ITK/Summer v4 2011 Meeting/A2D2/Deconvolution

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How our A2D2 will advance the field (of microscopy)

  • Deconvolution is commonly used to reduce blur in microscopy images
  • We provide algorithms to do this and data to evaluate them

Distribution

  • Code
    • New Deconvolution module
    • Point-spread function models for microscopy - external module
  • Data: MIDAS
  • Dependencies
    • FFT-based convolution filter (Cory will do, modification of Gaetan's Insight Journal contribution)

New Features and Classes in ITK

Two widefield microscope point-spread function models

  • itk::MicroscopePointSpreadFunctionImageSource.h
    • itk::OPDBasedWidefieldMicroscopePointSpreadFunctionImageSource
      • itk::GibsonLanniPointSpreadFunctionImageSource
      • itk::HaeberlePointSpreadFunctionImageSource
  • itk::OPDBasedWidefieldMicroscopePointSpreadFunctionIntegrand
  • itk::BeadSpreadFunctionImageSource
  • itk::ScanImageFilter
  • itk::SphereConvolutionFilter

Classes to enable fitting of parametric image models via the registration framework

  • itk::ParametricImageSource
  • itk::ImageToParametricImageSourceMetric

Four deconvolution algorithms

    • Wiener filter
    • Landweber algorithm
    • Richardson-Lucy maximum likelihood estimation
    • Parametric semi-blind deconvolution using parametric point-spread function model

New Features and Classes in ITK

Two widefield microscope point-spread function models

  • itk::MicroscopePointSpreadFunctionImageSource.h
    • itk::OPDBasedWidefieldMicroscopePointSpreadFunctionImageSource
      • itk::GibsonLanniPointSpreadFunctionImageSource
      • itk::HaeberlePointSpreadFunctionImageSource
  • itk::OPDBasedWidefieldMicroscopePointSpreadFunctionIntegrand
  • itk::BeadSpreadFunctionImageSource
  • itk::ScanImageFilter
  • itk::SphereConvolutionFilter

Classes to enable fitting of parametric image models via the registration framework

  • itk::ParametricImageSource
  • itk::ImageToParametricImageSourceMetric

Four deconvolution algorithms

    • Wiener filter
    • Landweber algorithm
    • Richardson-Lucy maximum likelihood estimation
    • Parametric semi-blind deconvolution using parametric point-spread function model

Data

Estimated size

1 GB

Sharing

  • Hosting on Kitware MIDAS installation
  • Some images contributed as test data

Images

Synthetic images of simple objects (50 images)

  • Spheres and cylinders convolved with example PSF
  • Corrupted by various levels of noise
  • 2 shapes X 5 different sizes for each shape X 5 different signal-to-noise ratios

Measured images of spherical beads (15 images )

  • We have widefield images of 100nm, 200nm, and 500nm beads from Dr. Kerry Bloom (size verified with scanning electron microscope)
  • 5 images of each bead size

Collaborator images (15-30 images)

  • 5 images and their associated PSFs from each collaborator (Bloom, Weinbert, and Superfine.)