gitter (version 1.1.1)

gitter: 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, verbose = "l", contrast = NULL, fast = NULL, plot = F, grid.save = getwd(), dat.save = getwd(), .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.

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.

.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)