gitter: Process a single plate image

In omarwagih/gitter: Quantification of Pinned Microbial Cultures

Process a single plate image

Description

The following function will grid and quantify a single plate image (for batch processing, see gitter.batch)

Usage

gitter(
  image.file = file.choose(),
  plate.format = c(32, 48),
  remove.noise = F,
  autorotate = F,
  inverse = F,
  image.align = T,
  verbose = "l",
  contrast = NULL,
  fast = NULL,
  plot = F,
  grid.save = getwd(),
  dat.save = getwd(),
  start.coords = NULL,
  increment.coords = NULL,
  dilation.factor = 0,
  .fx = 2,
  .is.ref = F,
  .params = NULL
)

Arguments

image.file	The path to the image. Defaults to a file choosing dialog.
plate.format	The plate format, accepted formats: 1536, 768, 384 and 96. Alternatively, you can provide the number of rows and columns on the plate as an integer vector for example c(32,48). Default is 1536.
remove.noise	Logical indicating noise/speckles should be remove from the thresholded image prior to analysis. Default is FALSE.
autorotate	Logical indicating if image should be auto-rotated prior to processing. Only select this option if image is extremely rotated. gitter is able to handle small variations in rotations (1-2 degrees) without auto-rotating. Default is FALSE.
inverse	Logical indicating if input image is inverted, meaning colonies are darker compared to their background. Default is FALSE.
image.align	Used when reference image is provided. Logical indicating if images should be aligned to reference. This corrects small camera shifts.
verbose	Shows details about the results of running job. For detailed logs "l", for a progress bar "p" or for no output "n". Default is "l".
contrast	Integer between 1 and 100 indicating how much contrast should be applied to the image, prior to processing. A value of NULL will not apply any contrast. Default is NULL.
fast	If set to integer value, the image will be resized to this width in pixels to speed up computation. This is useful for very large images that otherwise take a long time to process. We do not recommend resizing to fewer than 1500 pixels or greater that 4000 pixels in width. Default is NULL.
plot	Logical indicating whether intensity profiles should be plotted. Default is FALSE.
grid.save	Directory path to save gridded/thresholded images. Set to NULL if you do not want gridded images saved to disk. Default is the current working directory.
dat.save	Directory path to save resulting data files. Set to NULL if you do not want resulting data saved to disk. Default is the current working directory.
start.coords	Allows the user to specify a grid manually. This is a vector of length two with x,y coordinates of the top left most spot. Must be set in conjunction with increment.coords. By default grid is auto-detected.
increment.coords	Allows the user to specify a grid manually. This is a vector of length two with distances between colonies on the x-axis and y-axis. Must be set in conjunction with start.coords. By default grid is auto-detected.
dilation.factor	If specified, colonies will be dilated using a kernel of this size in pixels (value must be an odd number and >= 3). This dilation is only for fitting boundaries and will not be applied for counting colony pixels. This option is useful for spotted colonies, which are difficult to grid. By default, factor is 0 and no dialation is applied. See https://homepages.inf.ed.ac.uk/rbf/HIPR2/dilate.htm for more info.
.fx	If the central pixel is a zero, set constant boundary with with size of this value
.is.ref	Specifies if a reference property list is supplied. Warning: NOT for use by casual users.
.params	Reference property list. Warning: NOT for use by casual users.

Value

DAT file

Tab delimited file containing quantified colony sizes. There are two types of flags that can be associated with a data file (1) plate-level flags signify possible misgridding of the plate due to a high number of colonies with small size or low circularity. #' These flags can be viewed using the plate.warnings function (2) colony-based flags signify warnings associated with individual colonies. These flags can be viewed in the column named flags of #' the data file. row: row number col: column number size: quantified colony size circularity: circularity of the colony flags: colony-based flags: S - Colony spill or edge interference, C- Low colony circularity

Gridded image

Thresholded image showing the grid defined over the image

Examples

# Read sample image
f = system.file("extdata", "sample.jpg", package="gitter")
# Process it
dat = gitter(f)
# View head of the results
head(dat)

omarwagih/gitter documentation built on Feb. 6, 2023, 12:08 p.m.