Reproducible Research in Computational Science_综合

Reproducible Research in Computational Science

from: 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 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

Bayesian Structured Sparse Coding (BSSC)
Wavelet-basedsoft/hard thresholding and TI denoising Wavelab
Spatiallyadaptive image denoising under overcomplete expansion SA-OE
Low-complexity image denoising based on statistical modeling of wavelet coefficients code
BayesianLeast-Square Gaussian Scalar Mixture BLS-GSM
Wavelet-domainHMM for image denoising WHMT
Fields ofexperts model for image denoising FoE
Learningsparse representation for image denoising K-SVD
Shapeadaptive DCT based image denoising SA-DCT
Nonlocal meanbased image denoising code code2
Blockmatching 3D (BM3D) image denoising BM3D
Productof Edgeperts denoising PoEdges
TotalLeast-Square (TLS) image denoising TLS
AVMF colorimage denoising AVMF
MultiscleLMMSE-based image denoising code
Kernelregression based image denoising code
Beliefpropagation 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
Leaning simultaneous sparsity coding (LSSC) code (only runs on 64-bit Linux machine with MATLAB)
BM3D image denoising with shape - adaptive principal component analysis (BM3D-SAPCA) code
Learning Non-Local Range Markov Random Field for Image Restoration code
Image denoising via dictionary learning and structural clustering
From Learning Models of Natural Image Patches to Whole Image Restoration code
Image denoising: Can plain Neural Networks compete with BM3D?
Patch-based Locally Optimal Wiener Filtering for Image Denoising
Nonparametric Bayesian Dictionary Learning for Analysis of Noisy and Incomplete Images code
Spatially adaptive iterative singular-value threshodlign (SAIST) code
Image Denoising using the Higher Order Singular Value Decomposition code
Dual-Domain Image Denoising code
Progressive image denoising code

Image coding

JPEG-LS standardLOCO-I
Context-Based,Adaptive, Lossless Image Coding CALIC
Edge directedprediction for lossless image compression EDP
TMWlossless image compression DownloadCode (lost in cyberspace)
Minimum rateprediction with DP-based optimization Code
EmbeddedPredictive Wavelet Image Coder Code
SPIHTimage codec SPIHTMATLABcodes (third-party implementation)
Estimation Quantizationlossy image codec EQ
Least-SquareEstionation Quantization Codec LS-EQ
EBCOTcodec for JPEG2000 EBCOT
Multiple description coding with prediction compensation code
Multiple description image coding based on lagrangian rate allocation code

Image demosaicing

Primary-consistentsoft-decision (PCSD)-based scheme executable
Alternateprojection (AP)-based scheme AP
AdaptiveHomogeneity-Directed (AHD) demosaicing AHD
DLMMSEdemosaicing DLMMSE
Demosaicingby successive approximation SA
Demosaicingby 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 demosaicing
Color Demosaicking by Local Directional Interpolation and Non-local Adaptive Thresholding code
Residual Interpolation for color image demosaicking
Vector-Valued Image Processing by Parallel Level Sets
Exploitation of Inter-color correlation for Color Image Demosaicing

Image interpolation and Superresolution

Linear interpolation revitalized
New edge directed interpolation (NEDI) code
Signal Discrete Sinc-interpolation in DCT Domain code
Directionalfiltering and data fusion DFDF
Wavelet-basedtexture image interpolation wt_interp
Fast and robustsuperresolution (SR) toolbox UCSC-SR
Superresolutionfor synthetic zooming syn_zoom
EPFL'sfrequency-domain approach EPFL
Support vectormachine based image superresolution result
Imageinterpolation using multiscale geometric representations Code
Kriging-basedBest Linear Unbiased Estimator Code
Imageinterpolation by adaptive 2D autoregressive modeling and soft-decisionestimation Executable
Super-resolution GUI developedby Bahadir at LSU
Multi-frame image super-resolution
Super-resolutionvia sparse coding code
Super-resolution through neighbor embedding code
Super-resolutionwith 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
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
Fast direct super-resolution by simple functions
A+: adjusted anchored neighborhood regression for fast super-resolution
Image Super-Resolution Using Deep Convolutional Networks
Hyperspectral Image Super-resolution via Non-negative Structured Sparse Representation

