doCellSegmentation#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/cell_segmentation.R#L19

Description#

segment cells in Dapi image

Usage#

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

Arguments#

Argument

Description

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.