Universal precise large area colony scanning stage with measurement and selection tool integration

Colony scanning call for contributions.png

This project aims to develop a flexible, open-source platform for automatic plant and colony scanning, for morphological and long-term analysis.

The team are currently looking for contributors. Please contact Tobias Wenzel at tw347@cam.ac.uk.

The Idea

Plant or microbial cultivation and monitoring can be a time consuming and tedious process, especially, if precise analysis of plant/colony growth is required. Nonetheless, little automation is commonly used for this purpose in today’s laboratories. Generally, quantitative assessment of cultures has become vastly important for biological research, with great improvements in bioassay and drug discovery and monitoring, often achieved by microplate/multi-well analysis combined with absorptive or fluorescent photometry. The method produces fast and reliable results, but commercial devices are costly and limited to a narrow spectrum of experimentation. A simple expansion of the system could greatly improve the usability of plate readers for not only the current purposes, but also other fields, such as cell culture monitoring.

We propose an open-source platform for automatic (flat – e.g. Marchantia) plant and colony scanning, which extends the plate-reading-functionality to morphological and long-term analysis and will also be more flexible, considering growth plate size. This is an extension of the initiative of the Cambridge 2015 iGEM team, who developed an open source fluorescence microscope and want to integrate a similar optical analysis into colony scanning tools as part of the work of the Synthetic Biology Student Society in Cambridge.

For this technology vision to become a) technically viable, b) to be tested on biologically relevant questions and c) to ensure the establishment of a longer-term development community around the tool, we propose specifically:

a) The development of technological tools that combine video and optical microscopy techniques with CNC technology, currently used in 3D printers and CNC mills.

  • A more precise and more affordable CNC translation stage to seamlessly operate with optical microscopy devices
  • Technical interfaces that allow easy integration of open source measurement and preparation tools on the stage
  • A new open source tool that allows to identify and pick or mark colonies and their positions.

Optical analysis tools and their integration and testing will be performed as part of the SynBio Society work in their own time with microscope and technology developed by them and further collaborators. This aims to extend the functionality of the stage to the following: Scanning a cultivation area covered with growth plates; creating a map, which can then be navigated with a microscope; automatically focus and record time-lapse videos for each colony.

b) Testing and the stage and tools on seed germination experiments.

c) Replication the hardware as identical set for laboratories of this collaboration in Norwich, Cambridge and Slovenia to lay a foundation for easy feedback and collaboration.

The Team

Mr Tobias Wenzel,
Graduate Student, Department of Physics, University of Cambridge,

Dr Neil Pearson,
Postdoctoral Researcher, Earlham Institute, Norwich

Dr Luka Mustafa,
Institute IRNAS Race, Slovenia (http://irnas.eu/)

Dr Nick Pullen,
Postdoctoral Researcher, John Innes Centre, Norwich

Dr Ji Zhou,
Phenomics Project Leader, Earlham Institute, Norwich

Cambridge University Synthetic Biology Society (CUSBS),
University of Cambridge


Project Outputs

Project Report

Coming soon...

Project Proposal

Original proposal and application

software.png

Project Resources

Stage design documentation on Github.