doCellSegmentation: doCellSegmentation

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

doCellSegmentation

Description

segment cells in Dapi image

Usage

doCellSegmentation(
  raster_img,
  folder_path,
  reduce_resolution = 4,
  overlapping_pixels = 50,
  python_path = NULL
)

Arguments

raster_img	raster image; Dapi image of cells
folder_path	character; where to save the file
reduce_resolution	numeric; the original Dapi image from Vizgen works better in the Mesmer algorithm if its resolution is reduced 4 times.
overlapping_pixels	numeric; the number of pixels to overlap when calculating the rolling window
python_path	specify specific path to python if required

Details

This function is a wrapper for the Mesmer algorithm implemented in python. It segments the cells in tissue by applying a rolling window on the complete image. It saves all the files in the specified folder with the coordinates of the tile: sx (start x), ex (end x), sy, and ey.

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.