IMAGING AND VISUALISATION SEMINARS -------------------------------- Date and time: Friday 2nd November 2007 at 12:30 Location: Room 245, School of Computer Science Title: Serious Games -The Human Factor Speaker: Professor Bob Stone (http://www.eece.bham.ac.uk/Default.aspx?tabid=154) Institution: Electrical, Electronic & Computer Engineering (http://www.eece.bham.ac.uk/Home/tabid/53/Default.aspx) Host: Dr Jeremy Wyatt Abstract: Serious Games - The Human Factor The University of Birmingham’s Human Interface Technologies (HIT) Team (www.iecs.bham.ac.uk/hit/) has been pioneering the development and uptake of serious games technology for nearly 4 years, building on 20 years of experience in the domain of Virtual Reality. The Team’s participation within the UK’s Human Factors Integration Defence Technology Centre (www.hfidtc.com) has also provided a range of excellent opportunities to work closely with stakeholders and end users in the development of methodologies supporting human-centred design for serious games-based part-task trainers. In particular, the research is helping to avoid the technology push failures evident in the VR “era” of the 1990s by developing and evaluating demonstrators that emphasis the critical importance of exploiting human factors knowledge when specifying issues such as task and context fidelity, learning content, evaluation metrics and interactive technology appropriateness. This presentation will concentrate on a variety of ongoing serious games projects where early human factors attention has been crucial to the successful design, development and evaluation of a range of demonstrators. The examples to be presented include part-task trainers for close-range naval weapons procedures, submarine safety systems awareness, defence mental health therapy support, explosive ordnance disposal and marine archaeology (the Virtual Scylla artificial reef initiative – virtualscylla.org). -------------------------------- Date and time: Friday 9th November 2007 at 13:00 Location: Room 245, School of Computer Science Title: An Introduction to Upside-Down Remote Sensing Speaker: Dr Lee Chapman (http://www.gees.bham.ac.uk/people/index.asp?ID=374) Institution: School of Geography, Earth & Environmental Sciences (http://www.gees.bham.ac.uk/) Host: Professor Ela Claridge Abstract: An Introduction to Upside-Down Remote Sensing Over the last decade, a number of applications have been developed which utilise ground-based hemispherical photography. The collection of such imagery can be described as 'upside down remote sensing' as instead of viewing the earth from a platform in the sky, techniques are being employed to view the sky from the earth. This paper reviews the theory and potential applications of 'upside down remote sensing' across the electromagnetic spectrum. To date, apparatus has been developed to detect various wavelengths between ultra-violet and infrared. Potential applications using these wavelengths are numerous and include identification of plant and trees species, measurement of the sky-view factor, and automation of cloud cover measurements. -------------------------------- Date and time: Friday 16th November 2007 at 13:00 Location: Room 245, School of Computer Science Title: Flourescent Imaging and Visualisation of Organic Matter Speaker: Professor Andy Baker (http://www.gees.bham.ac.uk/people/index.asp?ID=260) Institution: School of Geography, Earth & Environmental Sciences (http://www.gees.bham.ac.uk/) Host: Professor Ela Claridge Abstract: Fluorescent Imaging and Visualisation of Organic Matter This seminar will introduce the various facilities available in the School of GEES to image, and characterise, fluorescent organic matter. The organic matter in question is that found in the environment, and includes soil derived humic material, and cellular and extra cellular material, found in soils, sediments, rivers and lakes; and anthropogenic pollutants such as optical brighteners, sewage and trade effluents. Imaging techniques include UV microscopy and UV luminescence spectrophotmetry, which can be applied to both solid and liquid samples at a range of scales from centimeter to micrometer. Case studies will be given, as well as an overview of more advanced techniques such as the use fluorescence quenching reactions. Various visualisation techniques will be presented that enable to the interpretation of fluorescence results which often comprise very large and complex datasets. -------------------------------- Date and time: Friday 7th December 2007 at 13:00 Location: Room 245, School of Computer Science Title: Near Infrared Optical Tomography for the detection of breast cancer Speaker: Dr Hamid Dehghani (http://newton.ex.ac.uk/research/biomedical/hd/) Institution: School of Physics, University of Exeter (http://www.ex.ac.uk/) Host: Professor Ela Claridge Abstract: Near Infrared Optical Tomography for the detection of breast cancer. Abstract: Near-Infrared (NIR) tomography has the potential for characterization of different tissue types based upon cellular and vascular alternations. This is especially useful for characterizing cancerous regions within normal tissue. Reconstructed images from NIR light propagation measurements through the female breast hold promise of providing clinically useful information about the patho-physiologic change of the tissue, specifically for the detection and characterization of cancer. Clinical optical imaging systems will be outlined as well as the developed numerical model and image reconstruction algorithms. Based on these algorithms, reconstructed images of the breast are presented, from multiple patient data. Additionally, the use of a-priori data such as spatial and spectral information are also presented and