Hyperspectral/Multispectral image processing

Hyperspectral and Multispectral Image Fusion based on a Sparse Representation code
Bayesian fusion of multi-band images code
Hyperspectral pansharpening: a review code
Minimum Volume Simplex Analysis: A Fast Algorithm for Linear Hyperspectral Unmixing code
Multiple Feature Learning for Hyperspectral Image Classification code
Generalized Composite Kernel Framework for Hyperspectral Image Classification code
Spectral-Spatial Classification of Hyperspectral Data Using Loopy Belief Propagation and Active Learning code
Spectral-Spatial Hyperspectral Image Segmentation Using Subspace Multinomial Logistic Regression and Markov Random Fields code
Hyperspectral Image Segmentation Using a New Bayesian Approach with Active Learning code
Semi-Supervised Hyperspectral Image Segmentation Using Multinomial Logistic Regression with Active Learning code
Hyperspectral Image Super-resolution via Non-negative Structured Sparse Representation

Image segmentation, parsing and matting

Image segmentationby normalized cut Ncut
Epitome-basedimage segmentation epitome
Bayesianmultiscale image segmentation SMAP
Graph-cutBased Image Segmentation segment Code2
EDISONSystem EDISON Code2
Pfindersystem Pfinder
Aclosed form solution to image matting matting
Spectralmatting code
Levelset evolution without reinitialization Code
Implicitactive contour driven by local binary fitting energy Code
Snakes, Shapes, and GradientVector Flow Code
Unsupervisedlearning of finite mixture model Code
DDMCMCImage Segmentation
Image Segmentationby Generalized SW-cuts
A generalized model for scratch detection
Biased normalized cut
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 Merging code
Interactive Images: Cuboid Proxies for Smart Image Manipulation
Efficient Inference in Fully Connected CRFs with Gaussian Edge Potentials
Image Segmentation with Cascaded Hierarchical Models and Logistic Disjunctive Normal Networks code
Nonlocal Matting
KNN matting
Unsupervised Joint Object Discovery and Segmentation in Internet Images

Image deblurring

Fourier-WaveletRegularized Deconvolution ForWard
PointwiseSA-DCT regularized deconvolution SA-DCT
Imagedeconvolution using a natural image prior Code
Total-Variation(TV) based image deblurring Code
Two-stepiterative shrinkage/thresholding algorithms for image restoration Code
Iterativemethods for image restoration Code
ICA Toolbox for blindimage separation
L0-AbSDeblur 1.0
Regularized Kernel Regression-Based Deblurring (AKTV)
Projection-baseddeblurring with fine-granularity and spatially adaptive regularization
Fast Gradient-Based Algorithms for Constrained Total Variation Image Deblurring code
Image deblurring by adaptive sparse domain selection and adaptive regularization code
Fast Image Deconvolution using Hyper-Laplacian Priors
BM3D Frames and Variational Image Deblurring code
Centralized Sparse Representation for Image Restoration code
Bayesian Structured Sparse Coding (BSSC)
Image Restoration Using Joint Statistical Modeling in Space-Transform Domain

Blind image deblurring

Removing Camera Shake from a Single Image code_request_form
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
Fast motion deblurring
Two-phase kernel estimation for robust motion deblurring
Blind deconvolution using a normalized sparsity measure
Efficient Deblurring for Shaken and Partially Saturated Images
Fast Removal of Non-uniform Camera Shake
Multi-frame Blind Deconvolution with Super-resolution and Saturation Correction
Robust Multichannel Blind Deconvolution via Fast Alternating Minimization
Benchmarking blind deconvolution with a real-world database (dataset only)
Frequency domain blind deconvolution in multiframe imaging using anisotropic spatially-adaptive denoising
Handling Noise in Single Image Deblurring using Directional Filters

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

Physics-based image processing

Single Image Haze Removal code (third-party implementation)
Efficient Image Dehazing with Boundary Constraint and Contextual Regularization code
Singel image dehazing (only toy example included)
Single Image Visibility Restoration Comparison
Automatic single-frame-based rain streak removal via image decomposition code
Removing Atmospheric Turbulence via Space-Invariant Deconvolution
Automatic Recovery of the Atmospheric Light in Hazy Images
Blind Separation of Superimposed Moving Images Using Image Statistics code

Image inpainting

Exemplar-basedimage inpainting code
Fields ofexperts model for image inpainting FoE
Imagerecovery via adaptive sparse representation code
Least-Squarebased sequential error concealment nsec
Patch-basednonlocal error concealment
Image recovery via hybrid sparse representation
Higher Order SVD Analysis for Dynamic Texture Synthesis
TV-based image inpainting code code2
Robust Locally Linear Analysis with Applications to Image Denoising and Blind Inpainting code
Non-Parametric Bayesian dictionary learning for sparse image representations code
Hierarchical super-resolustion-based 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
Vector-Valued Image Processing by Parallel Level Sets

