Focus Stacking for Teaching and Publication in Plant Sciences

This project aims to design a teaching tool and curriculum to teach focus stacked photography to secondary school children and undergraduates. This project follows on from Biomaker Challenge project Macrophotography of fern gametophytes using a DIY focus stacking system

The Idea

It has only recently become possible to take photographs of tiny plant specimens and have the full subject in focus. The technology is called focus stacking or deep focus photography. In this technique a large number of photographs are taken, while gradually moving the camera towards the subject. Each photograph has only some small areas in focus, and these focused areas are then cut out and merged together to make one, completely focused, image.

This technology is important for phenotyping in synthetic biology using Marchantia. It is also needed in very many other areas of biology research where the subject is very tiny. For example, in trichome research in Arabidopsis.

We aim to advance the use of deep focus photography in two ways:

  1. Develop a £100 teaching tool that can be used to teach the principles of deep focus photography, and a curriculum to accompany it.  
  2. Demonstrate and document how to convert the system so that it can take publishable photographs of the sort that can appear on the front cover of a journal, to be built for under £4000. Our system will accommodate subjects from 0.25mm to 1cm tall and beyond.

The Team

Dr Jennifer Deegan,
Visitor, Department of Plant Sciences, University of Cambridge

Dr Christopher Whitewoods,
Postdoctoral researcher, Cell and Developmental Biology, John Innes Centre

Dr Aleksandr Gavrin,
Research Associate, Sainsbury Laboratory, University of Cambridge

Mr Matthew Couchman,
Support Specialist, Computational and Systems Biology, John Innes Centre

Dr Richard Mortier,
University Lecturer, Computer Lab, University of Cambridge

Mr Tim Deegan,
External collaborator in the computing industry

Project Outputs

Project Report

This project is due to report in 2018.

Project Proposal

Original proposal and application


Project Resources

All resources are collated on this website. Documentation is also available on GITHUB, and youtube.