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
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Correct Lens Distortion
Count Division and Cell Death
Count Object Colocalization
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Create ROIs from Segments
Crop
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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
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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)
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Multi-Dimensional Open Information
Multi-Dimensional Open Stage Position
Multi-Dimensional Reload Channel
New Image
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Onset Image
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Optical Flow
Options
Pipeline
Pipeline Optimization
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Plot
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Plot Ratio
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Projection of Vectors from a Point
Ratio
Ratiometric ROI Classifiers
ReCount Division and Cell Death
Reevaluate Segments
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Rename
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ROI Classifiers
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Scalar Arithmetic (image-value math)
Scalar Arithmetic Multi
Secondary Watershed Segmentation
Select
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Sensor Noise Characteristics
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Set Segmentation Intensity Classifiers
Shift Time Scale
Simple 2D Cross-correlation
Simple Segmentation
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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

Thinness Ratio Optimization ( IATROptimize )

Parameters:

Name	Short Name	Type	Description
LBP minimum cut on ω	lmin	real	Cut on ω of the Low band pass Butterworth filter
LBP maximum cut off ω	lmax	real	Cut off ω of the Low band pass Butterworth filter
HBP minimum cut on ω	hmin	real	Cut on ω of the High band pass Butterworth filter
HBP maximum cut off ω	hmax	real	Cut off ω of the High band pass Butterworth filter
HBP cut on ω > LBP cut off ω	largerHBP	boolean	If Yes then the filter transmissions cannot overlap.
Spatial freq. (ω) unit	units	string	Sets the units of the above given ω values.
Order minimum	ordmin	real	Order of Butterworth filter
Order maximum	ordmax	real	Order of Butterworth filter
Filter normalization	normalization	string	Normalizes filter coefficients to keep an integral of 1 for the 1D or 2D filter function
Test ROI	roi	integer	Reads intensities from this ROI for the test
Number of baseline frames	baseline	integer	The image series consists of the given number of baseline frames followed by the given number of treated frames. This can be repeated any time in this order with the same number of frames.
Number of treatment frames	treatment	integer	The image series consists of the given number of baseline frames followed by the given number of treated frames. This can be repeated any time in this order with the same number of frames.
Direction of change	direction	string	Whether to look for an increasing or a decreasing signal
Use Mask	usemask	boolean	Whether to mask the filtered images with the mask image given above
Preserve edges	edges	boolean	Performs mirrored tiling to prevent edge artifacts. Slows down processing by 4x.
Enlarge paper	enlarge	boolean	Enlarges image by mirrored tiling to quadrangular. Prevents edge artifacts and distortions from non-quadrangular images.
Enlarge to 2^	enlargeto	integer	Size of image during filtering as power of 2.
Leave only phase	phase	boolean	Sets complex amplitudes in Fourier space to 1 keeping their original arc.
Absolute	absolute	boolean	Calculates absolute value after filtering. Required for intensity measurements on high pass and band pass filtered images.
Protect MASK	protectmask	boolean	Fills up masked areas and undetermined pixel values with zeros before processing. Required for masked images.

Description:

Thinness Ratio Filter Pair Optimization.
The Low Frequency band pass (LBP) and High Frequency band pass (HBP) filters are searched between the given cut on and cut off range. These filters are Butterworth band pass filters, and for simplicity all cut ons and cut offs have the same order which is sought between the "Order minimum" and "Order maximum".
The Thinness Ratio (TR) is calculated within the Test ROI. The basis of optimization is the comparison the TR in the baseline frames and the treatment frames. Given number of treatment frames follow the given number of baseline frames, and t-test is used to compare baseline and treatment TR values. The most significant change to the "Direction of change" is taken as the best filter pair.
Edge artifacts could be avoided by tiling a larger image with the original in a symmetric, thus periodic manner. To protect edges use "Preserve edges" when an image is quadrangular and size of power of 2.
Non-quadrangular images are unevenly filtered in x and y directions, therefore use "Enlarge paper" to tile a larger quadrangular image before filtering.
"Preserve edges" and "Enlarge paper" do not change the size or spatial calibration of the resultant image, the result is obtained by cropping the enlarged image to the original size. Fourier transformation is incompatible with masking (pixels without a real value), therefore the mask has to be filled up with zeros "Protect MASK" before filtering.