Huang: Agarose Slides for Imaging

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This protocol allows live bacterial cell imaging. We create a small, nutrient rich gel pad and inject the bacteria on top.


  • 500mg Agarose
  • 100 ml PBS buffer/bacterial media
  • 2 Glass microscope slides
  • 4 Glass cover slips
  • Nail Polish
  • Bacterial liquid culture (at least 10 μl, ideally in exponential phase)


  1. Mix Agarose with buffer solution, microwave until boiling.
  2. Prepare one glass slide and position 2 thin cover slips on each end, to create 2 edges.
  3. Pipet 25 μl of the Agarose solution onto the middle of the glass slide, while making sure not to touch the coverslips.
    1. Quickly position the second glass slide on top of the molten gel drop.
    2. Leave to dry for a few minutes.
  4. Remove the top glass slide.
  5. Add 2-4 μl of the liquid culture onto the hardened gel drop.
    1. Leave to dry for a couple of minutes
  6. Add a cover slip on top, seal with nail polish at all 4 corners.
  7. You are now ready to image some cells!


Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!