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
Gradient Magnitude Similarity Deviation: A Highly Efficient Perceptual Image Quality Index

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 Recognition code
Jialong He's Speaker Recognition (Identification) Tool
Unsupervised Salience Learning for Person Re-identification
Pose-free Facial Landmark Fitting via Optimized Part Mixtures and Deformable Shape Model
Robust Sparse Coding for Face Recognition code
Sparse Representation or Collaborative Representation: Which Helps Face Recognition? code

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
Image Smoothing via L 0 Gradient Minimization
Guided image filtering
Gaussian curvature filtering for spectrally regularized surfaces code

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/Image 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
Ensemble Projection for Semi-supervised Image Classification

Object detection/recognition

Adaboost method code
Biologically inspired object recognition code
Hierarchical Models of Object Recognition in Cortex code
Scalable recognition with a vocabulary tree Code
Shock graphscode
Shape contexts code
Robust nonrigid point matching Code
Histograms of Oriented Gradients (HOG) code
Pyramid histogram of oriented gradients (PHOG)
Beyond Bag of features Code
SuperParsing Code
Aggregating Gradient Distributions into Intensity Orders
Matching Local Self-Similarities across Images and Videos code (third-party implementation)
Deformed lattice detection in real-world images
Feature-Centric Efficient Subwindow Search code
Poselets: Body Part Detectors Trained Using 3D Human Pose Annotations code
Ensemble of Exemplar-SVMs for Object Detection and Beyond
Discriminative Learning of Relaxed Hierarchy for Large-scale Visual Recognition code
Multiple Kernels for Object Detection
Ensemble of Exemplar-SVMs for Object Detection and Beyond
Towards Total Scene Understanding: Classification, Annotation and Segmentation in an Automatic Framework
Object Bank: A High-Level Image Representation for Scene Classification and Semantic Feature Sparsification
Informative Feature Selection for Object Recognition via Sparse PCA code
Linear Spatial Pyramid Matching using Sparse Coding for Image Classification code
Locality-constrained Linear Coding for Image Classification code
MIT LabelMe Open Annotation tool
Stream-based Joint Exploration-Exploitation Active Learning code
BoF meets HOG: Feature Extraction based on Histograms of Oriented p.d.f Gradients for Image Classification code
Discriminatively trained deformable part models
Joint Deep Learning for Pedestrian Detection

Image registration/mosaicing/OFE

Affine SIFT (ASIFT) with online demo
SIFT Flow: Dense Correspondence across scenes
Lukas-Kanadealgorithm code code2
SIFT feature correspondence code code2 code3
Localbinary pattern (LBP) code
Speed up robust features (SURF)
Compact And Real-time Descriptors (CARD)
Maximallystable extremal regions (MSER) code
Graph-cutbased optical flow estimation code
Pyramid-basedhierarchical motion estimation Code
AffineMotion Estimation for Medical Image Registration Code
Afrequency-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 Images code
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
Pose-free Facial Landmark Fitting via Optimized Part Mixtures and Deformable Shape Model
Deformable Spatial Pyramid Matching for Fast Dense Correspondences
Nonlocal sparse and low-rank regularization for optical flow estimation code

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

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
HOGgles: Visualizing Object Detection Features
Visual tracking using appearance model and particle filters
Video Object Segmentation by Tracking Regions code
Visual tracking decomposition
Robust Visual Tracking using L1 Minimization code
Visual Tracking via Adaptive Structural Local Sparse Appearance Model
Robust Object Tracking via Sparsity-based Collaborative Model
Discrete-Continuous Optimization for Multi-Target Tracking
Multi-Target Tracking by Continuous Energy Minimization
Distribution Fields for Tracking
Least Soft-threshold Squares Tracking code
HOGgles: Visualizing Object Detection Features
Online Robust Non-negative Dictionary Learning for Visual Tracking
The Way They Move: Tracking Targets with Similar Appearance
Real-time compressive tracking

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
Efficient Salient Region Detection with Soft Image Abstraction
A Unified Approach to Salient Object Detection via Low Rank Matrix Recovery
Saliency Optimization from Robust Background Detection code

