#  Supplemental Metadata Descriptions

## HMBA Spatial Basal Ganglia data supplemental columns

Below we list column names and descriptions for the columns available in the
cell_supplemental_metadata table for the species in the spatial BG dataset.
The cell_metadata tables includes a the column
- 'qc_pass': aggregate of any/all QC metrics used to filter out low-quality cells

Additionally in the slab_plane_coordinates table the additional columns
['x_rotated_um', 'y_rotated_um']: Unofficial transformation of ['x', 'y'] that uses a manual midline annotation to correctly orient each section (dorsal up; midline left). These are retained for context
however, users should use the `x/y_slab_mm` coordinates which line up with the manually annotated polygons.

- All species
    - 'total_counts': detected counts of all spots, includes both genes and any control probes or codewords (controls differ slightly between MERSCOPE and Xenium platforms; see individual species for breakdown)
    - 'total_counts_genes': detected counts of gene transcripts
- Human (H22.30.001) & Macaque (QM23.50.001):
    - ['total_counts_Blank', 'pct_counts_Blank']: control for MERSCOPE platform
    - 'n_genes_by_counts': number of unique genes per cell
    - ['doublet_singlet_score_diff', 'doublet_diff_threshold']: parameters related to SOLO doublet detection
    - ['blanks_filter', 'genes_filter', 'counts_filter', 'doublets_filter']: QC pass boolean for each metric
    - 'qc_pass_and_singlet': boolean describing if a cell passed QC AND was predicted to be a singlet. Not usually used, but could be useful to have in the future.
- Macaque (QM23.50.001):
    - ['incongruous_genes_pct', 'incongruous_pairs_pct']: Segmentation QC metric on manually defined genes that shouldn't be expressed together
- Marmoset (CJ23.56.004):
    - ['total_counts_control_probe', 'total_counts_genomic_control', 'total_counts_control_codeword', 'total_counts_unassigned_codeword', 'total_counts_deprecated_codeword']: controls for Xenium platform
    - ['cell_area', 'nucleus_area', 'nucleus_count']: additional metadata generated by cell segmentation
    - 'segmentation_method': specifies which stain or method was used by the 10X Cell Segmentation Kit algorithm; categories include    ['Segmented by boundary stain (ATP1A1+CD45+E-Cadherin)', 'Segmented by interior stain (18S)', 'Segmented by nucleus expansion of 5.0µm']