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

Template Matching ( IATemplateMatching )

Parameters:
Name Short Name Type Description
Algorithm algorithmtype string Name of algorithm to be used for calculating match between template and image.
Result resulttype string Name of results to be returned.
Automatic Scaling autoscale boolean The template is scaled to the image based on x,y resolution data. If no, the scaling factor entered below is used.
Scaling factor scalingfactor real The template is scaled by this number to match the x,y resolution of the image. Applicable if not using automatic scaling. Use 1 for no scaling.
Working image size, exponent of 2 workingsize integer Images will be placed inside a 2^size quadrangular image, shrunken if required. No resizing if zero. Images sized as power of 2 are calculated faster.
Template may hang out of image padimage boolean Pads the image to allow finding template partially out of the image. FUTURE FUNCTION. THIS IS NOT IMPLEMENTED
Interpolation type interpolationtype string Interpolation used for the transformation. Affects the smoothness of the result.
Transform all linked images allinkedimages boolean If yes not just Image A, but all linked images are transformed. Valid only if B is not linked.
Multi frame matching multiframe string The way how image series are handled.
Number of best matches to return nbestmatch integer Multiple, non-overlapping best matches will be returned as an image series, regardless the goodness of the correlation.
Description:
Template Matching: finds a region of Image B that is the most similar to Image A.
Image A: template; Image B: the image where the match for the template is searched. The scaled x,y, size of the image must be bigger than the template.
The primary purpose of this function is to retrieve a matching region of a larger image (B) corresponding to the smaller image (template, A).Images of different magnification can be used. Images are scaled automatically according to image calibration, or by the "Scaling factor".
The best match is returned. The following results can be obtained:
"Image with ROI": The match is marked by an ROI in image B. The output is Image B.
"Cropped Image": The best match is scaled to the size of the template and returned as output as a new image. If "Transform all linked images" is selected, the same position in all linked channels is cropped, descaled and returned as new image windows linked to the output.
"Correlation Image": The output is a correlation image sized like Image A, where high pixel values mark centers of regions similar to the template.
The "Multi frame matching" parameter sets how image series of templates should behave. The "Repeated for all template frames" option results a ROI in B for each frame in A, or a cropped image series where each frame is the most similar part of image B, corresponding to each frame of A. For Image B always the actual frame is taken.
WARNING: Transforming all linked images is not parallel processing aware, so it requires proper pipeline design to prevent collision of this process with others. In such case use the "Wait for all inputs" function. To find multiple matches select "Correlation Image", and perform maximum search using image Segmentation, marking seeds.