cellPixels: cellPixels

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

cellPixels

Description

Main function for counting pixels in different regions

Usage

cellPixels(
  input_dir = NULL,
  apotome = FALSE,
  apotome_section = FALSE,
  nucleus_color = "blue",
  min_nucleus_size = NULL,
  min_cytosol_size = NULL,
  protein_in_nucleus_color = "none",
  protein_in_cytosol_color = "none",
  protein_in_membrane_color = "none",
  number_size_factor = 0.2,
  bit_depth = NULL,
  number_of_pixels_at_border_to_disregard = 3,
  add_scale_bar = FALSE,
  thresh_w_h_nucleus = NULL,
  thresh_w_h_cytosol = NULL,
  thresh_w_h_protein_in_nucleus = NULL,
  thresh_offset_nucleus = NULL,
  thresh_offset_protein_in_nucleus = NULL,
  thresh_offset_protein_in_cytosol = NULL,
  blur_sigma = NULL,
  use_histogram_equalized = FALSE,
  metadata_file = NULL,
  normalize_nuclei_layer = FALSE,
  magnification_objective = NULL
)

Arguments

input_dir	A character (directory that contains all images)
apotome	A boolean (TRUE if Apotome was used)
apotome_section	A boolean (TRUE is sectioned image shall be used)
nucleus_color	A character (color (layer) of nuclei)
min_nucleus_size	A number (minimum size in pixels of nuclei to be kept)
min_cytosol_size	A number (minimum size in pixels of cytosol to be kept)
protein_in_nucleus_color	A character (color (layer) of protein expected in nucleus)
protein_in_cytosol_color	A character (color (layer) of protein expected in cytosol)
protein_in_membrane_color	A character (color (layer) of protein expected in membrane)
number_size_factor	A number (factor to resize numbers for numbering nuclei)
bit_depth	A number (bit depth of the original czi image)
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)
add_scale_bar	A logic (add scale bar to all images that are saved if true)
thresh_w_h_nucleus	A number (width and height of moving rectangle for nucleus detection)
thresh_w_h_cytosol	A number (width and height of moving rectangle for cytosol detection)
thresh_w_h_protein_in_nucleus	A number (width and height of moving rectangle for protein in nucleus detection (different from detecting nuclei themselves))
thresh_offset_nucleus	A number (threshold for finding nuclei)
thresh_offset_protein_in_nucleus	A number (threshold for determining "positive" cells containing a certain protein in nucleus area)
thresh_offset_protein_in_cytosol	A number (threshold for determining "positive" cells containing a certain protein in cytosol area)
metadata_file	A character (file with meta data if tifs are used)
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)

Details

Input should be czi or tif-format with dim(z)>=1. We are counting the intensities of pixels of different color within and outside of the nuclei. We also add information about the entire image.

Author(s)

Kai Budde

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