clarification on overall method

[kguion1]

Hi,

thanks for a great package! I wanted to clarify your overall method. The resulting image in the shiny app shows one cell per spot (i think), and I wanted to clarify how that specific cell was chosen when in reality there are multiple cells per spot.

Does CellTrek map each cell to a specific spot so that each spot has multiple cells (and then choose one for the shiny app) or does it choose the best cell for each spot and leave many of the single cells without a spatial location?

Any clarification is appreciated!

[WandeRum]

Thank you for asking. The number of cells matched to spots was set to a maximum with spot_n. The mapping was based on an MNN graph with thresholding, thus not all cells will be mapped and not all spots will have cells in the default settings.
We intentionally keep a relatively sparse mapping to control the false positives considering 1) ST has RNA diffusion problems to some degree; 2) not all cells are in the slides (or in other words, the cell distribution of ST might be different from SC).
But you can play around with dist_thresh, spot_n, and intp_pnt to get more cells mapped. Also, trying different repel_r might give you slightly different visualization results.

[kguion1]

Okay, thank you. To clarify, the visualization in the shiny app then selects one cell per spot? even if spot_n is greater than 1?