Image processing functions in Image Analyst MKII
Image Analyst MKIIFunctions Glossary
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2D DFT Filter
2D DFT Filter Butterworth BP
2D DFT Filter Butterworth BP Tiled
2D Kernel Convolution
2D Median
2D Morphological Operator
2D Nonlinear Filter
2D Savitzky-Golay filter
Absolute Value
Affine Transformation
Align Channels
Align Series (Image Stabilizer)
Align Tiled Channels
Align Tiled Series (Image Stabilizer)
Anisotropic Diffusion Filter
Attach Intensity Gating Image
Attach Overlay Image
Automatic ROI drawing
Band Pass filter Optimization
Blind Spectral Unmix with NMF
Calculate Simple Crossbleed
Calculate Spatial Moments
Calibration Wizard Parameters
Clear Segmentation Classifiers
Close Image Window
Copy Image Window
Copy ROIs from Other Image
Correct Intensity Jump
Correct Lens Distortion
Count Division and Cell Death
Count Object Colocalization
Create ROI
Create ROIs from Segments
Crop
Crop Image in Place
Crop Image to Segments
Cross-correlation data
Cross-correlation image
Detect Nuclei Convolution
Differential Evolution Optimizer
Distance from Segments
Draw Model Mitochondrion
Draw Random Position Model Mitochondria
EndIf
Erase All ROIs
Excel Window Command
Export
Fill Mask
Fill or Mask Active ROI
FLIPR Calibration with [K+]ec steps and known [K+]ic and known kP
FLIPR Complete Calibration
FLIPR Complete Calibration with known kP
FLIPR Complete Calibration with known kP - Goldman
FLIPR Complete Iterative Calibration
FLIPR Estimate PN
FLIPR Short Calibration based on known potential during MDC and CDC
FLIPR Short Calibration between known baseline and CDC
FLIPR Short Calibration between known baseline and MDC
FLIPR Short Calibration between known baseline and separately measured fP0
FLIPR Short Calibration from Zero with fx=0
FunctionOptions
Get Image Information
Get Linked Channel
If
If Greater Than Zero
Image Arithmetic (image-image math)
Image Arithmetic In Place
Image Arithmetic Single Frame
Inpaint Mask
Input
Invert
Lens Correction Optimization
Link Image Windows
Load and Run Pipeline
Load ROIs
Mask Borders
Mask Frames by Plot Values
Mask Images
Measure Object Intensity
Measure Object Morphology
Mirror or Rotate (new image)
Mirror or Rotate in Place
Multi-Dimensional Open Information
Multi-Dimensional Open Stage Position
Multi-Dimensional Reload Channel
New Image
New Time Scale
Onset Image
Open File
Optical Flow
Options
Pipeline
Pipeline Optimization
Pipeline Optimization Parameter
Plot
Plot Correlation (Colocalization)
Plot Intensities Corresponding to Segments
Plot Morphological Parameters of Segments
Plot Ratio
Plot ROI Dimensions
Plot Tracking Parameters
Potential calibration constants
Potential calibration error propagation
Potential calibration expert overrides
Projection of Vectors from a Point
Ratio
Ratiometric ROI Classifiers
ReCount Division and Cell Death
Reevaluate Segments
Remove Blank Frames
Rename
Resample Image
ROI Classifiers
Run Membrane Potential Calibration
Save ROIs
Scalar Arithmetic (image-value math)
Scalar Arithmetic Multi
Secondary Watershed Segmentation
Select
Select by Number
Sensor Noise Characteristics
Set Reference Image
Set Scaling/LUT
Set Segmentation Classifiers
Set Segmentation Intensity Classifiers
Shift Time Scale
Simple 2D Cross-correlation
Simple Segmentation
Skeletonize
Spectral Unmix
Strip to Well Cell Count
Substitute Poisson Noise
Subtract Background or Normalize
T or Z-project
Template Matching
Temporal Average Filter
Temporal Block Filter
Temporal Median Filter
Temporal Rolling Projection
Temporal Savitzky-Golay Filter
Thinness Ratio Optimization
Threshold
Time Stamp and Scale Bar
TMRM Complete Calibration
TMRM Complete Calibration with known kT
TMRM Complete Calibration with known kT and K-steps
TMRM Short Calibration between known baseline and MDC or CDC
Track Objects
Truncate or Cut
Wait for All Inputs
Watershed Segmentation
Wiener filter
Window Menu Command
Write Back Scaled Values
ΔF/F0

Optical Flow ( IAOpticalFlow )

Parameters:
Name Short Name Type Description
Select dx kernel Kerdx string Row kernel for differentiation in x. Kernel defined in Preferences. Or use Savitzky-Golay below.
