (NEDI) code
- Signal Discrete Sinc-interpolation in DCT Domain code
- Directional filtering and data fusion DFDF
- Wavelet-based texture image interpolation wt_interp
- Fast and robust superresolution (SR) toolbox UCSC-SR
- Superresolution for synthetic zooming syn_zoom
- EPFL's frequency-domain approach EPFL
- Support vector machine based image superresolution result
- Image interpolation using multiscale geometric representations Code
- Kriging-based Best Linear Unbiased Estimator Code
- Image interpolation by adaptive 2D autoregressive modeling and soft-decision estimation Executable
- Super-resolution GUI developed by Bahadir at LSU
- Multi-frame image super-resolution
- Super-resolution via sparse coding code
- Super-resolution through neighbor embedding code
- Super-resolution with sparse mixing estimators
- Machine learning in multi-frame SR
- Example-based learning for super-resolution
- Super Resolution using Edge Prior and Single Image Detail Synthesis code
- Binary halftone image resolution increasing by decision tree learning
- Superresolution from a single image code (third-party implementation)
- Simultaneous motion deblurring and super-resolution
- Exploiting Self-Similarities for Single Frame Super-Resolution code
- Fast image/video upsampling (binary executables only)
- Image deblurring and supper-resolution by adaptive sparse domain selection and adaptive regularization code
- Image and video upsampling from local self-examples code(third-party implementation)
- Semi-Coupled Dictionary Learning with Applications to Image Super-resolution and Photo-Sketch Synthesis
- Sparse Representation based Image Interpolation with Nonlocal Autoregressive Modeling
- Structured Face Hallucination code
- Anchored Neighborhood Regression for Fast Example-Based Super-Resolution code
RGBD image processing
- Indoor Segmentation and Support Inference from RGBD Images
- Unsupervised Feature Learning for RGB-D Based Object Recognition
- Image Guided Depth Map Upsampling
Image segmentation/parsing and matting
- Image segmentation by normalized cut Ncut
- Epitome-based image segmentation epitome
- Bayesian multiscale image segmentation SMAP
- Graph-cut Based Image Segmentation segment Code2
- EDISON System EDISON Code2
- A closed form solution to image matting matting
- Level set evolution without reinitialization Code
- Implicit active contour driven by local binary fitting energy Code
- Snakes, Shapes, and Gradient Vector Flow Code
- Unsupervised learning of finite mixture model Code
- DDMCMC Image Segmentation
- Image Segmentation by Generalized SW-cuts
- A generalized model for scratch detection
- Power Watersheds (iccv'2009) code
- Global contrast based salient region detection
- Generalizing Swendsen-Wang to sampling arbitrary posterior probabilities code
- Interactive segmentation toolbox (GrabCut+LazySnap)
- Geodesic Star Convexity for Interactive Image Segmentation
- Distributed Cosegmentation via Submodular Optimization on Anisotropic Diffusion code
- Segmenting Scenes by Matching Image Composites
- Automatic Image Segmentation by Dynamic Region Mergingcode
- Interactive Images: Cuboid Proxies for Smart Image Manipulation
- Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials
Image deblurring
Blind image deblurring
Texture synthesis
- Reaction-diffusion textures code
- Texture synthesis via a noncausal nonparametric multiscale Markov random field code
- Pyramid Based Texture Analysis/Synthesis code
- Wavelet-domain parametric model code
- Texture synthesis by nonparametric sampling code (third-party implementation)
- Image quilting code code2
- Synthesizing Natural Textures code
- Texture Optimization for Example-based Synthesis code(third-party implementation)
- Parallel controllable texture synthesis code
- Graphcut Textures: Image and Video Synthesis Using Graph Cuts code (third-party implementation)
- Random Phase Textures: Theory and Synthesis code
- Higher Order SVD Analysis for Dynamic Texture Synthesis
- Symmetry-Guided Texture Synthesis and Manipulation
Image inpainting
PDE-based image processing
- Perona-Malik nonlinear diffusion code code2
- Total variation based image denoising code code2
- Curvature-Driven Diffusion based image inpainting code
- Shock filter for image enhancement code
- Weickert's anisotropic diffusion code
- Mean curvature diffusion (MCD) code
- A variational method for image recovery code
