calibrate: Calibrate cropping and rotation parameters
In EricEdwardBryant/screenmill: Tools for working with ScreenMill data

Description Usage Arguments Details

View source: R/calibrate.R

This function calibrates plate cropping and rotation parameters for an image with an arbritrarily sized grid of plates.

calibrate(
  dir = ".",
  grid_rows,
  grid_cols,
  rotate = 90,
  range = 2,
  thresh = 0.03,
  invert = TRUE,
  rough_pad = c(0, 0, 0, 0),
  fine_pad = c(0, 0, 0, 0),
  default_crop = NULL,
  overwrite = FALSE,
  display = TRUE,
  save_plate = !display,
  colony_radius = 1,
  max_smooth = 5
)

`dir`	Directory of images to process.
`grid_rows`	Number of expected rows in colony grid.
`grid_cols`	Number of expected columns in colony grid.
`rotate`	A rough angle in degrees clockwise to rotate each plate. The rotation angle will be further calibrated after applying this rotation. Defaults to `90`.
`range`	Range to explore (in degrees) when calibrating rotation angle. Defaults to `2`.
`thresh`	Fraction of foreground pixels needed to identify plate boundaries when rough cropping. Defaults to `0.03`.
`invert`	Should the image be inverted? Defaults to `TRUE`. Recommended `TRUE` if colonies are darker than the plate.
`default_crop`	If not `NULL` then use this dataframe as the default crop coordinates.
`overwrite`	Should existing crop calibration be overwritten? Defaults to `FALSE`.
`display`	Should cropped images be displayed for review? Defaults to `TRUE`.
`save_plate`	Should the calibrated plate be saved rather than displayed (useful when calibrating many plates)? Defaults to `!display`.
`colony_radius`	If <= 1, the box drawn around colonies will be this fraction of half the average distance between rows and columns (Defaults to 1). If > 1, the box will have a radius of this many pixels.
`max_smooth`	Maximum number of pixels to allow when smoothing row and column positions of individual colonies.

Crop calibration procedes through the following 3 steps:

Rough crop
Rotate
Fine crop

Rough cropping relies on high contrast between plates. If invert = TRUE plates should be light and the region between plates should be dark, and vice versa if invert = FALSE.

Fine cropping finds the nearest object edge (problematic for plates without any growth on the intended grid edges).

EricEdwardBryant/screenmill documentation built on March 13, 2020, 1:07 p.m.