process_img_dir: Process a folder of images

In ajfedorec/plateR:

Process a folder of images

Description

Process a folder of images

Usage

process_img_dir(
  dir_path,
  align_filename,
  invert = F,
  rotate = F,
  experiment_type = "colony",
  normalise = F,
  stencil_proportion = 1,
  proportion_centered = T,
  plate_type = "6-well",
  num_wells = 384,
  px_per_mm = NA,
  tl_corner = NA,
  well_ratio = NA,
  deg_rotation = NA,
  in_parallel = FALSE,
  blur = NA,
  img_settings_list,
  log_file = NA
)

Arguments

dir_path	path to directory containing plate images (.png images only)
align_filename	filename of image used to align well grid
invert	Boolean flag. Set to TRUE if the plate is inverted in the imager
rotate	Boolean flag. Set to TRUE if the images are upside-down i.e. row A on bottom of image
experiment_type	"colony" or "lawn"
normalise	Attempts to remove background. Negates pixel values in the first iteration of images, from all images.
stencil_proportion	Proportion of pixels covered by stencil to take values from.
proportion_centered	Boolean flag. If true discards the top and bottom "stencil_proportion/2" brightest pixels. If false, takes "stencil_proportion" brightest for blue panel or darkest for red panel.
plate_type	"6-well" or "1-well"
num_wells	Plate size used for output positions: 96, 384 or 1536
px_per_mm	If you already know the "px_per_mm" value (from previous alignment)
tl_corner	If you already know the "tl_corner" values (from previous alignment)
well_ratio	Proportion of space taken up by each "well". Can be scaled interactively.
deg_rotation	If you already know the "deg_rotation" values (from previous alignment)
in_parallel	process images in parallel (only available for R >= 4.0)
blur	Apply a Gaussian filter to blur the image. If NA, no blur is applied. If numeric, the value is used as the sigma for the Gaussian filter.
img_settings_list	a list of named vectors with meta-data for images in the order they were taken i.e."img_settings_list = list(c(panel="blue", exposure=20000, intensity=1),c(panel="red", exposure=4000, intensity=0.7))"

ajfedorec/plateR documentation built on April 25, 2022, 2:16 a.m.