Colon Spatial Transcriptomics Scale Factors

Source: R/data.R

Scale factors for the colon Visium example dataset

st_scalefactors

Format

A list containing:

spot_diameter_fullres

Spot diameter in full resolution pixels (~130)

tissue_hires_scalef

Scale factor for high-res image (~0.12)

tissue_lowres_scalef

Scale factor for low-res image (~0.037)

spot_diameter_um

Spot diameter in micrometers (55 um)

pixels_per_um

Pixels per micrometer (~2.37)

Details

These scale factors are essential for converting between pixel coordinates and physical distances (micrometers). The standard Visium spot diameter is 55 um, which is used to calculate the pixels_per_um conversion factor.

For spatial communication analysis, distances should be converted to micrometers to enable biologically meaningful distance thresholds.

See also

st_expr, st_meta

Examples

# \donttest{
data(st_scalefactors)

# Convert pixel distance to micrometers
pixel_distance <- 500
um_distance <- pixel_distance / st_scalefactors$pixels_per_um
cat("Distance:", um_distance, "um\n")
#> Distance: 211.1615 um
# }