Cell information not transferred

[roanvanscheppingen]

In CosMx data, the initial file contains a cell_ID column and a cell columns. This cell column is unique over all fovs. Cosmx starts recounting cell IDs per FOV. Hence you can have FOV 3 cell_ID 1 and FOV 10 cell_ID 1. The unique cell denominator helps to differentiate them.

Currently, this data is not transferred onto the transcript_metadata or cell_metadata output of proseg, making it difficult to compare individual cells. This is especially difficult since the centroids seem to shift a little due to the different boundaries and the cell order is not the same. In my output, a cell from fov 43 is now cell 0 of proseg output.

Transferring a column would help to compare cells head-on and make matching easier