Microbial Cell Counting in a Noisy Environment by Cameron Davidson-Pilon

Events PyMCon2020
1

Talk Abstract

In this LBAM, we’ll introduce the microbiological task of cell counting and understand all the potential sources of error involved. We’ll model each source of error probabilistically, introduce priors, and then discuss inference on the posterior. Finally, we’ll explore how we can extend our model to use in a calibration curve for other instruments. Only basic probability theory is required for this LBAM.
Cameron Davidson-Pilon Twitter @cmrn_dp

Talk

Cameron Davidson-Pilon

Cameron Davidson-Pilon has worked in many areas of applied statistics, from the evolutionary dynamics of genes to modeling of financial prices. His contributions to the community include lifelines, an implementation of survival analysis in Python, lifetimes, and Bayesian Methods for Hackers, an open source book & printed book on Bayesian analysis. Formally Director of Data Science at Shopify, Cameron is now applying data science to food microbiology.

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Speaker Tag: @CamDavidsonPilon

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This was really neat!

I gotta ask. What gear did you use for your microscope such that your iphone was able to capture that? I’m getting the impression that you’ve been able to get a pretty good bang for your buck gear-wise. Your talk kind of might have inspired me to consider yet another nerdy hobby.

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I have a similar project where I need to count the number of bacteria in 100 fields of view. Though the counting is done by a neural network, I think it would be interesting to incorporate Bayesian methods in this case as well. Thanks for the inspiration!

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Hi Cameron. This is an excellent talk – thanks very much! I am not sure I understand what you were saying near the end about moving uncertainty around like sand. You made it sound like there’s no benefit, as if using a better pipette would not reduce the uncertainty of the estimate. That’s not what you meant to say, is it?

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Thanks for the kind words, Allen!

Let me try to explain more carefully here. By using a better pipette, you would reduce the uncertainty. However, that uncertainty has not vanished - it has been concentrated near the point estimate. Like sand under a carpet, we can only move the sand around, and never remove it. Better measurements / more data move it (usually) to create a taller peak. However, there is the same uncertainty, just at a smaller scale. Graphically:

Screen Shot 2020-10-30 at 10.20.37 PM
Screen Shot 2020-10-30 at 10.20.37 PM1136×888 105 KB

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Great talk! I’m amazed how well "n = 1 observation" worked. I guess it was an observation of a handful of squares.

I work on survey statistics for measuring carbon in agricultural soil (for quantifying carbon credits), so it was fun to see analogs in your talk. I’m interested in Bayesian approaches to survey inference, and it seems your solution could be cast in that way, as a simple random sample of molecules from your beaker.

Thanks for the fun talk.

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I don’t understand this explanation, Mr Allen is right I think. Using better pipettes which results in more concentrated distributions reduces the “confidence interval” -which is a good thing- for your final decision making.

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A cool follow-up analysis could be:

  • we value uncertainty (e.g., the half width of the 90% interval divided by the estimated concentration) using such and such functional relationship (e.g., $100 for each percentage point of reduced uncertainty)
  • the fancy pipette costs $X
    At what price $X is it worth buying the fancy pipette?
1 Like