- Speckle reducing anisotropic diffusion code
- Parametric Maximum Flow Algorithmsfor Fast Total Variation Minimization code
- An Algorithm for Nonlocal TV Minimization
Image quality assessment
- Universal image quality index code
- Structural SIMilarity (SSIM) index code
- Degradation model code
- FSIM: A Feature Similarity Index for Image Quality Assessment code
- A No-Reference Objective Image Sharpness Metric Based on the Notion of Just Noticeable Blur code
- An Improved No-Reference Sharpness Metric Based on the Probability of Blur Detection code
Biometrics
HDR imaging
Gradient-domain image processing
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Distributed Gradient-Domain Processing of Planar and Spherical Images
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GradientShop:A Gradient-Domain Optimization Framework for Image and Video Filtering
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Local Laplacian Filters: Edge-aware Image Processing with a Laplacian Pyramid
- Domain Transform for Edge-Aware Image and Video Processing
- Image Smoothing via L 0 Gradient Minimization
Video coding
- MPEG-1/2 reference software
- H.263/H.263+ reference software
- MPEG4 reference software (MoMuSys version)
- H.264/AVC reference software
- 3D SPIHT video coding code
- DISCOVER video codec for DVC
- HEVC (H.265) Refence model in development
Texture/Shape classification
- Wavelet-based GDD and KL-distance code
- Local binary pattern (LBP) based
- Filter bank based at Visual Geometry Group
- A Completed Modeling of Local Binary Pattern Operator for Texture Classification code
- Shape Classification Using the Inner-Distance code
- Deformed Lattice Detector code
- Fast Directional Chamfer Matchingcode
Object detection/recognition
Image registration/mosaicing/OFE
- Affine SIFT (ASIFT) with online demo
- SIFT Flow: Dense Correspondence across scenes
- Lukas-Kanade algorithm code code2
- SIFT feature correspondence code code2 code3
- Local binary pattern (LBP) code
- Speed up robust features (SURF)
- Compact And Real-time Descriptors (CARD)
- Maximally stable extremal regions (MSER) code
- Graph-cut based optical flow estimation code
- Pyramid-based hierarchical motion estimation Code
- Affine Motion Estimation for Medical Image Registration Code
- A frequency-domain approach toward image registration Code
- Blended Intrinsic Maps
- An Efficient Earth Mover's Distance Algorithm for Robust Histogram Comparison code
- Diffusion Distance for Histogram Comparison code
- Coherency Sensitive Hashing
- Fast Template Matching in Non-Linear Tone-Mapped Imagescode
- BRIEF: Binary Robust Independent Elementary Features
- Autostitch developed for Apple iPhone
- Ztitch developed for Windows Phone
- Image Matching using Local Symmetry Features
- Secrets of optical flow estimation and their principles(Matlab code)
- Segmentation Based Variational Model for Accurate Optical Flow Estimation (Code)
- Total variation regularization of local-global optical flow
- Motion Detail Preserving Optical Flow Estimation
- Large displacement optical flow: descriptor matching in variational motion estimation code
- FAsT-Match: Fast Affine Template Matching
Action/event/scene recognition
- Human Activity Detection from RGBD Images
- Action MACH: a spatio-temporal maximum average correlation height filter for action recognition
- Evaluation of local spatio-temporal features for action recognition
- 2D Action Recognition Serves 3D Human Pose Estimation
- Hierarchical Mean Shift, Space-Time Segmentation and Action Recognition
- Human Activity Recognition with Metric Learning
- A Hough Transform-Based Voting Framework for Action Recognition
- Learning hierarchical spatio-temporal features for action recognition with independent subspace analysis
- Recognizing Scene Viewpoint using Panoramic Place Representation
- Multimodal Decomposable Models for Human Pose Estimation
Visual tracking
2D Phase Unwrapping
- Graph cut based 2D Phase unwrapping code
- Unwrapping MR phase images by a Markov random field model code
- Satellite radar interferometry - Two - dimensional phase unwrapping code
- Phase unwrapping algorithms for radar interferometry:residue-cut, least-squares, and synthesis algorithms code
Saliency/Objectness Detection
- Learning to Detect A Salient Object code (third-party implementation)
- Dynamic visual attention: searching for coding length increments code
- What is an object?
