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37. Eskandarian HA, Odermatt PD, Ven JXY et al
(2017) Division site selection linked to inherited cell surface wave troughs in mycobacteria.
Nat Microbiol 2:17094
38. Hannebelle MTM, Ven JXY, Toniolo C et al
(2020) A biphasic growth model for cell pole
elongation in mycobacteria. Nat Commun
11:452
39. Ueno H, Kato Y, Tabata KV et al (2019)
Revealing the metabolic activity of persisters
in mycobacteria by single-cell D 2 O Raman
imaging
spectroscopy.
Analyt
Chem
91:15171–15178
40. Whitesides G, Ostuni E, Takayama S et al
(2001) Soft lithography in biology and biochemistry. Annu Rev Biomed Eng 3:335–373
41. Weibel DB, Diluzio WR, Whitesides GM
(2007) Microfabrication meets microbiology.
Nat Rev Micro 5:209–218
42. Friend J, Yeo L (2010) Fabrication of microfluidic devices using polydimethylsiloxane. Biomicrofluidics 4:026502
43. Dhar N, Manina G (2015) Single-cell analysis
of mycobacteria using microfluidics and timelapse microscopy. In: Parish T, Roberts DM
(eds) Mycobacteria Protocols, 3rd edn.
Humana Press Springer, New York
44. Skylaki S, Hilsenbeck O, Schroeder T (2016)
Challenges in long-term imaging and quantification of single-cell dynamics. Nat Biotechnol
34:1137–1144
45. Wang Q, Niemi J, Tan C-M et al (2010) Image
segmentation and dynamic lineage analysis in
single-cell fluorescence microscopy. Cytom
Part A 77:101–110
46. Carpenter AE, Jones TR, Lamprecht MR et al
(2006) CellProfiler: image analysis software for
identifying and quantifying cell phenotypes.
Genome Biol 7:R100
47. Schindelin J, Arganda-Carreras I, Frise E et al
(2012) Fiji: an open-source platform for
biological-image analysis. Nat Methods
9:676–682
48. de Chaumont F, Dallongeville S, Chenouard N
et al (2012) Icy: an open bioimage informatics
platform for extended reproducible research.
Nat Methods 9:690–696
49. Ducret A, Quardokus E, Brun YV (2016)
MicrobeJ, a tool for high throughput bacterial
cell detection and quantitative analysis. Nat
Microbiol 1:16077
50. Ouyang W, Mueller F, Hjelmare M et al (2019)
ImJoy: an open-source computational platform
for the deep learning era. Nat Methods
16:1199–1200
51. van Raaphorst R, Kjos M, Veening JW (2020)
BactMAP: an R package for integrating, analyzing and visualizing bacterial microscopy
data. Mol Microbiol 113:297–308
52. Patino S, Alamo L, Cimino M et al (2008)
Autofluorescence of mycobacteria as a tool for
detection of Mycobacterium tuberculosis. J Clin
Microbiol 46:3296–3302
Microfluidic Microscopy of Mycobacteria
229