Citizen Science/Open Colony Counter Project

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Open Colony Counter Project

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Driving forces:

  • to provide an open source colony counter system
  • to ease access to quantitative equipment in Life Sciences
  • to deliver a low-cost / easy to reproduce design


Fleming's original culture plate


Vincent 13:06, 1 August 2010 (EDT): feel free to comment.


  • General:
    • can detect and count microbial colonies
    • accepted plate format: 60-90mm plates or multi-well plate format
    • desktop device for the wetlab bench
    • requires a PC (windows, osx, or linux)
    • Laser-cut design for the casing
    • lab automation friendly design
    • Open Source design
  • Available Measurements:
    • colony count
    • individual colony properties (size, roundness, position)
    • export in CSV format or local database
    • PDF/HTML report with overlaid image with detection results + colony statistics
  • Image processing:
    • one-step processing for the user
    • colony count in less than 3 seconds.
    • automatic background detection
    • utilizes LED illumination to optimize contrast between colonies and substrate.
    • possible manual colony count editing for improved count.
    • USB Webcam as an image acquisition device

User case: typical use

  1. the user places his/her plate inside the colony counter
  2. the user opens the colony counting application on the attached PC
  3. the user triggers the image acquistion and counting by pressing a single button
  4. results are displayed as an overlay on the acquired image
  5. if required, the user can adapt image processing parameters to improve detection
  6. the user can then export results in various format (CSV, HTML, PDF)

Technological stack under investigation:

  • Image acquisition device: USB Webcam-based
  • Light source: white LEDs, 470nm LEDs for GFP-like detection
  • Image processing engine: OpenCV library
  • Laser cut design for the casing

Vincent 13:06, 1 August 2010 (EDT): feel free to comment.