Select dy kernel Kerdy string Column kernel for differentiation in y. Kernel defined in Preferences. Or use Savitzky-Golay below.
Select dt kernel Kerdt string Column kernel for differentiation in t. Kernel defined in Preferences. Or use Savitzky-Golay below.
Average results for dt width AverageOFdtWidth boolean Calculates Optical Flow using spatial derivatives of each frame of the temporal differentiation kernel, and then take the average.
Block mode blockmode boolean Optical flow is calculated within consecutive blocks, each block has same number of frames as the dt kernel. Each block results one OF image. If disabled then Optical flow calculation is continuous, like a running differentiation. Must be disabled when using in Multi-Dimensional Load.
SG kernel for dx,dy width SGxyWidth integer Width of spatial Savitzky-Golay 1st derivative kernel
SG kernel for dx,dy order SGxyOrder integer Order of spatial Savitzky-Golay 1st derivative kernel
SG kernel for smooth width SGsmoothWidth integer Width of smooth Savitzky-Golay 0th derivative kernel
SG kernel for smooth order SGsmoothOrder integer Order of smooth Savitzky-Golay 0th derivative kernel
SG kernel for dt width SGtWidth integer Width of temporal Savitzky-Golay 1st derivative kernel
SG kernel for dt order SGtOrder integer Order of temporal Savitzky-Golay 1st derivative kernel
Aperture kernel size ApertureSize integer Optical flow is calculated within this sized neighborhood.
Aperture kernel shape ApertureShape string Optical flow is calculated within this shaped neighborhood.
Correct for bias by noise CorrectNoiseBias boolean
Correct low noisy gradients in time CorrectT boolean
Enforce constraints on gradients in space EliminateXY boolean
Variance factor for time constraint VarianceFactorCorrectionTime real
Variance factor for bias VarianceFactorCorrectionBias real
Variance factor for constraint 1 VarianceFactorConstraint1 real
Variance factor for constraint 2 VarianceFactorConstraint2 real
Detector offset DetectorOffset real Intensity measured in darkness, see "Sensor Noise Characteristics"
Detector variance vs. intensity Slope DetectorNoiseSlope real Slope of noise diagram, see "Sensor Noise Characteristics"
Detector Read out Variance DetectorReadOutNoise real Variance measured in darkness, see "Sensor Noise Characteristics"
Pixel size PixelSize real Results are multiplied with this value.
Output as Absolute value of vectors OutputAbs boolean Absolute velocity image is calculated.
Output as X and Y components of vectors OutputXY boolean X and Y vector component images are calculated.
Output as Absolute value of Projected Vectors OutputProjAbs boolean Radial - anterograde/retrograde velocity image is calculated. Needs a projection point ROI below.
Projection ROI ProjectionROI integer Center point ROI for radial projection.
Correct whole image drift OutputProjAbs boolean Sets the mean of X and Y component images to zero, then calculates absolute image. Warning: this works properly only if Correct noisy gradients in time is set to no!
Reject image if drift is larger than RejectDrift real If the calibrated mean vector of whole image is larger than this value, it is assumed to be caused by drift and the whole image will be masked.
Description:
Calculates velocity vector field or absolute velocities based on Optical Flow from image series.
See details in Gerencser and Nicholls, Biophys J. 2008 Sep 15;95(6):3079-99.
See online documentation for protocols.
Mathematica usage:
Kernel format instead of name= {{xseed,yseed},{{1,2,3},{1,2,3},{1,2,3}}}.