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

Threshold ( IAThreshold )

Parameters:
Name Short Name Type Description
Threshold value calculation method type string How is the threshold level calculated: "Pixel value", "Percentile by frames", "Percentile by series", "Percentile by reference", "Otsu by frames", "Otsu by series", "Otsu by reference"
Way way string How is the image modified at the threshold level: Setting values to 1 "Above" or "Below" value; or clipping at "Ceiling" or "Bottom"; or masking by "Mask Above", "Mask Below".
Value value real Pixel value, percentile, or factor times Otsu optimal threshold value (typically 1)
Determine boundaries at value2 real This is added to "value" when determining the boundary of local maxima/minima or the boundary is calculated at the given percent of each local maximum when Bound Maxima/Minima locally is selected below.
Threshold from local max/min type proctype string This enables local maximum or minimum search. Set "None" for simple thresholding. Available types: "Bound Maxima uniformly", "Bound Minima uniformly", "Bound Maxima locally", "Bound Minima locally".
Keep original mask keeporigmask boolean Originally masked areas are kept masked if Yes. Otherwise the mask will take zero, ceiling or bottom value.
Description:
Binarizes, masks or clips (ceilings/bottoms) the image at a given or calculated threshold value.
Above sets pixels greater or equal the threshold to 1, while below sets pixels smaller or equal the threshold to 1, the remaining pixels are set to 0.
Ceiling sets pixels greater or equal the threshold to the threshold value, while bottom sets pixels smaller or equal the threshold to the threshold value, the remaining pixels are unaffected.
Mask Above and Mask Below do not binarize the image, but sets corresponding pixels to MASK value.
The Otsu method calculates optimal threshold value. Optionally percentile or Otsu optimal threshold value is calculated from a reference image. To this end set an identical x,y sized image with identical channel number as Histogram reference image using the context menu.
Threshold from local max/min: "None" calculates simple threshold according to the threshold value, "Bound uniformly" calculates segment boundary with morphological reconstruction using a cap value given by the threshold value plus the "Determine boundaries at" value. Bound locally will bound local maxima at their given percent compared to the minimum or maximum of the image.
Determine boundaries at: when "Bound uniformly" is selected above, given in the same units and additive to the threshold value, and sets how far from the local maximum will the boundary of the object drawn. When "Bound locally" is selected, it is a value in percents of local maximum or minimum.
In practice, when local thresholding is used (for maxima) objects brighter than the local background by threshold value will be resulted. Using the "Determine boundaries at" value, the object boundaries can be extended or shrunken. When using "Bound locally" the boundaries are not determined by the threshold level, but taken individually for each local maximum or minimum.
Constraints: Ceiling or Bottom used together with "Bound locally" will ceiling for maxima and bottom for minima at the given percent of the local maximum. Ceiling and bottom are not available for "Bound uniformly" and for "Markers" and above or below thresholding is used instead.
Preexisting masks are kept as mask for Above and Below ways if "Keep original mask" is disabled.