Reads raw cell density timecourse data from Colonyzer output files
Reads in and binds together all of the Colonyzer output files in a directory, so they are checked and ready for bayesian or likelihood inference. Colonyzer is an open source image analysis tool for quantifying cell densities on agar plates: http://research.ncl.ac.uk/colonyzer/
The path to the folder containing the Colonyzer .dat files to be read: working directory by default.
Character vector giving locations of Colonyzer .dat files to be read - overrides path
Name of text file describing the inoculation times, library and plate number for unique plates. Taken relative to path if specified. File must be a tab-delimited text file with no header containing the following columns:
Path to a tab-delimited text file containing two columns (with no headers) associating unique, systematic strain identifiers (e.g. yeast ORF Y-numbers) with human readable gene names (e.g. standard names from SGD).
Tab-delimited text file describing the array strains present in each row-column coordinate of each plate in a series of rectangular arrayed libraries. Header row format is: "Library ORF Plate Row Column Notes". Columns are:
Unique experiment identifier (e.g. QFA00001)
An R data.frame where each row corresponds to a single observation on a single colony, with the value of the growth measurement in 'Growth', and the date and time of the measurement in 'Date.Time'. Other information about the observation is stored in the other columns. Several columns returned are direct copies of Colonyzer output and mapped as follows:
Image.Name - Image Name
Row - Spot Row
Col - Spot Column
X.Offset - X Offset
Y.Offset - Y Offset
Area - Area
Trimmed - Trimmed Area
Threshold - Threshold
Intensity - Intensity
Edge.Pixels - Edge Pixels
Colony.Color.R - Colony Color R
Colony.Color.G - Colony Color G
Colony.Color.B - Colony Color B
Background.Color.R - Background Color R
Background.Color.G - Background Color G
Background.Color.B - Background Color B
Edge.length - Edge length
Tile.Dimensions.X - Tile Dimensions X
Tile.Dimensions.Y - Tile Dimensions Y
Extra columns are automatically added as follows. Some of this information is derived from auxiliary files passed to the function such as the experimental description file, the orf-gene dictionary and the library description file:
Growth - A cell density surrogate built from trimmed Area normalised by tile area and maximum achievable pixel intensity: Trimmed/(Tile.Dimensions.X*Tile.Dimensions.Y*255)
Barcode - Plate identifier, essentially image name with date time and file extension stripped
Date.Time - Date time of image capture in YYYY-MM-DD_hh-mm-ss format
Inoc.Time - Date time that plate was inoculated. If plate is grown at a high temperature, date time at which plate was moved into high temperature incubator. The assumption in this case being that negligible growth occurred before plate temperature was shifted the the target temperature.
Treatments - Treatments applied to plate (e.g. temperature)
Medium - Medium contained in agar (e.g. nutrients or drugs added to agar)
Screen.Name - Unique identifier for experiment (usually identifies repeat number also if multiple repeats carried out).
RepQuad - Identifier for experiments scaling down from 1536 format plates to 384, indicating which quadrant on the original 1536 source plate the current 384 format plate belongs to.
MasterPlate.Number - Identifies which plate in the source library (as described in the library description file) corresponds to the current plate
Timeseries.order - Ordinal describing which photograph captured
Library.Name - Identifies which of the libraries identified in the library description file was used to construct this plate
ORF - Unique systematic identifier for the genotype of the strain at this location (e.g. yeast Y-number), as defined by library description file
Gene - Standard, human readable genotype identifier for the strain at this location, as defined by the ORF-Gene dictionary
Background - Tag identifying experiment, typically used to construct file names and axes titles in plots
Expt.Time - Number of days passed between inoculation (start of experiment) and current time
Finally, as well as returning the object above, this function prints a small report to screen, summarising the data returned. This includes number of unique barcodes read, number of photos read, number of genotypes in experiment, number of unique culture observations made, a list of treatments applied, a list of media used, a list of unique screen names (e.g. replicates carried out), the plate dimensions (e.g. 1536, 384 or 96 format) and a list of unique inoculation dates.
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