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Dataset for quantification of CFUs using AI

Cite this dataset

Egli, Adrian; Moucka, Michael (2022). Dataset for quantification of CFUs using AI [Dataset]. Dryad.


In recent years, smartphones and software have developed to help to automate imaging processes and thereby support digitalization in clinical microbiology laboratories. Due to the time-consuming nature of manual bacterial colony counting, diverse apps for smartphones have been developed to quantify the number of colony-forming units (CFUs) on agar plate images. 

Currently, at least four different apps with a colony counter function exist. Our study aimed to compare the accuracy of the apps compared to human visual manual counting. The images were acquired using four different colony counters with three apps on an iPhone 11 Pro Max (CFU.Ai, Promega Colony Counter, APD Colony Counter App PRO) and one app on a Samsung Galaxy A52 (@BactLAB). Two different measurement conditions were investigated. Firstly, standardized measurement in a handcrafted wooden apparatus, and secondly “freestyle measurement” manually holding the plate. The apparatus measurements were performed against a black background, apart from @BactLAB on a white background (as per the manufacturer’s instructions). We used three different types of media: blood agar, chrome agar, and LB. Four Escherichia coli isolates were used. We prepared a bacterial suspension of each strain, made a six-fold serial 1:10 dilution in saline and spread the dilutions “1:104”, “1:105”, and “1:106” at three different solution volumes (100μl, 50μl, and 25μl) homogeneously across the agar plates. We included a total of 108 agar plates.

This dataset contains all analyzed images. It may possibly be useful in order to assess and improve colony counter apps in the future. On the one hand, the dataset contains raw data (images before processing), on the other hand, it contains screenshots of our app measurement and thus enables accountability of our results (screenshots of all apps were uploaded apart from @BactLAB as from its screenshots nothing can be derived).

Usage notes

The dataset consists of five zip files. 

“Images iPhone” and “Images Samsung” contain all acquired images (before processing) from the iPhone and Samsung devices, respectively.

“CFU.Ai”, “Promega Colony Counter” and “APD Colony Counter App PRO” contain the screenshots of the various apps after the quantification process.