- Saliency Detection: A Spectral Residual Approach
- Image Classification: An Integration of Randomization and Discrimination
in A Dense Feature Representation - Saliency filters: contrast based filtering for salient region detection code
- Global Contrast based Salient Region Detection
- Frequency-tuned salient region detection
- Saliency, attention, and visual search: An information theoretic approach
- Saliency detection using maximum symmetric surround
- Segmenting salient objects from images and videos
- Static and space-time visual saliency detection by self-resemblance
- SUN: A bayesian framework for saliency using natural statistics
- Saliency estimation using a non-parametric low-level vision model
- model of saliency-based visual attention for rapid scene analysis
- Graph-based visual saliency
- Context-aware saliency detection
- Salient region detection and segmentation
- Automatic salient object segmentation based on context and shape prior
- Saliency Detection via Graph-based Manifold Ranking
- Kernel Null Space Methods for Novelty Detection
Low rank methods
Deep Learning
- DeepLearnToolbox
- Deep Belief Networks
- Convolutional deep belief network
- Learning Deep Boltzmann Machines
- Conditional RBMs/DBNs
- Niocognitron
- Convolutional/Deconvolutional networks
- Invariant scattering convolution network
- Marginalized Stacked Denoising Autoencoders
Manifold learning and embedding
- A Global Geometric Framework for Nonlinear Dimensionality Reduction code
- Nonlinear Dimensionality Reduction by Locally Linear Embedding code
- Laplacian Eigenmaps code
- Diffusion maps code
- Manifold learning toolbox&demo
- Learning distance metric
- Diffusion processes for retrieval
Wavelets and frames
- Emergence of simple-cell receptive field properties by learning a sparse code for natural images code
- A Wavelet Tour of Signal Processing Wavelab
- Steerable PyramidmatlabPyrtools.tar.gz
- Rice Wavelet Toolbox rwt.zip
- Contourlet and Ridgelet Toolbox download
- Beamlet and Curvelet Toolbox Beamlab
- Complex wavelet Toolbox download
- Wavelet/bandelet Toolbox at Matlab Central
- MCALab
- Differentiation of discrete multidimensional signals code
- The finite ridgelet transform for image representation code
- Framing pyramids code
- Contourlet transform: an efficient directional multiresolution image representation code
- Directional multiscale modeling of images using the contourlet transform code
- The nonsubsampled contourlet transform: Theory, design, and applications code
- Multidimensional directional filter banks and surfacelets code
Compressed Sensing
- l1-Magic
- SparseLab
- GPSR
- ell-1 LS: Simple Matlab Solver for ell-1-Regularized Least Squares Problems
- sparsify
- MPTK: Matching Pursuit Toolkit
- Bayesian Compressive Sensing
- SPGL1: A solver for large scale sparse reconstruction
- sparseMRI
- FPC
- CVX
- Chaining Pursuit
- Regularized OMP
- SPARCO: A toolbox for testing sparse reconstruction algorithms
- TwIST
- Compressed Sensing Codes
- Fast CS using SRM
- FPC_AS
- Fast Bayesian Matching Pursuit (FBMP)
- SL0
- Sparse recovery using sparse matrices
- PPPA
- Compressive sensing via belief propagation
- SpaRSA
- KF-CS: Kalman Filtered CS (and other sequential CS algorithms)
- Fast Bayesian CS with Laplace Priors
- YALL1
- TVAL3
- RecPF
- Basis Pursuit DeQuantization (BPDQ)
- k-t FOCUSS
- Sub-Nyquist sampling: The Modulated Wideband Converter
- Threshold-ISD
- A Sparse Learning Package
- Model-based Compressive Sensing Toolbox
- Sparse Modeling Software
- Spectral Compressive Sensing Toolbox
- CS-CHEST: A MATLAB Toolbox for Compressive Channel Estimation
- DictLearn: A MATLAB Implementation for Dictionary Learning
- SPAMS
- Peformance benchmark of l1-optimization algorithms
- BM3D-based compressed sensing
- Compressed sensing using belief propagation
- Model-based Compressed Sensing
- Bayesian Compressive Sensing
- Latent Variable Graphical Model Selection via Convex Optimization code
Biomedical Imaging
- SparseMRI Toolbox
- Image reconstruction toolbox
- medical image registration
- Level set based medical image segmentation
- Gradient vector flow
- Compressed sensing image reconstruction via recursive spatially adaptive filtering
- multiresolution celluar image classification
- multirate fluorescence microscopy image acquisition
- Nonlocal MRI Upsampling
- Joint image reconstruction and sensitivity estimation in SENSE (JSENSE) code
- Nonlinear GRAPPA: a kernel approach to parallel MRI reconstruction code
DTI and fiber tractography
- DSI Studio
- FMRIB
- dtiQuery
- Camino
- NAMIC
Data Clustering
- Unsupervised learning of finite mixture models code
- Affinity propagation
- On Spectral Clustering: Analysis and an algorithm codecode2 code3
- Nonnegative matrix factorization (NMF) code2 code3
- Computing nonnegative tensor factorizations
- Fast kmeans via triangle inequality
- FastANN and FastCluster for approximate kmeans
- kdtree-based NN/kNN search fast kNN search code2
- RANSAC toolbox for robust fitting
- Clustering Through Ranking On Manifolds code
- Correlation clustering optimization
- Hybrid Linear Modeling via Local Best Flats code
Stereo matching& Multiview geometry
- A taxonomy and evaluation of dense two-frame stereo correspondence algorithms code
