> 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/technical-notes.md).

# Technical Notes

- [Expected Input](https://help.codex.bio/codex/processor/technical-notes/expected-input.md)
- [Expected Output](https://help.codex.bio/codex/processor/technical-notes/expected-output.md)
- [Cycle Alignment](https://help.codex.bio/codex/processor/technical-notes/cycle-alignment.md)
- [Background Subtraction](https://help.codex.bio/codex/processor/technical-notes/background-subtraction.md)
- [Deconvolution](https://help.codex.bio/codex/processor/technical-notes/deconvolution.md)
- [Extended Depth of Field](https://help.codex.bio/codex/processor/technical-notes/extended-depth-of-field.md)
- [Shading Correction](https://help.codex.bio/codex/processor/technical-notes/shading-correction.md)
- [Tile Registration](https://help.codex.bio/codex/processor/technical-notes/tile-registration.md)
- [Segmentation & Spillover](https://help.codex.bio/codex/processor/technical-notes/segmentation-and-spillover.md)
- [t-SNE](https://help.codex.bio/codex/processor/technical-notes/t-sne.md)
- [FCS Format](https://help.codex.bio/codex/processor/technical-notes/fcs-format.md)