> For the complete documentation index, see [llms.txt](https://help.codex.bio/codex/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.codex.bio/codex/processor/user-instructions/processing-options.md).

# 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)              |

![](/files/-Ly1Cj_UaJPueT52DJ6w)

### 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                                               |

![](/files/-Ly1FL3_hvOpIXFr5T1M)