Difference between revisions of "Supported algorithms"

From MIPAV
Jump to: navigation, search
m
m
 
Line 1: Line 1:
−
Note: Many of these algorithms are implemented for both monochromatic and RGB images
+
Many of these algorithms are implemented for 2D, 2.5D, 3D, monochromatic, and RGB images. Refer to the Image types section, to learn about image types for a specific algorithm.
  
−
* Autocorrelation coefficients
+
== MIPAV Algorithms ==
−
* Autocovariance coefficients
+
*[[Understanding MIPAV capabilities]]
−
* Brain tools
+
*[[Developing new tools using the API]]
−
** Face de-identification
+
*[[Using MIPAV Algorithms | Overview of MIPAV Algorithms]]
−
** Extract brain surface (BET)
+
**[[Cost functions used in MIPAV algorithms]]
−
** Extract Brain surface (BSE)
+
**[[Interpolation methods used in MIPAV]]
−
* Density based clustering
+
**[[Degrees of freedom]]
−
* Edge detection
+
**[[Algorithms used to draw VOI]]
−
* Extract surface (marching cubes)
+
<div id="AutoCorrelation"></div>
−
* Filtering
+
**[[Autocorrelation Coefficients]]
−
** FFT
+
**[[Autocovariance Coefficients]]
−
*** Gaussian filter
+
**[[Barrel Distortion Correction]]
−
*** Butterworth
+
<div id="DtiAlgorithms"></div>
−
*** Highpass
+
**[[DTI: Create List File]]
−
*** Lowpass
+
**[[DTI Color Display]]
−
*** Bandpass
+
**[[DTI Estimate tensor | DTI Estimate tensor - under construction]]
−
** Filters (frequency)
+
**[[DTI Pipeline]]
−
** Filters (Gabor)
+
<div id="EdgeDetection"></div>
−
** Filters (homomorphic)
+
**[[Edge Detection: Zero X Laplacian]]
−
** Filters (spatial)
+
**[[Edge Detection: Zero X Non-Maximum Suppression]]
−
*** Adaptive histogram equalization
+
<div id="ExtractSurface"></div>
−
*** Regional (for speed)
+
**[[Extract Brain: Extract Brain Surface (BET)]]
−
*** Neighborhood (for precision)
+
**[[Extract Brain: Extract Brain Surface (BSE)]]
−
*** Anisotropic diffusion
+
**[[Extract Surface (Marching Cubes)]]
−
*** Coherence enhancing diffusion
+
**[[Face Anonymizer (BET)]]
−
*** Gaussian blurring
+
<div id="FilterAlgorithms"></div>
−
*** Gradient magnitude
+
**[[Filters (Frequency)]]
−
*** Laplacian
+
**[[Fast Fourier Transformation (FFT)]]
−
*** Mean
+
**[[Filters (Spatial): Adaptive Noise Reduction]]
−
*** Median
+
**[[Filters (Spatial): Adaptive Path Smooth]]
−
*** Mode
+
**[[Filters (Spatial) Anisotropic Diffusion]]
−
*** Non-linear noise reduction
+
**[[Filters (Spatial): Coherence-Enhancing Diffusion]]
−
*** Nonmaximum supression
+
**[[Filters (Spatial): Gaussian Blur]]
−
*** Regularized isotopic diffusion
+
**[[Filters (Spatial): Gradient Magnitude]]
−
*** Slice averaging
+
**[[Filters (Spatial): Haralick Texture]]
−
*** Unsharp mask
+
**[[Filters (Spatial) Laplacian]]
−
** Filters (wavelet)
+
**[[Filters (Spatial): Local Normalization]]
−
* Histogram Tools
+
**[[Filters (Spatial): Mean]]
−
** 2D Histogram
+
**[[Filters (Spatial): Median]]
−
** Histogram equalization
+
**[[Filters (Spatial): Mode]]
−
*** Neighbourhood adaptive
+
**[[Filters (Spatial): Nonlinear Noise Reduction]]
−
*** Regional adaptive
+
**[[Filters (Spatial): Nonmaximum Suppression]]
−
** Histogram matching
+
**[[Filters (Spatial): Regularized Isotropic (Nonlinear) Diffusion]]
−
** Histogram summary
+
**[[Filters (Spatial): Slice Averaging]]
−
* Insight toolkit (ITK)
+
**[[Filters (Spatial): Unsharp Mask]]
−
** Gaussian blur
+
**[[Filters (Wavelet): De-noising BLS GSM]]
−
* Microscopy
+
**[[Filters (Wavelet): Thresholding]]
−
** Colocalization
+
**[[Fuzzy C-Means: Multispectral and Single Channel Algorithms]]
−
*** Expectation maximization
+
<div id="HistogramAlgorithms"></div>
−
*** Orthogonal regression
+
**[[Cumulative Histogram|Histogram cumulative]]
−
** FRAP
+
**[[Histogram Equalization: Regional Adaptive]]
−
** FRET
+
**[[Histogram Equalization: Neighborhood Adaptive]]
−
** FRET bleedthru
+
**[[Histogram Matching]]
−
** FRET efficiency
+
**[[2D Histogram]]
−
** Subtract VOI background
+
**[[Histogram summary]]
−
