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. 2020 Jun 17;14(10):2461–2473. doi: 10.1038/s41396-020-0700-9

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Maximum intensity projection of an unlabelled JM105 colony acquired using reflection confocal mesoscopy, with a single isolated optical section shown. Reflection imaging determined that intra-colony channels were not occupied by material of differing refractive index to the biomass. The colony-medium interface can be observed clearly, while there is no evident structure within the colony. b Signal from non-viable cells (yellow) was subtracted from viable cells to negate any spectral overlap in the emission of Sytox Green and HcRed1. A composite maximum intensity projection of the entire colony is presented. Intra-colony channels in the viable cell population (cyan) did not contain any non-viable cells. c Alexa594-WGA-stained EPS residues (magenta) were not present in the intra-colony channels when compared with elsewhere in the biofilm, meaning channels were not composed of an EPS-based matrix. The high background signal in the surrounding agar is likely owed to non-specific binding of the WGA dye with gycan components of the agar substrate. d Nile red-stained lipids (red) clustered in the centre of E. coli biofilms while intra-colony channels remain unstained by Nile Red. Therefore, intra-colony channels were not composed of lipids. e Emission of SYPRO Ruby-stained extracellular proteins (magenta) mimicked the spatial patterns of intra-colony channels, showing that channels were filled by a protein-based matrix.