User:Pakpoom Subsoontorn/Notebook/Shape Determination in Bacteria/2008/10/09

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miniProject: Microfluidic device for monitoring the dynamics of bacterial cell shapes

  • GOAL: In this project, we design the microfluidic system that we can flow bacterial cells into the pipe,

fix them to the wall and image them dividing and changing cell shape. We should also be able to flow in new media and wash away the old one.

TO DO list

  • Meet with Tony tomorrow, chat about the chip
  • Finish-up Autocat design
    • How to create different layers
    • Select the lines or rectangles and extend/shrink them
    • Draw lines with specific lengths
    • Specify the height, width of the flow lines and control lines
    • Specify the size of the chip, the size of the mask and how to fit them in.
    • Install VM and Autocat on laptop/ get office key from KC
    • read microfluidic design guideline
    • check the design the people at foundry
  • Get all microscope detail
  • discuss image quality: illumination, focus, background, balance(try 96 wells)
  • FM646 and other dye absorption/emission
  • 200 ms instead of 100 ms
  • ask about 3D position

figure out how to set and run microfluidic chip on it

Question to think about

  1. How to fix bacterial cell to the pipe wall? Note that we want them to stay while we washing the pipe with

new media. We don't want cells to pile up. Also, we want to be able to un-fix the cells and wash all of them out once we finish


  • A simple two-pipe and four-pipe design
  • 100 um depth, 15 mm by 0.6 mm

Progress note

  • 10/09/08 chat about the goal and basic design with KC