# 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)              |

![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-Ly180Y2WFVH7ZiNRzmT%2F-Ly1Cj_UaJPueT52DJ6w%2F2019-12-17%2009_46_21-CODEX%20Processor%201.7.0.0-WONMEAN-DESKTOP%20-%20Copy%20\(3\).png?alt=media\&token=3c1a9643-110a-4cec-9e3b-dcd82d08a0b4)

### 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                                               |

![](https://1268872846-files.gitbook.io/~/files/v0/b/gitbook-legacy-files/o/assets%2F-LWT7bo4Xbl2jOnmH1yB%2F-Ly1EThTS2Y8NtslAqe3%2F-Ly1FL3_hvOpIXFr5T1M%2F2019-12-17%2009_46_25-CODEX%20Processor%201.7.0.0-WONMEAN-DESKTOP.png?alt=media\&token=0a587683-92ed-472c-9f75-6da83161dc73)


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