Low rank methods

Efficient Computation of Robust Low-Rank Matrix Approximations in the Presence of Missing Data using the L1 Norm code
Low-Rank Matrix Recovery and Completion via Convex Optimization
Predictive low-rank decomposition for kernel methods
Improved Nystr?m Low-rank Approximation for Scalable Manifold Learning
RASL: Robust Batch Alignment of Images by Sparse and Low-Rank Decomposition
TILT: Transform Invariant Low-rank Textures
Nonlocal sparsity regularized image restoration: a low-rank approach code
Bayesian Robust Matrix Factorization for Image and Video Processing
Motion Saliency Detection Using Low-rank and Sparse Decomposition code
Low-rank Modeling and its Applications in Image Analysis
Moving Object Detection by Detecting Contiguous Outliers in the Low-Rank Representation

Deep Learning

DeepLearnToolbox
Deep Belief Networks
Convolutional deep belief network
Learning Deep Boltzmann Machines
Conditional RBMs/DBNs
Neocognitron
Convolutional/Deconvolutional networks
Invariant scattering convolution network
Marginalized Stacked Denoising Autoencoders
Joint Deep Learning for Pedestrian Detection
Pedestrian Parsing via Deep Decompositional Neural Network
Deep Learning Identity Preserving Face Space
Deep Convolutional Network Cascade for Facial Point Detection

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
3D Discrete Shearlet Transform and Video Processing 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

HDR/RGBD 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
Binocular Tone Mapping
High dynamic range imaging and tonemapping
Indoor Segmentation and Support Inference from RGBD Images
Unsupervised Feature Learning for RGB-D Based Object Recognition
Image Guided Depth Map Upsampling

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
MR image reconstruction from highly undersampled k-space data by dictionary learning
k-t FOCUSS
k-t SLR: Accelerated dynamic MRI using low rank and sparse penalties
Low-Rank Modeling of Local k-Space Neighborhoods (LORAKS) for Constrained MRI
k-t SPARSE SENSE
ESPIRiT: Programming Library and Software Toolbox for Compressed Sensing and Parallel Imaging

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

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 code code2 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

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
RECON: Scale-Adaptive Robust Estimation via Residual Consensus code
How Do Humans Sketch Objects?
Manifold Exploration: A Markov Chain Monte Carlo technique for rendering scenes with difficult specular transport
Exploring Collections of 3D Models using Fuzzy Correspondences
Illuminant Chromaticity from Image Sequences
Network Principles for SfM: Disambiguating Repeated Structures with Local Context

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&Physics-based Simulation

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
Illuminant Chromaticity from Image Sequences

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 packagefor undirected graphical models
Kernel smoothingtoolbox
CMUstatistics library collections
Rice DSP software release
Complexnetwork toolbox
DistLearnKit: a MATLABToolkit for distance metric learning
Subspace segmentationsource 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 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
Image Processing Online (IPOL) (many excellent c-coded source codes)

