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