keep_cells {synapsis}R Documentation

keep_cells

Description

Deletes objects in mask which are too small, large, oblong i.e. unlikely to be a cell

Usage

keep_cells(
  candidate,
  max_cell_area,
  min_cell_area,
  cell_aspect_ratio,
  crowded_cells,
  annotation
)

Arguments

candidate

Mask of individual cell candidates

max_cell_area,

Maximum pixel area of a cell candidate

min_cell_area,

Minimum pixel area of a cell candidate

cell_aspect_ratio

Maximum aspect ratio of blob to be defined as a cell

crowded_cells

TRUE or FALSE, defaults to FALSE. Set to TRUE if you

annotation,

Choice to output pipeline choices (recommended to knit) have many cells in a frame that almost touch

Value

Mask of cell candidates which meet size criteria


[Package synapsis version 1.0.0 Index]