> 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/fcs-format.md).

# FCS Format

To facilitate the use of outside analysis tools, processor outputs FCS files that Multiplex Analysis Viewer requires. Equivalent CSV files are written out in the same folder.

| Header                        | Description                                                                                             |
| ----------------------------- | ------------------------------------------------------------------------------------------------------- |
| cell\_id:cell\_id             | Cell ID unique to experiment                                                                            |
| region:region                 | Region 1-index within the experiment                                                                    |
| tile\_num:tile\_num           | Tile 1-index within the corresponding region                                                            |
| x:x                           | Location of cell center, 0 to tileWidth \* regionWidth                                                  |
| y:y                           | Location of cell center, 0 to tileHeight \* regionHeight                                                |
| z:z                           | Location of cell center, 0 to numZSlices                                                                |
| x\_tile:x\_tile               | Location of cell center within the corresponding tile, 0 to tileWidth                                   |
| y\_tile:y\_tile               | Location of cell center within the corresponding tile, 0 to tileHeight                                  |
| size:size                     | Number of voxels within the segmented cell                                                              |
| cyc001\_ch001:\<marker\_name> | Integrated pixel intensity of all voxels within the segmented cell, can be compensated or uncompensated |
| ...                           | ...                                                                                                     |
| tsne\_x:tsne\_x               | t-SNE x coordinate unique to region                                                                     |
| tsne\_y:tsne\_y               | t-SNE y coordinate unique to region                                                                     |
| homogeneity:homogeneity       | <p>A measure of expression homogeneity.<br>sum(expression) / sqrt(sum(expression^2))</p>                |


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