spot_assay_processor.nb

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The Mathematica \[OpenCurlyDoubleQuote]Spot Assay Processor\
\[CloseCurlyDoubleQuote] notebook is designed to quantify cell growth on \
solid media plates incubated under the influence of different environmental \
factors. It does so by measuring the size of the colonies formed by the \
growing cells in pictures taken from the solid media plate with colonies at \
regular intervals. The colonies are laid out on a grid using a \
\[OpenCurlyDoubleQuote]spotting\[CloseCurlyDoubleQuote] technique commonly \
having rows for the different strains or mutants of the organisms under study \
and a dilution series as columns.

The notebook processes these images in the following successive steps:\
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Detect colonies on the background using a sequence of image processing \
techniques:\
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Threshold filter to better define colonies and boundaries between colony and \
medium. This filter uses cluster variance maximization \
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image thresholding on grayscale images.\
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Binarization to convert the pixels of the detected colonies to 1 (white) and \
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ensure that each partition is of equal pixels size and compensate for minor \
misalignment of colonies in the grid cells. The latter prevents the edges of \
one colony to flow over into the grid cell of another colony leading to false \
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Count the 1\[CloseCurlyQuote]s in the binary matrices after partitioning as a \
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In case of a reference plate, the pixel counts in the assay are normalized by \
the pixel counts in the reference. This may lead the less pixels than the \
reference image in which case the organism/cell growth rate is reduced \
(sensitivity) under influence of the environmental factor, no effect or more \
pixels in which case colony growth in increased under influence of the \
environmental factor. This notebook focuses on sensitivity and therefor all \
pixel counts higher than the control are set to equal the control (growth \
cannot be higher than the control).\
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In case of a control image, a final value for sensitivity is calculated by \
averaging the difference in growth over the dilution series.\
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to process and optionally a reference image using a common system file \
selection dialog. You can test the script by using the test images shipped \
with the software (condition-x.png and the reference image control.png). \
Mathematica will handle most common image file formats automatically.\n\nOf \
the 4 program parameters you can set (",
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