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
AI Create Training Set
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
Brightfield Color Deconvolution with PCA
Calculate Simple Crossbleed
Calculate Spatial Moments
Calibration Wizard Parameters
Clear Segmentation Classifiers (Gating)
Close
Copy
Copy ROIs from Other Image
Correct Intensity Jump
Correct Lens Distortion
Count Division and Cell Death
Count Object Colocalization
Create ROI
Create ROI Grid
Create ROIs from Segments
Create Segments from ROIs
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
Find ROIs and Annotations
Fix Vignetting
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 Calibration with known kP - Goldman with Neural Network
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
Ion Concentration Calibration Constants
Ion Concentration Calibration Error Propagation
Ion Concentration Calibration Overrides
Ion Concentration Calibration Wizard Parameters
Lens Correction Optimization
Link
Load and Run Pipeline
Load ROIs
Mask Borders
Mask Frames by Plot Values
Mask Images
Measure Object Intensity
Measure Object Morphology
Mirror or Rotate
Mirror or Rotate in Place (clipping)
Model Out of Focus Blur
Multi-Dimensional Open Information
Multi-Dimensional Open Position
Multi-Dimensional Reload Channel
New Image
New Time Scale
Onset Image
Open File
Optical Flow
Options
Peak Bioenergetic Power Analysis
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 Spectral Parameter with PCA
Plot Spectrum (Periodogram)
Plot Tracking Parameters
Potential calibration constants
Potential calibration error propagation
Potential calibration expert overrides
Projection of Vectors from a Point
Ratio
Ratiometric Ion Concentration with Grynkiewicz Equation - Complete Internal
Ratiometric ROI Classifiers (Gating)
ReCount Division and Cell Death
Reevaluate Segments (Apply Gate)
Remove Blank or Unsharp Frames
Rename
Replace or Modify ROIs
Resample Image
Resize Image
Revvity Harmony Options
ROI Classifiers (Gating)
Run EXE
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 ROI Annotation
Set Scaling/LUT
Set Segmentation Classifiers (Gating)
Set Segmentation Intensity Classifiers (Gating)
Shift Time Scale
Simple 2D Cross-correlation
Simple Segmentation
Skeletonize
Spectral Unmix
Stitch Series
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

TMRM Short Calibration between known baseline and MDC or CDC ( IATMRMShortBaselineMDCorCDC )

Parameters:
Name Short Name Type Description
Range definitions in time courses rangedef string Defines whether the ranges given below refer to frames or seconds in the recordings
Baseline Range BaselineRange string Defines the range of the baseline (in the above defined time units). Longer baseline results more accurate calibration.
VF (mitochondria:cell volume fraction) VF real Confocal stereologic volume fraction of mitochondria (inner boundary membrane) to whole cell (including nucleus)
VFM (matrix:mitochondrion volume fraction) VFM real EM stereologic volume fraction of matrix to mitochondrion (inner boundary membrane)
aR` (matrix:cytosol apparent activity coefficient ratio) aR real Apparent activity coefficient ratio measured by confocal microscopy
ΔψM at baseline (mV) MMP0 real Previously measured value of ΔψM at baseline.
MDC/CDC Range MDCRange string The complete range of Mitochondrial and/or Complete Depolarization Cocktail addition (in the above defined time units). Ideally a range of consecutive additions of MDC and CDC are selected.
Assume equilibrium for MDC/CDC Range AssumeEquilibrium boolean Assumes equilibrium, thus uses DT=0.
kT kT real Previously measured value of kT
fT0-fTX Allowed Range fT0MinusfTXRange string Trace selection criterion: the minimum and maximum allowed value of fT0-fTX
Quality control based on MDC calibrates to zero QCMDC boolean Removes traces where MDC does not calibrate to zero, or noisy. Set threshold below.
Limit smallest offset from zero during MDC (mV) QCMDCdeviation real Traces where the absolute mean of the last third MDC Range is larger than this number are removed. Zero value disables checking. Applied when "Quality control based on MDC calibrates to zero" is enabled.
Limit standard deviation during MDC (mV) QCMDCSD real Traces where the SD of the entire MDC Range is larger than this number are removed. Zero value disables checking. Applied when "Quality control based on MDC calibrates to zero" is enabled.
Description:
This method calculates mitochondrial membrane potential (ΔψM) time course based on previously known baseline potential and kP. The zero point of the calibration is MDC or CDC.
Required experimental protocol: baseline, any time lapse, followed by mitochondrial or complete depolarization,
If the baseline is not steady, use the "Do not assume equilibrium baseline" switch in the Constants tab.