_borderpos = border positions of all plates in the experiment
1 border for 384 density, 2 for 1536 and 4 for 6144
_pos2coor = position ids and their corresponding plate coordinate
unique position ids for all possible colony positions in the experiment and thei correspoing plate coordinates ie colony density, plate number, row number and column number
_pos2orf_name = position ids and the corresponding orf-name (or mutant name)
_pos2rep = position ids of lowest density plates to their replicates at higher density plates based on the upscale pattern
for internal use
_pos2strain_id = position ids and their corresponding strain ids
_strainid2orf_name = same as excel table from above
Pixel count estimation from pictures using the MATLAB Colony Analyzer Toolkit
imageanalyzer.m
Information to keep in handy before proceeding:
Location of any smudges on the plates ie the colonies you want to remove from the analysis because of any technical issues
plate number, row number, column number
User will be asked to verify binary files before uploading raw pixel count data
Each image will now have 3 additional files - .binary, .cs.txt and .info.mat
View the .binary file (using Preview in Mac) to verify if the colonies have been correctly identified
Successful run will create the following tables:
_RAW = raw colony size estimations per hour per position id of all the images
image1, image2 and image3 columns correspond to the three images per plate
average column is the mean of the pixel count estimation from the three images
image1 = image2 = image3 = average if there is a single image per plate
_smudgebox = position ids corresponding to the user defined coordinates
_JPEG = similar to _RAW with
pixel count estimations for borders and smudgebox NULL'd
and any pixel count estimation < 10 is also NULL'd - likely to be a light artifact
If the images are already analyzed using a different software then make sure the colony sizes in the _JPEG table are arranged in ascending order of hours, plate number, column number, row number.