Source Code Collection for Reproducible Research

【 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 on 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 through Reproducible 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

Wavelet-based soft/hard thresholding and TI denoising Wavelab
Spatially adaptive image denoising under overcomplete expansion SA-OE
Low-complexity image denoising based on statistical modeling of wavelet coefficientscode
Bayesian Least-Square Gaussian Scalar Mixture BLS-GSM
Wavelet-domain HMM for image denoising WHMT
Fields of experts model for image denoising FoE
Learning sparse representation for image denoising K-SVD
Shape adaptive DCT based image denoising SA-DCT
Nonlocal mean based image denoising codecode2
Block matching 3D (BM3D) image denoising BM3D
Product of Edgeperts denoising PoEdges
Total Least-Square (TLS) image denoising TLS
AVMF color image denoising AVMF
Multiscle LMMSE-based image denoising code
Kernel regression based image denoising code
Belief propagation for image restoration code
Gaussian Field-of-Expert (GFoE) denoising code
Active random field learning code
Clustering-based Denoising using Locally Learned Dictionaries (K-LLD)
Local Pixel Grouping (LPG)-PCA image denoising
Learning Non-Local Range Markov Random Field for Image Restoration code
Image denoising via dictionary learning and structural clustering

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 CoderCode
SPIHT image codec SPIHTMATLAB codes (third-party implementation)
Estimation Quantization lossy image codec EQ
Least-Square Estionation Quantization CodecLS-EQ
EBCOT codec for JPEG2000 EBCOT

Image demosaicing

Primary-consistent soft-decision (PCSD)-based scheme executable
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
Lukac's demosaicing toolbox Download
A Model of Retinal Local Adaptation for the Tone Mapping of Color Filter Array Images

Image interpolation and Superresolution

Linear interpolation revitalized
New edge directed interpolation (NEDI) 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
Super-resolution via sparse coding 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
Simultaneous motion deblurring and super-resolution

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
EDISON System EDISON
Pfinder system Pfinder
A closed form solution to image matting matting
Spectral matting code
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
Biased normalized cut
Global contrast based salient region detection
Generalizing Swendsen-Wang to sampling arbitrary posterior probabilities code

Stereo matching& SfM

A taxonomy and evaluation of dense two-frame stereo correspondence algorithms code
Graph cut based stereo matching code
Belief propagation based stereo matchingcode
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

Image deblurring

Fourier-Wavelet Regularized Deconvolution ForWard
Pointwise SA-DCT regularized deconvolution SA-DCT
Image deconvolution using a natural image prior Code
Total-Variation (TV) based image deblurring Code
Two-step iterative shrinkage/thresholding algorithms for image restoration Code
Iterative methods for image restoration Code
ICA Toolbox for blind image separation
L0-AbS Deblur 1.0
Regularized Kernel Regression-Based Deblurring (AKTV)
Projection-based deblurring with fine-granularity and spatially adaptive regularization
Fast Gradient-Based Algorithms for Constrained Total Variation Image Deblurringcode
Image deblurring by adaptive sparse domain selection and adaptive regularization code

Blind image deblurring

Removing Camera Shake from a Single Image code_request_form
Coded exposure for motion deblurring
Invertible Motion Blur in Video
High-quality blind motion deblurring (executables only)
Quality measure for Blind deblurring methods
Eficient Marginal Likelihood Optimization in Blind Deconvolution code
Analyzing spatially varying blur
blind deconvolution using a normalized sparsity measure
Blur Kernel Estimation using the Radon Transform code

Image inpainting/Texture synthesis

Exemplar-based image inpainting code
Fields of experts model for image inpainting FoE
Image recovery via adaptive sparse representation code
Least-Square based sequential error concealment nsec
Patch-based nonlocal error concealment
Wavelet-domain parametric model code
Image recovery via hybrid sparse representation
Higher Order SVD Analysis for Dynamic Texture Synthesis

PDE-based image processing

Perona-Malik nonlinear diffusion code code2
Total variation based image denoising codecode2
Shock filter for image enhancement code
Weickert's anisotropic diffusion code
Mean curvature diffusion (MCD) code
A variational method for image recovery code

