generate_spix: Generate super pixels from ST

In patrickCNMartin/Vesalius: Vesalius: Dissecting Tissue Anatomy from Spatial Transcriptomic Data

Generate super pixels from ST

Description

Generate super pixels from ST

Usage

generate_spix(
  vesalius_assay,
  dimensions = seq(1, 3),
  embedding = "last",
  method = "kmeans",
  col_resolution = 10,
  compactness = 1,
  scaling = 0.5,
  threshold = 0.9,
  index_selection = "bubble",
  verbose = TRUE
)

Arguments

vesalius_assay	a vesalius_assay object
dimensions	numeric vector of latent space dimensions to use.
embedding	character string describing which embedding should be used.
method	character string for which method should be used for segmentation. Select from "slic", "leiden_slic","louvain_slic"
col_resolution	numeric colour resolution used for segmentation. (see details)
compactness	numeric - factor defining super pixel compaction.
scaling	numeric - scaling image ration during super pixel segmentation.
threshold	numeric [0,1] - correlation threshold between nearest neighbors when generating segments from super pixels.
verbose	logical - progress message output.
k	numeric - number of closest super pixel neighbors to consider when generating segments from super pixels

Value

a vesalius_assay object

patrickCNMartin/Vesalius documentation built on April 17, 2025, 11:31 p.m.