Citizen Science/Open Colony Counter Project

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[[Image:Open-Colony-Counter-Project-Image.jpg|350px|Synthetic Biology Foundations Prism]]
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[[Image:Open-Colony-Counter-Project-Image.jpg|350px|Fleming's original culture plate|Fleming's original culture plate]]
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==Specifications==
==Specifications==
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[[User:Vincent Rouilly|Vincent]] 13:06, 1 August 2010 (EDT): feel free to comment.
===Features===
===Features===
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* General
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* '''General:'''
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** bacterial colonies or DAPI stained mammalian cells
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** can detect and count microbial colonies
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**  
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** accepted plate format: 60-90mm plates or multi-well plate format
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* Image processing-related
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** desktop device for the wetlab bench
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** Colony count in less than 3 seconds.
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** requires a PC (windows, osx, or linux)
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*  
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** Laser-cut design for the casing
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* Open source design
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** lab automation friendly design
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* Image acquisition device: USB Webcam-based
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** Open Source design
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* Light sources: white LEDs
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* '''Available Measurements:'''
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* Image processing engine: OpenCV library-based
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** colony count
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* Calibration Mode / Automatic Mode
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** individual colony properties (size, roundness, position)
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* Colony Counting mode / Colony Picking mode (if interfaced with a robotic platform)
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** export in CSV format or local database
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* Lab automation friendly design
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** PDF/HTML report with overlaid image with detection results + colony statistics
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* '''Image processing:'''
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** one-step processing for the user
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** colony count in less than 3 seconds.
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** automatic background detection
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** utilizes LED illumination to optimize contrast between colonies and substrate.
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** possible manual colony count editing for improved count.
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** USB Webcam as an image acquisition device
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===Optional Features===
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==User case: typical use==
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# the user places his/her plate inside the colony counter
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# the user opens the colony counting application on the attached PC
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# the user triggers the image acquistion and counting by pressing a single button
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# results are displayed as an overlay on the acquired image
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# if required, the user can adapt image processing parameters to improve detection
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# the user can then export results in various format (CSV, HTML, PDF)
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==Technological stack under investigation:==
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===Requirements===
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* Image acquisition device: USB Webcam-based
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* Light source: white LEDs, 470nm LEDs for GFP-like detection
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* Image processing engine: OpenCV library
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* Laser cut design for the casing
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[[User:Vincent Rouilly|Vincent]] 13:06, 1 August 2010 (EDT): feel free to comment.

Current revision

Open Colony Counter Project

Home        Documentation        Applications        Resources

visit counter for blogspot

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

Team:

Fleming's original culture plate

Specifications

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

Features

  • 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.
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