ImageSegmentation

Matlab Image Segmentation scripts

Required packages

• SPM12: https://www.fil.ion.ucl.ac.uk/spm/software/spm12/
• MixEst: https://github.com/utvisionlab/mixest
• GCO (used only in TestGCO.m): https://vision.cs.uwaterloo.ca/code/

Experiments

FMRI

• prepros_nyu_data.R -- preprocess NYU fmri data (https://www.nitrc.org/projects/nyu_trt)
• fmriTestScript -- runs HMRF-MCEM, HMRF-VEM, HMRF-EM, GrabCut on preprocessed NYU fmri data

Synthetic data

• MultipleIterationsOfTheExperiment -- generates synthetic data and runs HMRF-MCEM, HMRF-VEM, HMRF-EM, GrabCut on that data
• CalculateMetricsForExperiments -- calculates metrics for synthetic data experiments and saves them to csv
• AnalyzeExperimentMetrics -- reads calculated metrics and displays boxplots

Other

• CompareMethodsBinarySegmentation -- segments 2D image using ICM, Simulated Annealing and GraphCuts
• CompareMethodsNonBinarySegmentation -- segments 2D image into 3 classes using ICM, Simulated Annealing and GraphCuts
• CompareTime -- compares the time it takes to run HMRF-MCEM and HMRF-VEM
• GraphCutOnStarplusData -- attempt to segment Starplus fmri data
• TestGCO -- an example of using GCO library to segment an image with label costs

Functions

• AUC -- calculates AUC metric for a given ground truth and posterior distribution
• C -- vMF normalization const
• logC -- log vMF normalization const
• CalculateFinalEnergy -- calculates energy of an image
• CalculateLikelihoodProbabilities -- calculates likelihood probabilities for vMF distribution
• CalculateScores -- calculates Simple Similarity Score, Jaccard Coefficient and SSIM for a given image and ground truth
• EstimateParametersGrabCut -- estimates parameters for GrabCut algorithm
• EstimateParametersHMRFEM -- estimates parameters for HMRF-EM algorithm
• EstimateParametersHMRFMCEM -- estimates parameters for HMRF-MCEM algorithm
• FitGMMWithUnsetNumberOfComponents -- attempts to fit gmms with variable number of components and chooses best by AIC
• GenerateSynteticData -- generates syntetic data using Potts model and von Mises Fisher distribution
• GetNeighbours -- provides a list of neighbour indexes for a list of points
• GibbsSamplerPotts -- Gibbs sampler for Potts model
• GibbsSamplerLabelCost -- Gibbs sampler with a possibility to provide label costs
• Grab_Cut -- an implementation of GrabCut algorithm
• HMRF_EM -- an implementation of HMRF-EM algorithm
• HMRF_MCEM -- an implementation of HMRF-MCEM algorithm
• HMRF_VEM -- an implementation of HMRF-VEM algorithm
• ICM -- iterated conditional modes for MRF
• MetropolisHastings -- an implementation of Metropolis Hastings algorithm
• MLE -- calculates segmentation based maximum likelihood probability
• MRF_MAP_GraphCutABSwap -- an implementation of GraphCut Alpha-Beta Swap algorithm
• MRF_MAP_GraphCutAExpansion -- an implementation of GraphCut Alpha Expansion algorithm
• NormalizeToUnitLength -- normalizes vectors to N-dimensional unit sphere
• PadData -- adds zero padding to the matrix
• PlotDistanceToTruth -- plots the difference between true values and estimated values
• RealignDataByMask -- applies mask to data and removes zeroes on the edges of the data
• RotateMatrix -- rotates matrix 90 degress around a given dimension
• SaveImage -- saves segmented image to file using same colors as imagesc
• ShowImageWithLabels -- shows slice of 3d dimensional image overlayed with its labels
• ShowMultipleSlicesWithLabels -- shows multiple slices of 3d dimensional image overlayed with its labels
• SimilarityScore -- calculates Jaccard similarity score
• SimpleSimilarityScore -- calcultates simple similarity score
• SimulatedAnnealing -- an implementation of Simulated Annealing for MRF
• TruePositiveNegativeRates -- calculate sensitivity and recall metrics
• Read4DArrayFromStarplus -- reads 4D array from Starplus fmri data (http://www.cs.cmu.edu/afs/cs.cmu.edu/project/theo-81/www/)
• ReadROIFromStarplus -- reads provided ROI from Starplus fmri data