Data & Software

Software tools:

BiofilmQ, a software tool for quantitative image analysis of microbial biofilm communities
R. Hartmann*, H. Jeckel*, E. Jelli*, P.K. Singh, S. Vaidya, M. Bayer, L. Vidakovic, F. Díaz-Pascual, J.C.N. Fong, A. Dragoš, O. Besharova, C.D. Nadell, V. Sourjik, A.T. Kovács, F.H. Yildiz, K. Drescher
submitted (2019). (* equal contribution) [bioRxiv] [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
submitted (2018). (* equal contribution) [bioRxiv] [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
Proceedings of the National Academy of Sciences, online (2018). [journal link] [dataset explorer]

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, online ahead of print (2018). [journal link] [bioRxiv] [data repository]