Team:Cambridge-JIC/Attributions

CAMBRIDGE-JIC

Attributions

We would like to thank our supervisor, advisors, and the many people who have generously shared their time and expertise with us, and without whom this project would not have been possible, let alone finished in time…

Special thanks to:

Dr Richard Bowman, NanoPhotonics Center, University of Cambridge
For inspiring our entire project, and providing the basis for our microscope stage with his PiScope (an open-source, inverted, bright-field microscope). See here for more information about PiScope [1].

Prof Jim Haseloff, Department of Plant Sciences, University of Cambridge
For his support and patience as our PI. Particularly for organising consultation meetings, logistics and helping at every step of the way.

Kate Armfield, PhD student, University of Glasgow
For being a wonderful full-time advisor, who has helped us in all aspects of our project, including logistics, press releases and lab supervision.

Barbara Landamore, Department of Plant Sciences, University of Cambridge
For helping with risk assessments and lab protocols, and sourcing key materials.

Dr George Sirinakis and Dr Alex Sossick, Gurdon Institute, University of Cambridge
For their advice on how to improve the optical performance of our microscope.

Prof. Dale Sanders, Head of the John Innes Centre, and Prof. Duncan Maskell, Head of the School of Biological Sciences, University of Cambridge
For enthusiastic leadership and generous support.

BBSRC/EPSRC OpenPlant Synthetic Biology Research Centre
For funding support.

Tobias Wenzel, Department of Physics, University of Cambridge
For his constant guidance with optical pathway design and illumination.

Luka Mustafa, Shuttleworth Fellow, IRNAS
For his appraisal of our hardware design and advice on custom PCBs.

Bernardo Pollak, Department of Plant Sciences, University of Cambridge
For his assistance with samples for imaging, and advice about Marchantia.


[1] Sharkey, J., Foo, D., Kabla, A., Baumberg, J. and Bowman, R. (2015). A one-piece 3D printed microscope and flexure translation stage.[online] Arxiv.org. [Accessed 18 Sep. 2015].

Thanks also to:

Professor Emeritus Dennis Bray, Department of Physiology, Development and Neuroscience, University of Cambridge
For his talk on bacterial chemotaxis.

Dr James Locke, Sainsbury Laboratory, University of Cambridge
For his advice on the Evolvinator concept.

Dr Nicola Patron, The Sainsbury Laboratory, Norwich
For her feedback on our presentation and microscope at a visit day in Norwich that she helped organise.

Dr Jenny Molloy, Department of Plant Sciences, University of Cambridge
For her feedback on our Human Practices project.

Dr Alexandre Kabla, Department of Engineering, University of Cambridge
For assisting with funding, courtesy of the Department of Engineering.

Dr Jim Ajioka, University of Cambridge
For his mentorship and help in Cambridge.

Professor George Lomonossoff
For coordination with the John Innes Centre.

Dr Pietro Cicuta Physics Department, University of Cambridge
For support in the Physics Department.

Dr Paul Grant, Department of Plant Sciences, University of Cambridge
For supervision in the laboratory and guiding us through transformations.

Sarah Collins, Dr Tom Almeroth-Williams, Sue Long and Dr Louise Walsh, Cambridge University Press
For helping with our press releases and our outreach event.

Amanda Whitehead and Dr Shaila Kotadia, Synthetic Dance-ology
For picking our microscope as the focus of their dance workshop.

Prof Clemens Kaminski, Laser Analytics Group, University of Cambridge
For his stimulating talk on Optical Superresolution Imaging.

Dr Tim Weil, Department of Zoology, University of Cambridge
For his incredible help in providing samples for our outreach day.

Dr Fernán Federici, Dr James Brown and all the other people who have encouraged us and given us feedback.

In terms of collaboration, thanks to:

Glasgow and William & Mary iGEM teams
For sending us some samples to image.

The Westminster iGEM team
For helping us organise a microscopy workshop at their UK iGEM meetup.

Teamwork

Mechanical Design

Simon, Katerina

Optical Design

Simon, Katerina, Ocean

Electronics and Hardware

Souradip, Rajiv, Simon

Software

Will, Souradip, Ocean, Rajiv

Human Practices

Atti

Outreach

Ocean, Olivia, María, Will

Wiki

Will, Souradip, Simon, Katerina, Atti, Lorenzo

Graphics Design

Simon, Ocean, Olivia

Documentation

Atti, Souradip, Simon, María, Katerina

Sponsorship

Lorenzo, Atti, María


Open Source Projects

Software

Below is a list of software programs that we have found useful for developing open-source documentation, supplemented with other commonly used programs:

  1. OpenSCAD – a free, open-source, parametric CAD platform used to design 3D objects for printing (available from here)

  2. Tracker – a free, open-source, video analysis and modelling tool. Used to track moving objects in videos and extract data (available from here)

  3. Cura 3D – a free, open-source 3D printer interface from Ultimaker. Used to control printer settings (available from here)

  4. Fiji - a free, open-source image processing and analysis platform. Particularly useful for microscopy (available from here)

  5. Inkscape – a free, open-source vector graphics package. Extremely useful for 2D design followed by linear extrusion (available from here)

  6. DesignSpark – a free electronics design software for PCB prototyping. Has an online library of over 80,000 parts (available from here)

  7. Scribus – a free, open-source graphics software. Particularly useful for publishing (available from here)

  8. Python – a free, open-source, programming language that allowed us to put together software quickly

  9. Nginx – A FOSS lightweight web server on top of which we built our web interfaces.

  10. OpenCV – A FOSS released under a BSD license that provides a library for image processing software (available from here)

For a detailed list of free, open-source software programs available, look here.


Hardware

  1. Arduino – A low-cost, open-source microprocessor with a number of available add-ons. Includes its own specific programming software and language (available here).

  2. Raspberry Pi – A low-cost, linux-based computer board with a wide range of compatible modules including cameras and Wi-Fi adapters (available here).