1. What mcDETECT expects

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1.1 Platform type

Value	Use case
"discrete"	Z is a small set of optical planes (MERSCOPE, CosMx). Unique global_z values define the internal z-grid.
"continuous"	Z is continuous (e.g. Xenium).

MERSCOPE: use "discrete".

1.2 Transcript table (pandas.DataFrame)

Each row is one transcript. The detector relies on:

Column	Role
global_x, global_y, global_z	Spatial coordinates (same units as eps, grid_len, sphere radii).
target	Gene name string; granule markers must appear here and in gnl_genes.
overlaps_nucleus	Boolean or 0/1; used to compute in-soma ratio per sphere.
cell_id	Optional; if you set record_cell_id=True in dbscan / detect, each sphere gets a modal cell_id.

Negative controls are passed as nc_genes and matched via target when filtering is enabled.

Next: Step A — Construct mcDETECT