Preprocessing the the spatial experiment data for SimpleSeg output.

Preprocessing the the spatial experiment data for SimpleSeg output.

readSimpleSeg(
  spe,
  mask,
  img_id = "imageID",
  cell_id = "cell_id",
  use_BPPARAM = BiocParallel::SerialParam(),
  method_name = "SimpleSeg",
  verbose = TRUE
)

Arguments

spe

A Spatial Experiment object for multiple image ID

mask

The mask results from simpleSeg

img_id

A string indicates the image ID column in SpatialExperiment object.

cell_id

A string indicates the cell ID column in SpatialExperiment object.

use_BPPARAM

BiocParallelParam instance.

method_name

A string indicates the method name of the cell segmentation.

verbose

A logical value indicates whether to print out running messages.