Links to other individual's reproducible research

Abhinav Gupta 's research code release
Adrian Barbu's research codes release
Al Hero's Lab and his reproducible research
Alexei Efros' research codes release
Allen Yang's research codes release
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 his reproducible research
Anat Levin's matlab codes release
Andrew Davison's work on Computational neuroscience
Ann Lee's Diffusionmaps and treelet
Andrew Zisserman'svisual geometry group source codes
Antonio Torralba's research codes release
Ashok Veeraraghavan's reproducible research code release
Ayan Chakrabarti's reproducible research code release
Bahadir Gunturk's 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 his reproducible research
Chih-Chung Hsu's research code release
Chih-Jian Lin's machine learning software release
Chih-Yuan Yang's research code release
Christopher Kanan's reproducible research code release
Chuck Anderson's matlab codes on NNs and reinforcement learning
Chunming Li's research code release
Claude Knaus' research codes release
Dafeng Sun's matlab codes release
Dan Ellis' MATLAB Audio Processing Examples
Daniel DeMenthon's research code release
Daniel Huttenlocher 's research code release
Daniel Zoran's research code release
Danny Harari's software release
David Heeger's toolboxes
Deqing Sun's reproducible research code release
Derek Hoiem's research software release
Deva Ramanan's work on object recognition
Dror Baron's research software release
Dimitri Van De Ville 's research codes release
Emmanuel Candes' software release
Emanuel Todorov's research codes release
EPFL CVLab's research codes release
Eugene M. Izhikevich's matlab codes on NNs
Fei-fei Li's research code release
Gaofeng Meng's research code release
Guoping Qiu's research codes release
Graham Taylor's source codes release
Guy Gilboa's matlab codes on PDE-based image processing
Haibin Ling's research codes release
Haichao Zhang's research codes release
Hanchun Peng's software release
Hao Jiang's research code release
H.J. Seo's interesting collection of everything
Honglak Lee's research code release
Huchuan Lu's research codes release
Huifung Poo's research codes release
Human sensing @CMU's software release
INRIA LEAR research codes release
IPL (Politechnico di Torino)'s research codes release
Jason Corso's research codes release
Jalal Fadili's source codes on sparse representation
James Hays' research code release
Javier Portilla's research codes release
Jelena Kovacevic's bimagicLab: Software
Jeffrey A. Fessler's matlab codes release
Jia-bin Huang's Awesome Computer Vision website
Jian Sun's research code release
Jian Zhang's research code release
Jianbo Shi's software release
JianChao Yang's sourcecodes on image classification and super-resolution
Jianxiong Xiao's research codes release
Jiaya Jia's programs and executables
Jieping Ye's research codes release
John Paisley's research code release
Jon Wellner's work on statistics
Jose M. Bioucas Dias' research codes release
Julien Mairal's research code release
Jun Li's research codes release
Junzhou Huang's research codes release
Justin Haldar's research code release
Kai Yu's reproducible research codes release
Kaihua Zhang's research code release
Keigo Hirakara's research codes release
Kilian Q. Weinberger 's research code release
Kevin Murphy's Bayes Net Toolbox for Matlab
Kyoung Mu Lee 's software release
Laurens van der Maaten's software collection
LaurentPerrinet's SparseHebbianlearning source codes
Lawrence Carin's research code release
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 reproducible research
Leslie Ying's research codes release
Lina Karam's research software release
Mahdi Soltanolkotabi 's research code release
MalcolmA. MacIver's AnimalLab
Marco Zuliani's reproducible research codes release
Mariana S. C. Almeida 's reproducible research code release
Mark A. Davenport's research code release
Mark Schmidt's reseach on learning on probabilistic graphical models
MATTHIAS J. EHRHARDT's research code release
Matthew Zeiler's reproducible research code release
MD Anderson Cancer Center: Bioinformatics
Michael Elad'ssource code collection on his research
Michael J. Brown's research codes release
Michal Cernansky's research code release
Michael Lustig's research code release
Miguel ?. Carreira-Perpi?án 's research software release
Mikel Rodriguez's source codes release
Minmin Chen's reproducible research code release
Ming-ming Chen's reproducible research code release
Ming-Hsuan Yang's reproducible research works
Mingyuan Zhou's research codes release
Naiyan Wang's research codes release
Neil Lawrence's reproducible research in machine learning
Ofir Pele's research codes release
Onur Guleryuz's research codes release
Owen Carmichael's software release
Pascal Getreuer's software release
Patrik O Hoyer's source code collection on his reproducible research
Paven Turaga's research code release
Pedro Domingos' research codes release
PF Felzenszwalb 's research codes release
Penn State LPAC research code release
Peter Getreuer's reproducible research code release
Peter Kovesi's matlab functions for CV and image processing
Peyman Milanfar'sresearch code release
Philipp Krahenbuhl's research codes release
Qi Wei's research code release
Qingxiong Yang's research codes release
Quoc V. Le's research codes release
Rene Vidal's Visionlab reproducible research code release
Raj Gupta's reproducible research code release
Radu Timofte's research code release
Raquel Urtasun 's research codes release
Rick Chartland's release on his reproducible research
Robert Nowak's source code release
Ruslan Salakhutdinov's research codes release
Scott Acton's research software releases
Shai Bagon's Matlab Code
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
Stanley Chan's research codes release
Takumi Kobayashi's research code release
Thomas Brox's research codes release
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
Vladimir Kolmogorov's research codes release
Wavelab (at Univ. of Salzburg) software release
WILLOW's research code release
Wotao Yin's research code release
Xavier Bresson's source codes accompanying his papers on image processing
Xiaodi Hou's research codes release
Xiaofei He's dimensionality reduction source code collection
Xiaofeng Ren's research codes release
Xiaogang Wang's research codes release
Xiaolin Wu's research codes release
Xiaoming Huo's software release
Xiaoou Tang's MM Lab research code release
Xiaowei Zhou's research code release
Xubo Song's matlab codes on her reproducible research
Yair Weiss' research codes release
Yi Ma's source code collection on his reproducible research
Yi Wang's research codes release
York vision research center's software release
Yu-wing Tai's reproducible research code releases
Yuanjie Zheng's source codes release
Yue M Lu's source codes on his reproducible research
Yue Wang at VT-CBIL's research code release
Zhilin Zhang's research codes release
Zhoulin Jiang's research code release
Zhuowen Tu's research code releases

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 the source 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.

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