Geometric Viability Assay (GVA)
GVA is a high throughput cell viability assay for microbiology. Akin to the classic CFU assay, GVA measures the number of viable microbes in a sample based on counting discrete colonies. The classic CFU assay uses a dilution series to measure viable cell concentrations across the many orders of magnitude that exist in nature; but this comes at the expense of time and resources. In contrast, GVA leverages the geometry of a cone to allow nature to run the dilution series for you at 30X the speed! Fortunately, you likely have a cone sitting on your bench in the form of a pipette tip.
How to set up a GVA assay
While there are several approaches to counting your cells, the protocol always begins with embedding cells within a hydrogel (e.g., agarose) in a pipette tip. Start with a sample containing microbes, mix it with a liquid gel, then allow the gel to solidify inside the pipette tip. After incubating the pipette tips until each bacterium forms a colony, measure the colony positions using one of the three approaches detailed below. Happy counting!
Preparing your Samples
[video:https://youtu.be/9tAIbpZ_uOw]
Did GVA help advance your research?
Please acknowledge us in your publications by citing the following:
Meyer, C.T., Lynch, G.K., Stamo, D.F. et al. A high-throughput and low-waste viability assay for microbes. Nat Microbiol (2023).
doi: https://doi.org/10.1038/s41564-023-01513-9
Choose Your Counting Platform
There are a few ways to analyze and quantify your cells after you've embedded them in the agarose. Each technique comes with its own unique advantages and disadvantages.
You can count your cells by eye (with an optional magnifying glass) or with a MATLAB-based software that offers additional analysis to improve accuracy and speed. If you count your cells by eye, simply generate a printable worksheet matching the geometry of your pipette tips to quantify your samples using the software in the Paper link below. Higher dynamic range can be achieved when imaging the tips either with a DSLR camera or a Smartphone which allows for visualizing the smallest colonies at the higher concentrations. Once you've gathered your images, download and run our MATLAB software to analyze each sample. The software has been compiled and can be used without a license (Windows only) or run from the source code (Windows, Mac, Linux).
Images tips with a high-resolution camera. The increased resolution expands your dynamic range.
*Image 12 tips at a time
~$3K to set up
Uses 3D printed parts to stereotypically position tips in front of a macro lens.
*Images 1 tip at a time
~$100 (not including phone)
Align tips to a ruled grid on a piece of paper and use a magnifying glass to count colonies.
*Counts 1 tip at a time
~$5 (assuming access to a printer)