Calculate the baseline metrics of cell from cell segmentation output

Calculate the baseline metrics of cell from cell segmentation output

calBaselineAllMetrics(
  spe,
  metrics = c("total_transciprts", "total_genes", "total_cells", "meanExprsPct_cells",
    "cell_area", "elongation", "compactness", "eccentricity", "sphericity", "solidity",
    "convexity", "circularity", "density"),
  use_BPPARAM = BiocParallel::SerialParam(),
  rerun = TRUE,
  verbose = TRUE
)

Arguments

spe

A Spatial Experiment object

metrics

A character vector indicating the metrics to be calculated

use_BPPARAM

a BiocParallelParam instance determining the parallel back-end to be used during evaluation.

rerun

A logical value indicates whether to recalculate existing metrics.

verbose

A logical value indicates whether to print out running messages.

Value

A SpatialExperiment object