Reproducible Research in Computational Science

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

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“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

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"As a method for finding things out, science lives by its disdain for authority and its reliance on experimentation." - Chris Quigg

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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
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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

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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

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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 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
• Open Remote Sensing Website

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 á. 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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