** Restoration
+
**[[Hough Transform]]
−
*** XCOSM_EM
+
**[[Image Calculator]]
−
*** Maximum likelihood Iterative blind deconvulution
+
**[[Manual 2D Series]]
−
* Principal Component
+
**[[Mask]]
−
* Registration
+
<div id="MicroscopyAlgorithms"></div>
−
** Align patient position
+
**[[Microscopy Colocalization Orthogonal Regression]]
−
** B-spline automatic registration 2D/3D
+
**[[Microscopy: Fluorescence Resonance Energy Transfer (FRET)-Acceptor]]
−
** B-spline automatic registration 2.5D
+
**[[Microscopy: FRAP (Fluorescence Recovery After Photobleaching)]]
−
** Constrained optimized automatic registration
+
**[[Microscopy: Fluorescent Resonance Energy Transfer (FRET) Bleed Through and Efficiency]]
−
** Display pixel similarity cost functions
+
**[[Microscopy: Blind Deconvolution]]
−
** Landmark
+
<div id="TransformationAlgorithms"></div>
−
*** Least squares
+
**[[Midsagittal line alignment]]
−
*** Thin-plate spline
+
**[[Morphology]]
−
** Manual 2D series
+
***[[Morphology#Background Distance map|Background Distance map]]
−
** Mosaic
+
***[[Morphology#Close|Close]]
−
** Optimized automatic registration
+
***[[Morphology#Delete Objects| Delete Objects]]
−
** Optimized automatic registration 2.5D
+
***[[Morphology#Dilate|Dilate]]
−
** Optimized automatic registration 3.5D
+
***[[Morphology#Distance Map|Distance Map]]
−
** Time series optimized automatic registration
+
***[[Morphology#Erode|Erode]]
−
** VOI landmark
+
***[[Morphology#Evaluate Segmentation|Evaluate Segmentation]]
−
* Segmentation
+
***[[Morphology#Fill holes|Fill holes]]
−
** Evaluate VOI segmentation
+
***[[Morphology#Find Edges|Find Edges]]
−
** Fuzzy C-means
+
***[[Morphology#ID objects|ID objects]]
−
*** Single-channel
+
***[[Morphology#Morphological Filter|Morphological Filter]]
−
*** Multispectral
+
***[[Morphology#Open|Open]]
−
** Graph based
+
***[[Morphology#Particle Analysis|Particle Analysis]]
−
** Levelset
+
***[[Morphology#Skeletonize|Skeletonize]]
−
** Levelset diffusion
+
***[[Morphology#Skeletonize 3D pot field|Skeletonize 3D pot field]]
−
** Threshold
+
***[[Morphology#Ultimate erode|Ultimate erode]]
−
** Watershed
+
**[[Muscle Segmentation]]
−
* Shading Correction
+
**[[NEIRetinalRegistration | NEI Build macular pigment maps]]
−
** Entropy Minimization
+
<div id="RegistrationAlgorithms"></div>
−
** Inhomogeneity N3 Correction
+
**[[B-Spline Automatic Registration | Registration: B-Spline Automatic Registration ]]
−
** MRI combined info
+
***[[Detect folding]]
−
* Transformation (i.e. affine)
+
***[[User Dialogs in MIPAV|B-Spline Automatic Registration Dialog box]]
−
** Reslicing / iso-tropic voxels
+
**[[Optimized automatic registration 3D | Registration: Optimized automatic registration 3D and 3.5D]]
−
** Subsample
+
**[[Registration: Landmark-Least Squares]]
−
** Transform
+
**[[Registration: Landmark-TPSpline]]
−
** [[Transform nonlinear]]
+
**[[Registration: Manual 2D Series]]
−
** Transform to power of 2
+
**[[Midsagittal line alignment | Registration: Midsagittal line alignment]]
 +
**[[Reslice-Isotropic Voxels | Registration: Reslice-Isotropic Voxels]]
 +
**[[Registration: Time Series Optimized Automatic Registration]]
 +
**[[Reslice-Isotropic Voxels]]
 +
**[[Watershed|Segmentation: Watershed]]
 +
**[[Shading Correction: Inhomogeneity N3 Correction]]
 +
**[[Standard Deviation Threshold]]
 +
**[[Subsampling images]]
 +
**[[Threshold]]
 +
**[[Transform]]
 +
**[[Transform to power of 2]]
 +
**[[Transform: Conformal Mapping Algorithms]]
 +
**[[Transform nonlinear]]
 +
**[[Volume Renderer]]
 +
 
 +
[[Category:Help]]
 +
[[Category:Help:Algorithms]]

Latest revision as of 19:27, 10 September 2013

Many of these algorithms are implemented for 2D, 2.5D, 3D, monochromatic, and RGB images. Refer to the Image types section, to learn about image types for a specific algorithm.

MIPAV Algorithms

Retrieved from "http://mipav.cit.nih.gov/pubwiki/index.php?title=Supported_algorithms&oldid=47229"