Description Usage Arguments Value Examples
The following function will grid and quantify a single plate image (for batch processing, see gitter.batch
)
1 2 3 4 |
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 |
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 |
inverse |
Logical indicating if input image is inverted, meaning colonies are darker compared to their background. Default is |
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 |
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 |
plot |
Logical indicating whether intensity profiles should be plotted. Default is |
grid.save |
Directory path to save gridded/thresholded images. Set to |
dat.save |
Directory path to save resulting data files. Set to |
.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. |
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
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Gridded image |
Thresholded image showing the grid defined over the image |
1 2 3 4 5 6 | # Read sample image
f = system.file("extdata", "sample.jpg", package="gitter")
# Process it
dat = gitter(f)
# View head of the results
head(dat)
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