Quantified-imaging and Visualisation

Biological images and data provide little insight into the underlying process until these are quantified and thus turned into useful information.

Professor John Girkin

The physical methods including atomic force, electron and visible light microscopy, X-ray crystallography, fluorescence and magnetic resonance are all aimed at probing the structure and function of biological systems with quantified information. Researchers at Durham have a specific expertise in developing novel optical instrumentation both at the microscopic imaging level and also for large samples. With all of the imaging work undertaken "pretty pictures" provide little information to help biological understanding. Thus a strong emphasis in the BSI is converting the data recorded, either from an imaging instrument or say a spectrometer, into quantified data with a strong emphasis on then presenting this data in a visual form.

Linked with data collection and visual presentation, is work to explore how people visualise in general:  Linking visual perception in psychology with, for example, three dimensional data projection systems. An example of the breadth of the work in this field: research is underway that looks at the way the lens develops with the aim of helping to prevent cataracts and other ophthalmic complications.

Areas of Research

The BSI is very keen to collaborate to solve challenging life science imaging and visualisation problems from observing high-speed mitochondrial movement to the imaging of the removal of fat from clothes. Some of the current projects and programmes of work are outlined below.

Novel Optical Imaging

An underlying thread within the BSI is the development of novel imaging methods for a range of biological challenges. Current projects include:

• Single Plane Illumination Microscopy (SPIM) linked with a heart synchronisation method to image beating Zebra fish hearts.  For a podcast about the Beating Hearts at High Resolution project please see the right hand navigation bar.
• Biospectroscopy where a fibre optic based imaging spectroscope, normally used in astronomical telescopes, has been applied to a microscope to study local changes in the spectra emitted by samples.
• Adaptive optics applied to widefield, confocal and non-linear microscopy to correct for tissue aberrations.
• Micro-endoscopes (under 1mm in diameter) and cameras for long term embedded in vivo imaging.

Contact: Professor John Girkin

3D Visualisation

Through the BSI's collaborations with computer science, engineering, psychology and physics, complex data sets are being analysed and presented in 3D. As well as presenting the information in this manner research is underway as to how this is perceived and understood by the user.

• Stereo Tumour Imaging is a project exploring the way clinicians assess images in 3D in relation to cancer diagnosis. Visualisation is a collaborative project with Professor Marty Banks (Berkeley) looking at 3D perception of vision and how the eye and brain focus on an image. Manipulation of Microscopy Images is a multifaceted project developing software for 3D visualisation of original data sets from the novel instruments developed within Durham, and beyond. 3D Television is a project looking at the psychological and physiological issues associated with 3D television.

Contact: Dr Nick Holliman 

Structural Determination

A large focus of the BSI that cuts across several departments is the use of X-ray diffraction and electron microscopy to look at structures at different levels.  Research in Protein Structural Analysis and Electron Microscopy makes a large contribution to this area.

 Contact: Dr Ehmke Pohl

The 4^th Dimension in Imaging

With the developments in optical imaging more data sets are emerging with time along with the 3D information. Thus BSI researchers are involved in several projects looking at how this data can be recorded and gathered and crucially subsequently processed:

• Lens cell movement is an area looking at GFP transfected fish to study how the lens develops using complex 4D data sets, tracking individual cell movement. Mitochondrial tracking is a project with collaborators in Durham, Newcastle, Strathclyde using a number of different models from fish to stem cells and blood vessels all of which have the common theme of high speed mitochondrial movement. SPIM: Another aspect of the SPIM project with Zebra fish is the tracking over extended periods of time of cell migration, including apoptosis, in developing embryos and plants. Intermediate Filaments and Optical Tweezing is a series of projects linking both data collection using optical tweezers to probe the local cell environment and theoretical modelling of the processes taking place.

Contact: Professor John Girkin