@article {wang2016probing,
	title = {Probing phenotypic growth in expanding Bacillus subtilis biofilms},
	journal = {Applied microbiology and biotechnology},
	volume = {100},
	number = {10},
	year = {2016},
	pages = {4607{\textendash}4615},
	publisher = {Springer Berlin Heidelberg},
	abstract = {
	
		We develop an optical imaging technique for spatially and temporally tracking biofilm growth and the distribution of the main phenotypes of a\&nbsp;Bacillus subtilis\&nbsp;strain with a triple-fluorescent reporter for motility, matrix production, and sporulation. We develop a calibration procedure for determining the biofilm thickness from the transmission images, which is based on Beer-Lambert{\textquoteright}s law and involves cross-sectioning of biofilms. To obtain the phenotype distribution, we assume a linear relationship between the number of cells and their fluorescence and determine the best combination of calibration coefficients that matches the total number of cells for all three phenotypes and with the total number of cells from the transmission images. Based on this analysis, we resolve the composition of the biofilm in terms of motile, matrix-producing, sporulating cells and low-fluorescent materials which includes matrix and cells that are dead or have low fluorescent gene expression. We take advantage of the circular growth to make kymograph plots of all three phenotypes and the dominant phenotype in terms of radial distance and time. To visualize the nonlocal character of biofilm growth, we also make kymographs using the local colonization time. Our technique is suitable for real-time, noninvasive, quantitative studies of the growth and phenotype distribution of biofilms which are either exposed to different conditions such as biocides, nutrient depletion, dehydration, or waste accumulation.
	

},
	url = {https://link.springer.com/article/10.1007/s00253-016-7461-4},
	author = {Wang, Xiaoling and Koehler, Stephan A. and Wilking, James N. and Sinha, Naveen N. and Cabeen, Matthew T and Srinivasan, Siddarth and Seminara, Agnese and Shmuel Rubinstein and Sun, Qingping and Michael P. Brenner and others}
}
