Research Interests
Contents
Optical Tomography
My current work is in optical tomography, using the MONSTIR imaging system. Much of our work is in collaboration with the UCL Centre for Perinatal Brain Injury and Repair and the Medical Imaging Group of the Department of Computer Science.
BORL meetings
BORL has weekly meetings and a Journal Club.TOAST documentation
We use the TOAST image reconstruction software, written by Martin Schweiger and Simon Arridge.Tutorial
Here is a tutorial, explaining in tedious detail how to do 2D and 3D forward modelling and reconstruction in toast.Format of def files
Most of the options available in toast are accessible through the definition file which is described here as html and as postscript.I used latex2html v99.1 to generate these html pages. To get it to work with my version of Linux (Redhat 7.0), I had to also install giftrans and modify the latex2html perl script according to these details.
Blob moving across a tank
absorption blob scatter blob
Some reconstruction details:
The blob had 5x higher mua and mus than the background properties of mua=0.01mm-1, mus=1.0mm-1. It was a cylinder, 7mm diameter and 7mm tall, moved in steps of 5mm from the centre to 25mm across a cylindrical tank. The tank was 70 mm diameter and 140 mm tall. Images were reconstructed on a 12 x 12 x 16 linear pixel basis using intensity ratio and meantime difference datatypes. The finite element mesh had 40513 nodes and 26268 quadratic elements. The images above are displayed by selecting only those nodes which had values of greater than 90% of the peak change in the image.3D meshing
To reconstruct images using TOAST, we need a good 3D finite element mesh. Generating such a mesh for an irregular, complex shape such as the head is difficult. The picture below on the left shows an optical phantom, designed to simulate a baby's head, being imaged with MONSTIR. We then generated meshes of the phantom using Netgen. We took a CT scan of the phantom, generated a surface mesh using this software (below middle), and modified it using VTK before generating the volume mesh (below right). At the bottom, there are some preliminary reconstructed images showing the attenuation (mua) and scatter (mus) of light in slices through the head.
Student Supervision
PhD
- Ben Price
- David Sen Wong
- Roberto Aguilera
- Teresa Correia
- Christos Panagiotou: Prior information in Diffuse Optical Tomography. 2005-2008.
- Caroline Reid: Spectroscopic techniques for medical diagnosis at optical and terahertz wavelengths. 2005-2008 First year talk
- Dave Jennions: Advences in optical tomography instrumentation. 2003-2006
- Tara Yates: Time-resolved optical tomography for the detection and specification of breast disease 2003-2005
2007
- MSc - Kaiban Shen: A compressible optical/MR phantom
- BSc - Saman Dallali: A new user interface for frequency-multiplexed near-infrared topography system for imaging functional activation in the brain
- BSc - Rahmatulai Maane: Exploring the effect of coupling fluid properties ion optical mammography images
- BSc - John Fiallos: Optical tomography of tissues using non-contact sources and detectors
- BSc - Daniel Hopper: Comparison between three hemispherical cups used for opticla imaging of the breast
2006
- MSc - Girvani Manoharan: Reconstruction of optical mammography images using prior information
- Intercalated BSc - Sheetal Patel: Investigating and compensating for the effect of hair on imaging the brain with optical tomography.
- Intercalated BSc - Nick Norton: Characterising the optical properties of the human heel and a tissue-equivalent phantom.
- BSc - Ali Moghanchi: Data analysis and image reconstruction in optical imaging.
- BSc - Ben Price: Design and construction of a breast phantom with realistic x-ray, optical, and elasticity properties.
2005
- MSc - Gurps Rehal: Combined x-ray/optical mammography reconstruction
- MSc - Arron Dowdall: A phantom for combined MR/optical imaging
- BSc - Rebecca Anderson: Study of the potential for a combined optical and x-ray mammography system using a compressed breast phantom
- Intercalated BSc - Nina Breunung: A combined imaging system for mammography using x-ray and optical methods
- BSc - Matthew Panayiotou: Three-dimensional imaging of an unfertilised chicken egg using optical tomography
- BSc - Elisabeth Deutsch: Characterisation of the scattering anisotropy of muscle fibres using near-infrared light
- Intercalated BSc - Chris Pawley: Development of a simple "Monte Carlo" computer program for simulating light travel in biological tissue
2004
- Intercalated BSc - Oliver Pearce: Measurement of the spectral response of the eye
- Intercalated BSc - Will Kieffer: Optical imaging of blood volume and oxygenation changes within the finger
2003
- MRes - Dave Jennions, CAIS
- BSc Group Project - Blood pressure monitoring
- Intercalated BSc - Asad Khan: A Phantom for evaluating the effect of Cerebro-spinal fluid on the optical imaging of the brains of the newborn
2002
- Intercalated BSc - Ed Matthews: Design and Construction of a Blood filled Phantom
- Intercalated BSc - Andrew Matheson: Near infrared spectroscopy across the adult chest: in vivo measurements and computer modelling
Electrical Impedance Tomography
See my PhD thesis and a website I helped to set up.