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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