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

Biometrics

Fingerprint enhancement and matching
Daugman's iris recognition algorithm implementation
Photorealistic Models for Pupil Light Reflex and Iridal Pattern Deformation
Gabor Feature based Sparse Representation for Face Recognition code
Robust Sparse Coding for Face Recognitioncode
Face recognition software at face-rec.org
Ling Feng's speaker recognition sources

HDR imaging

HDR image rendering using a retinex-based adaptive filter
Digital Camera Workflow for HDR Images Using a Model of Retinal Processing
HDR image rendering by iCAM06 model
Rafal Mantiuk's research on HDR imaging

Gradient-domain image processing

Distributed Gradient-Domain Processing of Planar and Spherical Images
GradientShop:A Gradient-Domain Optimization Framework for Image and Video Filtering
Local Laplacian Filters: Edge-aware Image Processing with a Laplacian Pyramid
Domain Transform for Edge-Aware Image and Video Processing

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 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

Object recognition

Adaboost method code
Biologically inspired object recognition code
Hierarchical Models of Object Recognition in Cortex code
Scalable recognition with a vocabulary treeCode
Shock graphscode
Shape contexts code
Robust nonrigid point matching Code
Recognizing and learning object categories (short course at ICCV2005)
Beyond Bag of features Code
SuperParsing Code
Aggregating Gradient Distributions into Intensity Orders

Blind source separation

Shiro Ikeda's page of Blind Source Separation
Independent Component Analysis by JV Stone
Blind source separation via Independent component analysis
Two-microphone Separation of Speech Mixturescode

Image registration

Affine SIFT (ASIFT) with online demo
Lukas-Kanade algorithm code code2
SIFT feature correspondence code code2 code3
Local binary pattern (LBP) code
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

Visual tracking

Object detection and tracking in motion sequence
Incremental Learning for Robust Visual Tracking code
Online Visual Tracking with Histograms and Articulating Blocks code
Kanade-Lucas-Tomasi Feature Tracker
SIFT keypoint detector code2 code3
Speeded-Up Robust Features (SURF)
Histogram of oriented gradients (HOG) based human detection
Visual tracking using appearance model and particle filters (plug-in to opencv)
Video Object Segmentation by Tracking Regions code

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

Wavelets and frames

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

Compressed Sensing

l1-Magic
SparseLab
GPSR
ell-1 LS: Simple Matlab Solver for ell-1-Regularized Least Squares Problems
sparsify
MPTK: Matching Pursuit Toolkit [See also related conference publication: ICASSP 2006]
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 [See also relatedtechnical report ]
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

Evolutionary computing

Ant colony optimization
Genetic algorithm toolbox
Particle Swarm Optimization Toolbox

Networking Research

The network simulator (ns-2)
NetSim at Tetcos
LBNL's software releases

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

Data Clustering

Unsupervised learning of finite mixture models code
Affinity propagation
On Spectral Clustering: Analysis and an algorithm code code2 code3
Nonnegative matrix factorization (NMF) code2code3
Fast kmeans via triangle inequality
kdtree-based NN/kNN search fast kNN searchcode2
RANSAC toolbox for robust fitting
Clustering Through Ranking On Manifolds code

Sampling&Simulation

Poisson-disk sampling
Filtering solid Gabor noise

Graphics, Cartoons&Motion

Apparent Layer Operations for the Manipulation of Deformable Objects
2.5D cartoon models
3D modeling with sihouettes
Real-time Large-deformation Substructuring
Generalized biped walking control
Locomotion Skills for Simulated Quadrupeds
Action Recognition from a Distributed Representation of Pose and Appearance

Machine learning&Neural Networks

Deep Boltzmann Machines
Support vector machine
SVM and kernel method toolbox
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
Echo state networks for harnessing nonlinearity code
Image segmentation by LEGION network code

Miscellaneous

Simple model of spiking neurons spike train analysis
Direct LS-based ellipsis fitting code
Graph cut based 2D Phase unwrapping code
DACE: a MATLAB Kriging toolbox
Inference package for undirected graphical models
Kernel smoothing toolbox
CMU statistics library collections
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

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
Physics-Based Human Motion Modelling for People Tracking
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

