Data & Software

Software tools:

Quantitative image analysis of microbial communities with BiofilmQ
R. Hartmann*, H. Jeckel*, E. Jelli*, P.K. Singh, S. Vaidya, M. Bayer, D. Rode, L. Vidakovic, F. Díaz-Pascual, J.C.N. Fong, A. Dragoš, O. Besharova, J.G. Thöming, N. Netter, S. Häussler, C.D. Nadell, V. Sourjik, A.T. Kovács, F.H. Yildiz, K. Drescher
Nature Microbiology 6, 151-156 (2021). (* equal contribution) [journal link]
       -- download/use the BiofilmQ software tool, view video tutorials.

BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology
R. Hartmann*, M.C.F. van Teeseling*, M. Thanbichler, K. Drescher
Molecular Microbiology 114, 140-150 (2020). (* equal contribution) [journal link]
       -- download/use the BacStalk software tool
       -- view video tutorials for using BacStalk software

Data sets:

Learning the space-time phase diagram of bacterial swarm expansion
H. Jeckel, E. Jelli, R. Hartmann, P.K. Singh, R. Mok, J.F. Totz, L. Vidakovic, B. Eckhardt, J. Dunkel, K. Drescher
PNAS 116, 1489-1494 (2019). [Open Access] [dataset explorer]
       -- Youtube video summary.

Emergence of three-dimensional order and structure in growing biofilms
R. Hartmann, P.K. Singh, P. Pearce, R. Mok, B. Song, F. Diaz-Pascual, J. Dunkel, K. Drescher
Nature Physics 15, 251-256 (2019). (* equal contribution) [journal link] [Europe PMC] [data repository]
       -- see Jordi Garcia-Ojalvo's Perspective in Nature Physics.
       -- see Phil Pearce's "Behind the paper" story.