cell.load.alt: Cargar el output de cell-id

In gerbeldo/tidycell: CellID Data Analysis Inside the Tidyverse

Cargar el output de cell-id

Description

Cargar el output de cell-id

Usage

cell.load.alt(
  path,
  pdata = NULL,
  position.pattern = ".*Position(\\d+).*",
  fluorescence.pattern = "^([GCYRT]FP|[GCYRT]\\d{2})_Position\\d+_time\\d+.tif$",
  ucid.zero.pad = 4,
  append.posfix = NULL,
  ...
)

Arguments

path	Path to images directory
pdata	Path to metadata CSV file
position.pattern	Regex describing what the position string looks like (default ".*Position(\d+).*") including a capturing group for the position ID number (coerced to integer).
fluorescence.pattern	Regex describing what the fluorescence/channel ID string looks like (default "^([GCYRT]FP|[GCYRT]\d2)_Position\d+_time\d+.tif$")
ucid.zero.pad	Amount of decimal digits for the cellID (defaults 4, corresponding to a maximum of 9.999 cellIDs and 9999 positions).
append.posfix	String appended to the channel ID extracted by 'fluorescence.pattern' ('NULL' by default, but "FP" is usual).
...	Arguments passed on to cargar.out_all. Patterns for "out" files, fluorescence channel, and other options may be changed here.

Value

A list of dataframes: data (CellID data), images (images metadata and paths), image_maping (extra mapping metadata from CellID: BF to FL correspondence, channel flag, bf_as_fl flag, and one-letter channel encoding).

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