Antibiotics Change the Growth Rate Heterogeneity and Morphology of Bacteria

Each experiment was conducted on the Multipad Agarose Plate (MAP) and is labelled with BE followed by a number. This repository contains four main elements:

1. The file Condition map MAP P2.json describes how the MAP platforms were set up for each experiment. Some datasets also include data that was discarded.  
2. The folder Benchmarking contains data for how we validated the performance of our PadAnalyser package. Originals have a set of images from bacteria affected by antibiotics to produce different morphologies. Annotated_raw is the human-labelled version of these, and Annotated are these converted to a format that can be used by code for comparison. Segmentation Benchmarking.ipynb is a Jupyter Notebook that segments the cells and compares the output to the annotated data. 
3. The folder Dataframes contains Pandas data frames from all experiments, classified by bacteria species. 
4. The folder Videos contains debug videos visualizing how the segmentation algorithm performed on the different datasets. Contact us for access to the raw data. Videos in the format *_ssi.mp4 contain single cell masks, and *_css.mp4 contains colony masks.