Published February 9, 2023 | Version v1

Radial topographies of biofilm colonies

  • 1. Georgia Institute of Technology

Description

During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing diverse biophysical models empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a novel and detailed empirical characterization of vertical growth dynamics. This dataset corresponds to the profiles of developing biofilms, measured through white-light interferometry. This dataset represents novel high-resolution characterizations of developing biofilms in the vertical direction, empirical measurements that can be utilized to test models for biofilm development, ranging from bulk-dynamics to surface fluctuations. 

Notes

All interferometric measurements are provided in csv format. For a detailed description of the files refer to the README.md document and the accompanying article. 

For analysis and topography analysis scripts:

- Python for cleaning script, and loading sample .datx data.

- Julia for differential equation modeling, and parameter optimization.

Funding provided by: National Institute of General Medical Sciences
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000057
Award Number: 1R35GM138354-01

Funding provided by: National Science Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000001
Award Number: BMAT2003721

Files

all_bootstrap.csv

Files (762.3 MB)

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Additional details

Related works

Is cited by
10.1101/2022.08.11.503641 (DOI)
Is derived from
10.5281/zenodo.7478333 (DOI)