Optimization and Fabrication of Multi-Level Microchannels for Long-Term Imaging of Bacterial Growth and Expansion

Hsieh Fu Tsai, Daniel W. Carlson, Anzhelika Koldaeva, Simone Pigolotti, Amy Q. Shen

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Bacteria are unicellular organisms whose length is usually around a few micrometers. Advances in microfabrication techniques have enabled the design and implementation of microdevices to confine and observe bacterial colony growth. Microstructures hosting the bacteria and microchannels for nutrient perfusion usually require separate microfabrication procedures due to different feature size requirements. This fact increases the complexity of device integration and assembly process. Furthermore, long-term imaging of bacterial dynamics over tens of hours requires stability in the microscope focusing mechanism to ensure less than one-micron drift in the focal axis. In this work, we design and fabricate an integrated multi-level, hydrodynamically-optimized microfluidic chip to study long-term Escherichia coli population dynamics in confined microchannels. Reliable long-term microscopy imaging and analysis has been limited by focus drifting and ghost effect, probably caused by the shear viscosity changes of aging microscopy immersion oil. By selecting a microscopy immersion oil with the most stable viscosity, we demonstrate successful captures of focally stable time-lapse bacterial images for ≥72 h. Our fabrication and imaging methodology should be applicable to other single-cell studies requiring long-term imaging.

Original languageEnglish (US)
Article number576
Issue number4
StatePublished - Apr 7 2022


  • E. coli
  • bacterial population dynamics
  • computational fluid dynamics
  • focus drifting
  • immersion oil viscosity
  • live cell imaging
  • long-term microscopy imaging
  • mother machine
  • multi-level microfluidic device
  • single-cell studies

ASJC Scopus subject areas

  • Control and Systems Engineering
  • Mechanical Engineering
  • Electrical and Electronic Engineering


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