Toolbox Documentation—Table of Contents

1. Overview of PMI Toolbox
2. License
3. The SD Structure
4. The Measurement List
5. The Medium Structure
6. Toolbox Functions
   1. pmipath - setup search paths for toolbox
   2. Data Processing Tools
      1. Working with PMI formatted data files, readPMIData, writePMIData
      2. Fitting background optical properties, fitMua, fitMusp
      3. Simultaneous background optical property fitting, fitBackground, newFitBackground
      4. Calibrating forward models to data, fitSD, fitSDAmp, fitSDPhs
   3. Computing the Forward Problem
      1. Born Approximation (includes Rytov and FullBorn)
         1. Calculate the unperturbed fluence, DPDWHelmholtz
         2. Calculate the Born forward matrix, genBornMat
         3. Calculate the total fluence, genBornData
         4. Frequency-Domain Imaging, FD2pt and FD3pt
         5. Time-Domain Imaging, TD2pt and TD3pt
      2. Analytical Sphere Solution
         1. Calculate total fluence given a spherical perturbation, genSphereData
         2. Calculate fluence scattered off of spherical perturbations, exactSphere
      3. tMCimg and tFDimg
         1. PMItoFD, PMItoMC
         2. MCConfig
         3. loadMC2pt
         4. readMCHis
         5. readSig
      4. Calculating Jacobians
         • genMuJacobian
         • genSDJacobian
         • genPosJacobian
         • genJacobianFrom2pts
   4. Adding Simulated Noise, addElecNoise, addShotNoise
   5. Data Reconstruction
      1. Tikhonov Reconstruction
      2. Filtered Back-projection
      3. Regularized Least-squares
      4. Truncated Conjugate Gradient
      5. Algebraic Reconstruction Technique
      6. Simultaneous Iterative Reconstruction Technique
      7. Truncated Singular Value Decomposition
   6. Data Visualization
      1. 2-D data visualization, plotData, showImage
      2. 3-D data visualization, showVolume, ishowVolume
   7. Useful Utility Routines
      1. isFD, isTD
      2. SetOptode
      3. calcAffine
      4. calcSep
      5. genMeasList
      6. cm256, gray256
      7. mergeSD
      8. sampleVolume
7. Sample Programs
8. Additional programming notes for developers and users writing their own PMI toolbox based applications.