iscc.data.Visium

Visium(count_model='dm', batch_label=None, n_reads=None, spot_pitch=None, spot_radius=None, mu_counts=None, sigma_counts=None, field_lengthscale=None, field_sigma=None, edge_sigma=None, diffusion_sigma=None, sigma_batch=None, ambient_frac=None, kappa=None, nb_dispersion=None, n_spots_x=None, n_spots_y=None, seed=42)

Bases: Assay

Visium spatial assay: lays spots over the section, aggregates cells, applies a VisiumBatch.

Any hyper-parameter below can be overridden explicitly (None keeps the default, which is calibrated to a real 10x Visium section). Legacy aliases are accepted: n_reads maps onto mu_counts, and a spot grid requested via n_spots_x / n_spots_y derives spot_pitch from grid_side at run time. The number of spots (and cells per spot) follows from grid_side (passed to run) and the sampled cell_data, so there is no n_cells.

Parameters:

Name	Type	Description	Default
count_model	str	Final count-emission model: "dm" Dirichlet-multinomial (compositional per-spot capture, the Visium default) or "nb" negative-binomial (independent per-gene).	"dm"
batch_label	str	Section/batch label; defaults to f"visium{seed}".	None
n_reads	float	Legacy alias for mu_counts (mean per-spot library size).	None
spot_pitch	float	Spot centre-to-centre spacing (coordinate units); sets spot density / number of spots. Overridden at run time if n_spots_x / n_spots_y are given.	2.0
spot_radius	float	Spot capture radius: cells within this distance of a spot centre are pooled into it (~1-10 cells / spot).	1.0
mu_counts	float	Mean per-spot library size (total UMIs / spot); ell_s ~ LogNormal(log mu_counts, sigma_counts^2) × capture_field.	20000.0
sigma_counts	float	Per-spot library-size LogNormal sd (spot-to-spot depth variation).	0.45
field_lengthscale	float	Spatial autocorrelation length of the capture-efficiency field (the squared-exponential GP length-scale, in coordinate units); larger -> smoother field -> higher Moran's I.	18.0
field_sigma	float	Capture-field strength (log-space sd of the smooth positive field); 0 -> flat field (no spatial capture bias).	0.70
edge_sigma	float	Tissue-boundary capture falloff: the very edge of the section is reduced by this fraction, the interior stays ~1. 0 disables; a value < 1 keeps efficiency positive.	0.30
diffusion_sigma	float	Lateral mRNA-bleed Gaussian kernel sd, spreading each spot's expression into its neighbours before counting; 0 disables (no bleed).	0.0
sigma_batch	float	Per-gene batch-factor LogNormal sd, shared across spots (Splatter batch.facScale).	0.10
ambient_frac	float	Fraction of each spot's library drawn as ambient "soup" contamination.	0.05
kappa	float	Dirichlet-multinomial concentration (only for count_model="dm"); large -> ~ multinomial, small -> lumpy proportions.	50.0
nb_dispersion	float	Negative-binomial overdispersion phi (var = mu + phi*mu^2; only for count_model="nb").	0.30
n_spots_x	int	Legacy alias: request a fixed spot-grid width. When both n_spots_x and n_spots_y are set, the pitch is derived as grid_side / max(n_spots_x, n_spots_y) at run time instead of using spot_pitch.	None
n_spots_y	int	Legacy alias: request a fixed spot-grid height (see n_spots_x).	None
seed	int	RNG seed. Fixes the technical signature (per-gene batch factor, spatial capture field, per-spot depth) and is reproducible.	42

Methods:

Name	Description
run	Assay a 10x Visium spatial-transcriptomics section over the sampled cells.

run

run(cell_data, grid_side)

Assay a 10x Visium spatial-transcriptomics section over the sampled cells.

Lays out a grid_side x grid_side grid of spots, pools each spot's cells, applies lateral mRNA diffusion and a smooth spatial capture field, and draws per-spot UMI counts.

Parameters:

Name	Type	Description	Default
cell_data	dict	Per-cell ground-truth tables from the sampling stage; uses the expression table cell_exp and the spatial coordinates cell_crd.	required
grid_side	int	Number of spots along each side of the (square) section.	required

Returns:

Type	Description
Visium	self, with the spot-by-gene UMI matrix in spot_counts, spot coordinates in spot_coords, and the per-spot ground-truth/QC table in obs. Call to_anndata or write to export.

Technology presets

Platform	Parameters	Notes
10x Visium	defaults (spot_pitch = 2, spot_radius = 1, mu_counts ≈ 20000)	~55 µm spots, ~1–10 cells / spot.
Visium HD	smaller spot_pitch / spot_radius, lower mu_counts	High-resolution (near-single-cell): many more, smaller spots.