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


Synthetic Biology Foundations Prism



  • 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)
    • 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

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