2D vs 3D tracking in bacterial motility analysis

Jacqueline Acres; Jay Nadeau; Jacqueline Acres; Jay Nadeau

doi:10.3934/biophy.2021030

AIMS Biophysics

2021, Volume 8, Issue 4: 385-399. doi: 10.3934/biophy.2021030

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2D vs 3D tracking in bacterial motility analysis

Jacqueline Acres ,
Jay Nadeau ^,

Department of Physics, Portland State University, 1719 SW 10th Ave., Portland, OR 97201, USA

Received: 02 October 2021 Accepted: 24 November 2021 Published: 09 December 2021

Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fashion. However, computational tools for tracking large 4D datasets remain lacking. In this paper, we examine the errors introduced by tracking bacterial motion as 2D projections vs. 3D volumes under different circumstances: bacteria free in liquid media and bacteria near a glass surface. We find that while XYZ speeds are generally equal to or larger than XY speeds, they are still within empirical uncertainties. Additionally, when studying dynamic surface behavior, the Z coordinate cannot be neglected.
- holographic microscopy,
- microbial motility,
- Vibrio,
- reverse and flick,
- chemotaxis,
- tracking
Citation: Jacqueline Acres, Jay Nadeau. 2D vs 3D tracking in bacterial motility analysis[J]. AIMS Biophysics, 2021, 8(4): 385-399. doi: 10.3934/biophy.2021030

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Abstract

Digital holographic microscopy provides the ability to observe throughout a large volume without refocusing. This capability enables simultaneous observations of large numbers of microorganisms swimming in an essentially unconstrained fashion. However, computational tools for tracking large 4D datasets remain lacking. In this paper, we examine the errors introduced by tracking bacterial motion as 2D projections vs. 3D volumes under different circumstances: bacteria free in liquid media and bacteria near a glass surface. We find that while XYZ speeds are generally equal to or larger than XY speeds, they are still within empirical uncertainties. Additionally, when studying dynamic surface behavior, the Z coordinate cannot be neglected.

Acknowledgments

The authors acknowledge the support of the National Science Foundation Grant Number 1828793. Portions of this work were supported under a contract from the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration. We thank Louis Sumrall for the S. putrefaciens dataset.

Conflict of interest

The authors declare no conflict of interest.

Author contributions:

Acres—processed DHM data, performed tracking, prepared figures, wrote paper.
Nadeau—collected and processed DHM data, wrote paper.

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