Links to other individual's reproducible research

Adrian Barbu's research codes release
Al Hero's Lab and his reproducible research
Amir Beck's work on optimization theory and applications
Amir Saffari's reproducible reseach code releases
Amit Agrawal's Matlab and C codes
Anand Rangarajan 's matlab codes on hisreproducible research
Anat Levin's matlab codes release
Andrew Davison's work on Computational neuroscience
Ann Lee's Diffusion maps and treelet
Andrew Zisserman's visual geometry group source codes
Antonio Torralba's research codes release
Ashok Veeraraghavan's reproducible research code release
Ayan Chakrabarti's reproducible research code release
Bill Freeman's software release on his group's reproducible research
Bob Kass' research codes on neuronal data analysis
Ce Liu's software release on hisreproducible research
Christopher Kanan's reproducible research code release
Chuck Anderson's matlab codes on NNs and reinforcement learning
Dan Ellis' MATLAB Audio Processing Examples
David Heeger's toolboxes
Deliang Wang's research codes release
Deqing Sun's reproducible research code release
Deva Ramanan's work on object recognition
Eugene M. Izhikevich's matlab codes on NNs
Guy Gilboa's matlab codes on PDE-based image processing
Leo Grady's Graph Analysis Toolbox for Image Processing
Jalal Fadili's source codes on sparse representation
Jelena Kovacevic: bimagicLab: Software
Jeffrey A. Fessler's matlab codes release
Jian Sun's research code release
JianChao Yang's source codes on image classification and super-resolution
Jiaya Jia's programs and executables
Jon Wellner's work on statistics
Julien Mairal's matlab toolbox for sparse coding and dictionary learning
Kai Yu's reproducible research codes release
Kevin Murphy's Bayes Net Toolbox for Matlab
Laurens van der Maaten's software collection
Laurent Perrinet's SparseHebbianlearning source codes
LCAV's reproducible research at EPFL
LEAR's learning and recognition in vision
Lei Zhang's MATLAB codes releases
Leo Grady's matlab codes on his reproducibleresearch
Malcolm A. MacIver's AnimalLab
Marco Zuliani's reproducible research codes release
Mariana S. C. Almeida 's reproducibleresearch code release
Mark Schmidt's reseach on learning on probabilistic graphical models
Matthew Zeiler's reproducible research code release
MD Anderson Cancer Center: Bioinformatics
Michael Elad's source code collection on his research
Micheal Jordan's research code release
Ming-ming Chen's reproducible research code release
Ming-Hsuan Yang's reproducible research works
Neil Lawrence's reproducible research in machine learning
Onur Guleryuz's research codes release
Patrik O Hoyer's source code collection on his reproducible research
Peter Getreuer's reproducible research code release
Peyman Milanfar's source code collection on his reproducible research
Rene Vidal's Visionlab reproducible research code release
Raj Gupta's reproducible research code release
Rick Chartland's release on his reproducibleresearch
Shaoting Zhang's reproducible research code release
Simoncelli's LCV reproducible research codes release
Sinisa Todorovic's reproducible research codes release
Song-chun Zhu's source codes on image segmentation and active basis
Tony Xu Han's reproducible research code release
UCF vision lab source code collection
UIUC's salient patch feature collection
USC's iLab Neuromorphic Vision C++ Toolkit
UWO vision lab reproducible research code release
Vanderbilt's StatReport
Wotao Yin's research code release
Xavier Bresson's source codes accompanying his papers on image processing
Xiaofei He's dimensionality reduction source code collection
Xubo Song's matlab codes on her reproducibleresearch
Yi Ma's source code collection on hisreproducible research
Yu-wing Tai's reproducible research code releases
Yue M Lu's source codes on his reproducibleresearch

Google Scholar is great but if most papers in computational sciences could be accessed along with their source codes (not just the citation number), the world for scientific researchers will be even better. It is easy to find papers these days but when can finding thesource codes of a paper become easy too? I think Don Knuth's old-day advices on Literate Programming are still relevant to the current state of reproducible research. I believe that the time is ripe for significantly promoting experimentally reproducible research (just like mathemathetical theories - mentally reproducible research), and that we can best achieve this by considering research codes to be works of literature (so they can be easily picked up by other researchers). Only when the reproducibility of research in computational science becomes a default instead of a luxury, can we look further by standing on each other's shoulders.

一个好的资源整合网址：

http://www.csee.wvu.edu/~xinl/source.html