cellSpreading: cellSpreading

In SFB-ELAINE/cellPixels: Detect nuclei (and cells) and count pixel intensities in these regions

cellSpreading

Description

Main function for counting pixels in different regions

Usage

cellSpreading(
  input_dir = NULL,
  nucleus_color = "blue",
  cell_body_color = "red",
  number_of_pixels_at_border_to_disregard = 3,
  use_histogram_equalized = FALSE,
  normalize_nuclei_layer = FALSE,
  magnification_objective = NULL,
  apotome_section = FALSE,
  blur_sigma = NULL,
  thresh_w_h_nuc = NULL,
  thresh_offset = NULL,
  number_size_factor = 1,
  add_scale_bar = FALSE
)

Arguments

input_dir	A character (directory that contains all images)
nucleus_color	A character (color (layer) of nuclei)
cell_body_color	A character (color (layer) of cell body)
number_of_pixels_at_border_to_disregard	A number (number of pixels at the border of the image (rows and columns) that define the region where found cells are disregarded)
use_histogram_equalized	A boolean (use histogram equalized images for everything)
normalize_nuclei_layer	A boolean (state whether nucleus layer should be normalized)
magnification_objective	A number (magnification of objective if not given in metadata or if metadata is wrong)
apotome_section	A boolean (TRUE is sectioned image shall be used)
blur_sigma	A number (blurring factor)
thresh_w_h_nuc	A number (width and heigth for thresholding)
thresh_offset	A number (offset for thresholding)
number_size_factor	A number (factor to resize numbers for numbering nuclei)
add_scale_bar	A logic (add scale bar to all images that are saved if true)

Details

Input should be czi or tif-format with dim(z)>=1. We are trying to identify different cells by using nuclei and Actin layers.

Author(s)

Kai Budde

SFB-ELAINE/cellPixels documentation built on Oct. 12, 2024, 8:45 p.m.