- Graph cut based stereo matching code
- Belief propagation based stereo matching code
- A roadmap to the integration of early visual modules Code
- Adaptive support-weight approach Code
- Energy minization based stereo matching
- Energy Based Multiple Model Fitting for Non-Rigid Structure from Motion code
- Recognizing Scene Viewpoint using Panoramic Place Representation
- A Closed-Form Solution to Uncalibrated Photometric Stereo via Diffuse Maxima
- Patch-based Multi-view Stereo (PMVS)
- Library for Efficient Large-scale Stereo Matching
Graphics, Cartoons,Motion&3D
Machine learning&Neural Networks
- Resource collection at UC-Merced
- Belief propagation/Sum-Product Algorithm code
- Deep Boltzmann Machines
- Shape Boltzmann machine: a strong model of object shapes
- Support vector machine
- Liblinear for large linear classification
- Object detection with Boosting
- Convolutional/Deconvolutional networks
- Hopfield networks code
- Self-organizing map (SOM) Toolbox
- Reservoir Computing Toolbox
- Polychronization: Computation With Spikes
- Slowly coupled oscillators: phase dynamics and sync
- Liquid State Machines(LSM) code
- Sparse Coding Neural Gas code
- Echo state networks for harnessing nonlinearity code
- Fast Approximate Nearest Neighbors with Automatic Algorithm Configuration
- Sum-Product Networks: A New Deep Architecture code
- Deformable graph matching code
Blind source separation
- Shiro Ikeda's page of Blind Source Separation
- Independent Component Analysis by JV Stone
- Blind source separation via Independent component analysis
- ICALab for image processing
- Separating a Real-Life Nonlinear Image Mixture
Camera calibration
- A toolbox containing several camera calibration techniques
- A flexible new technique for camera calibration
- Geometric Camera Calibration Using Circular Control Points
- A New Mirror-based Extrinsic Camera Calibration Using an Orthogonality Constraint
Sampling&Simulation
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Poisson-disk sampling
- Filtering solid Gabor noise
- Gabor Noise by Example
- Guided Exploration of Physically Valid Shapes for Furniture Design
- Efficient Geometrically Exact Continuous Collision Detection
Evolutionary computing/Optimization
- Ant colony optimization
- Genetic algorithm toolbox
- Particle Swarm Optimization Toolbox
- Cache-efficient graph cuts on structured grids
Networking Research
- The network simulator (ns-2)
- NetSim at Tetcos
- LBNL's software releases
Miscellaneous
- Simple model of spiking neurons spike train analysis
- Visual pattern recognition by moment invariants code
- Direct LS-based ellipsis fitting code
- DACE: a MATLAB Kriging toolbox
- Inference package for undirected graphical models
- Kernel smoothing toolbox
- CMU statistics library collections
- Rice DSP software release
- Complex network toolbox
- DistLearnKit: a MATLAB Toolkit for distance metric learning
- Subspace segmentation source code distribution
- Multiview geometry and 3D reconstruction
- A probabilistic image jigsaw puzzle solver
- Non-Iterative Approach for Fast and Accurate Vanishing Point Detection code
- Affine registration of 2d point sets
- Rotation Invariant Nonrigid Point Set Matching in Cluttered Scenes code
- Tensor Product model transformation (for control design)
- N-way toolbox (more versatile than the above one but slower)
- Simple Formulas For Quasiconformal Plane Deformations
- An Analytic Model for Full Spectral Sky-Dome Radiance
- Implementation of a Low-Depth of Field Picture Classifier
- Decoding, Calibration and Rectification for Lenselet-Based Cameras
Links to other communities' reproducible research effort
- Geostatistics toolbox mgstat DACE
- Error Correcting Codes (ECC)
- Face recognition software at face-rec.org
- Computer graphics graphics papers on the web
- Computer vision CV papers on the web
- Machine learning
- Google Sites on Compressed Sensing
- Google Sites on Matrix Factorization
- DMOZ Open Directory Project
- MATLAB toolbox collection at Plymouth
- Neurophysiological data analysis
- VLFeat library for open-source CV
- Algorithms and source code for Quality&Technology
- Video-based human action detection resources
- Data compression resources
- Deep learning (including DBM and RBM)
- Computational Topology
Links to reproducible books/journals/tutorials
- Image Processing Online (IPOL)
- Gradient Domain Manipulation Techniques in Vision and Graphics
-
Statistical and Structural Recognition of Human Actions
- Distance functions and metric learning
- Feature Learning for Image Classification
- Recognizing and Learning Object Categories
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Physics-Based Human Motion Modelling for People Tracking
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3d Shape Reconstruction from Photographs: a Multi-View Stereo Approach
- Deblurring Images: Matrices, Spectra, and Filtering
- Natural image statistics
- Spikes, decisions & actions
- Multiple view geometry in computer vision
- Collective Animal Behavior
- Signal Processing Techniques for Spike Train Analysis using MatLab
- Image Processing Online (IPOL) (many excellent c-coded source codes)
Links to other individual's reproducible research
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