parameters.default: Default parameters list for Cell-ID

In gerbeldo/tidycell: CellID Data Analysis Inside the Tidyverse

Default parameters list for Cell-ID

Description

Returns a list of key-value pairs, for the default Cell-ID parameters.

Usage

parameters.default(
  max_split_over_minor = 0.5,
  max_dist_over_waist = 8,
  max_pixels_per_cell = 2000,
  min_pixels_per_cell = 75,
  background_reject_factor = 0.75,
  tracking_comparison = 0.2,
  align_individual_cells = F,
  align_fl_to_bf = T,
  image_type = "brightfield",
  bf_fl_mapping = "list"
)

Arguments

max_split_over_minor	To-do: document or link to explanation.
max_dist_over_waist	To-do: document or link to explanation.
max_pixels_per_cell	To-do: document or link to explanation.
min_pixels_per_cell	To-do: document or link to explanation.
background_reject_factor	To-do: document or link to explanation.
tracking_comparison	To-do: document or link to explanation.
align_individual_cells	To-do: document or link to explanation.
align_fl_to_bf	To-do: document or link to explanation.
image_type	To-do: document or link to explanation.
bf_fl_mapping	To-do: document or link to explanation.

Details

Documentation for each parameter can be found at: https://github.com/darksideoftheshmoo/cellID-linux#parameters

Boolean values are for "flag" type parameters which enable a feature when present (eg. "align_fl_to_bf"), or, if absent, indicate default behavior.

Other parameters have values which must end up separated from names by a space " " in the parameters.txt file format that Cell-ID uses:

max_split_over_minor 0.5
max_dist_over_waist 8
max_pixels_per_cell 2000
min_pixels_per_cell 75
background_reject_factor 0.75
tracking_comparison 0.2
align_fl_to_bf
image_type brightfield
bf_fl_mapping list

Value

A nice list of parameters.

See Also

parameters.write, arguments

gerbeldo/tidycell documentation built on Aug. 15, 2022, 2:35 p.m.