How the age of AI is changing the way we hunt for phages: Accelerating phage workflow with OnePetri

Artificial Intelligence simply means the use of programming technology to imitate human thought and action by analyzing data and surroundings, solving or anticipating problems, learning of self-teaching, or adapting to a variety of tasks. AI can relieve humans of various repetitive tasks. The technology can learn work once and repeat it, as many times as desired by its human programmer. AI makes it possible for machines to learn from experience, adjust to new inputs and perform human-like tasks, from chess-playing computers to self-driving cars, which rely heavily on deep learning and natural language processing. AI has set foot in the world of phage enthusiasts, development of different tools that will aid and simplify the tasks that a human scientist was supposed to do are rising.


OnePetri developed by Michael Shamash, a microbiologist by training, who is currently pursuing his Master’s degree in the lab of Dr. Corinne Maurice at McGill University in Canada is one of the tools dedicated to aiding scientists with the plaque counting tasks. Plaque counting is one of the key steps in many phage protocols and can be incredibly time-consuming but with OnePetri it only takes a couple of seconds. Once installed in your device OnePetri uses your phone camera to detect plaques from a petri dish, the image can be live scanned or an image from your gallery. After a release of a beta version of the app, those who tested realized that besides counting plaques an app is capable of counting bacterial colonies for the purpose of determining colony forming units on a petri dish. That was an expected plus for the app.
Importing an image on OnePetri


In an interview with The phage, when asked what inspired him to make such a tool Michael said " I wanted to create a tool which could hopefully help a good chunk of those who do these counts on a regular basis so they can save potentially hours per week and use that time for something more productive. I also was really interested in machine learning and object detection in images in general, so this was the perfect chance for me to learn more about this cutting-edge technology while also helping others in the phage field!"
OnePetri is not Michael's first app release, although as a sole developer this is his first. In 2014 and 2015 together with his partner released a suite of iOS applications for flight simulation hobbyists/enthusiasts like himself. The apps were a great companion for those who enjoy doing flight simulation on the computer, providing live map and location information, as well as flight routing information. Unfortunately, he had to remove these apps from the App Store in early 2021 due to him not having enough time to keep them up to date and fully functioning.
Michael revealed that OnePetri was probably the quickest app project he has had go from idea to published application on the App Store. In total it took about 6 weeks, including a beta test period
where other members of the phage community helped test the app on their own datasets and Petri dishes. OnePetri is currently available only for ios and currently, the developer is working on the android version of the app adding to that Michael made his project currently free for everyone to use! In fact, the app’s source code is available publicly online under the GPL-v3 license, with the models and training data also available. If you’d like to contribute to the project, please visit the project GitHub page here.
OnePetri needs no signing in or registration In fact, OnePetri doesn’t collect any data or statistics about your use of the app. Michael said "My goal when making the app was to make it as simple and as quick to use as possible, while also being fully useable without internet access. In the future, I may add an account system as part of additional features I’m working on, but registration/login will never be required for core app functionality".
OnePetri AI plaque counting on action


when asked about his plans Michael said "In terms of features for the iOS app, I’d also like to add support for bacterial CFU counting (though I have heard anecdotally that the plaque detection AI models work quite well for CFUs too!), as well as additional assay types. Ultimately I’d like OnePetri to be one app that supports a wide range of common Petri dish assay types, beyond just CFU and PFU counting, and am open to suggestions from the community on what they’d like to see next!"
The world of phage scientists is still waiting for more and more apps like this that put their innovation and dedication at reducing tiresome on-bench repetitive tasks.

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4 Comments

  1. That's amazing tool Michael, can the app measure the diameter of a single plaque? If not can that feature be added?

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    Replies
    1. Hi Walya, thanks for your interest in OnePetri! We do not currently support measuring plaque diameter, however this is something I'm considering adding a future update. It would be an estimate though.

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    2. Thanks Michael. cant wait to see the update

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