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Processing Options

Processing options can be found in the main tab.
Name
Details
Background Subtraction
Enable auto-fluorescence subtraction using "blank" cycles
Deconvolution
Enable deconvolution which can reduce out of focus light
Extended Depth of Field
Enable collapse of a z-stack into a single best focus image
Shading Correction
Enable correction for optical shading or vignetting
Diagnostic output
Enable output of additional diagnostic images
t-SNE
Enable t-SNE calculation (may take 15% longer)
Advanced Processing Options
Name
Details
Reference Cycle
Reference marker to be used for cycle alignment
Reference Channel
​Reference marker to be used for cycle alignment
3D Cycle Alignment
Disable to lock cycles in the z-axis during alignment
Blind Deconvolution
Unnecessary for typical 20x air imaging
Deconvolution Iterations
For advanced users; non-default values may degrade image quality
Deconvolution Model
For advanced users
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Quick Start

Segmentation Options

Last modified 3yr ago

Name	Details
Background Subtraction	Enable auto-fluorescence subtraction using "blank" cycles
Deconvolution	Enable deconvolution which can reduce out of focus light
Extended Depth of Field	Enable collapse of a z-stack into a single best focus image
Shading Correction	Enable correction for optical shading or vignetting
Diagnostic output	Enable output of additional diagnostic images
t-SNE	Enable t-SNE calculation (may take 15% longer)

Name	Details
Reference Cycle	Reference marker to be used for cycle alignment
Reference Channel	Reference marker to be used for cycle alignment
3D Cycle Alignment	Disable to lock cycles in the z-axis during alignment
Blind Deconvolution	Unnecessary for typical 20x air imaging
Deconvolution Iterations	For advanced users; non-default values may degrade image quality
Deconvolution Model	For advanced users