ITK/Summer v4 2011 Meeting/A2D2/Deconvolution: Difference between revisions
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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 = | = 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:: | * 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 | ** Wiener filter | ||
** Landweber algorithm | ** Landweber algorithm | ||
** Richardson-Lucy maximum likelihood estimation | ** Richardson-Lucy maximum likelihood estimation | ||
** Parametric semi-blind deconvolution using parametric point-spread function model | ** 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.) | |||
Latest revision as of 01:18, 11 February 2012
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::OPDBasedWidefieldMicroscopePointSpreadFunctionImageSource
- 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::OPDBasedWidefieldMicroscopePointSpreadFunctionImageSource
- 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.)
