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