Processing Options
Processing options can be found in the main tab.
Background Subtraction
Enable auto-fluorescence subtraction using "blank" cycles
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
Enable t-SNE calculation (may take 15% longer)

Advanced Processing Options

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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