m1vg/taxispy repository overview

⁠TaxisPy: A Python-based Software for the Quantitative Analysis of Bacterial Chemotaxis

Several species of bacteria are able to modify their swimming pattern in response to chemical attractants or repellents. Methods for the quantitative analysis of bacterial chemotaxis such as quantitative capillary assays are tedious and time-consuming. Computer-based video analysis of swimming bacteria represents a valuable method to directly assess the chemotactic response of bacteria. Even though multiple studies have used this approach to elucidate various aspects of the bacterial chemotaxis, to date, no computer software for such analyses is freely available. Here, we introduce TaxisPy, a Python-based software for the quantitative analysis of bacterial chemotaxis. The software comes with an intuitive graphical user interface and can be easily accessed through Docker on any operating system. Using a video of freely swimming cells as input, TaxisPy estimates the culture’s average tumbling frequency over time. We demonstrate the utility of the software by assessing the effect of different concentrations of the attractant shikimate on the swimming behavior of Pseudomonas putida F1 and by capturing the adaptation process that Escherichia coli undergoes after being exposed to L-aspartate.

⁠Docker Image

This repository contains a stable version of TaxisPy. See Tags tab for details. TaxisPy is currently under development by Miguel A. Valderrama-Gómez ([email protected]⁠) in the Savageau Laboratory (https://savageaulab.wordpress.com/⁠) @ UC Davis

⁠Getting Started

To use the TaxisPy Docker Image:

1. Download Image: docker pull m1vg/taxispy

2. Create Container: docker run -d -p 8888:8888 m1vg/taxispy

3. Open http://localhost:8888⁠ in a browser window