discussed. -------------------------------- Date and time: Friday 1st February 2008 at 13:00 Location: UG40, School of Computer Science Title: Optical Coherence Tomography: an emerging clinical imaging modality Speaker: Dr Gordon McKenzie (gordon.mckenzie@md-ltd.co.uk) Institution: Michelson Diagnostics Ltd (http://www.md-ltd.co.uk/) Host: Professor Ela Claridge Abstract: Optical Coherence Tomography: an emerging clinical imaging modality. Optical Coherence Tomography is an optical analogue of ultrasound, offering real time, non-ionising, micron resolution imaging of tissue. It has found great acceptance within the Ophthalmic clinical community, and has rapidly become the gold standard to whilch all other retinal imaging techniques are compared. The use of OCT in other clinical areas has not yet become the norm, although with technological advances this is changing rapidly. Recent studies have concluded that OCT is able to usefully distinguish clinically relevant tissue subtypes in-situ. This talk will give a background to the technique, explore the strengths and drawbacks of its capabilities, and outline where the technique is going. It will also examine the challenges involved in moving from researching OCT to research using OCT, and in moving OCT from the lab to the clinic. About the speaker Gordon McKenzie is a founder director of Michelson Diagnostics. He has a PhD in Biomedical Optical Engineering from the University of Warwick. MDL is a start-up company founded in 2006 by five ex-employees of Sira, and focused on bringing novel OCT instrumentation to the clinical and research markets. Gordon.McKenzie@md-ltd.co.uk http://www.michelsondiagnostics.com -------------------------------- Date and time: Friday 8th February 2008 at 13:00 Location: UG40, School of Computer Science Title: The Future of Aquatic Dissolved Organic Matter Monitoring: High Resolution Spatial and Temporal Measurements by In-Situ Instrumentation Speaker: Dr Rob Spencer (rgspencer@ucdavis.edu) Institution: University of California (http://www.ucdavis.edu/index.html) Host: Professor Ela Claridge -------------------------------- Date and time: Friday 15th February 2008 at 13:00 Location: UG40, School of Computer Science Title: Diffuse optical tomography of the breast and infant brain Speaker: Professor Jem Hebden (http://www.medphys.ucl.ac.uk/~jem) Institution: University College London (http://www.medphys.ucl.ac.uk/) Host: Professor Ela Claridge Abstract: Diffuse optical tomography of the breast and infant brain When light passes through tissue, differences between the absorption spectra of oxygenated and non-oxygenated haemoglobin enable changes in the amount of blood in the tissue and its degree of oxygenation to be determined. This has led to the development of near-infrared spectroscopy and imaging techniques for monitoring haemo-dynamics and oxygenation in vivo. However, light is strongly scattered in tissue so that transmission images across large (> 1 cm) thicknesses exhibit very little internal detail. To help overcome this problem, instruments have been built which measure times-of-flight of transmitted photons, which give much greater information about the internal optical properties of the tissue. In addition, sophisticated image reconstruction algorithms have been developed which convert measurements between multiple positions on the surface into three-dimensional (3D) distributions of absorbing and scattering properties [ ]. The development of so-called diffuse optical tomography has focussed primarily on two clinical problems: imaging blood oxygenation and functional activity within the brain, and the detection and specification of breast cancer. Two distinct approaches have been investigated for brain imaging. One involves placing a pad of optical fibres on the surface of the head, and measuring light that is diffusely reflected by brain tissues immediately the below the probe. This method has been widely used to display small localised changes in blood volume and oxygenation occurring in the cortex of the brain in response to sensory stimulation and cognitive activity [ ]. Meanwhile, a second approach involves reconstructing a full 3D image of the brain using transmission measurements. Our group at University College London (UCL) has used a 32-channel time-resolved instrument and a non-linear image reconstruction algorithm to obtain the first 3D optical images of the brains of premature infants in intensive care [ , ]. This technique is being developed as a means of diagnosing hypoxic-ischaemic brain injury in newborn infants and monitoring response to new forms of treatment. Figure 1 below shows an infant wearing a helmet which holds 32 optical fibre bundles in contact with the head during a scan. Figure 1. A fibre holder helmet on head of an infant during imaging scan Figure 2. 3D absorption images of infant brain in response to increase in ventilated CO2. Figure 3. Right and left breast images of a patient with a tumour in the right breast. One of the first studies involved reconstructing the differences in the optical properties which occurred in the brain of a mechanically-ventilated infant resulting from small alterations in ventilator settings [4]. Figure 2 shows coronal and sagittal slices revealing the changes in absorption at 815 nm due to an increase in carbon dioxide pressure. The associated increase in blood volume produced increased absorption, concentrated within the cerebral hemispheres. Several research groups are also exploring diffuse optical imaging techniques as means of detecting breast disease [1]. At UCL we have performed studies on about 80 patients and healthy volunteers using our time-resolved optical imaging system [ ,6]. A scan lasting about 5 minutes provides absorption and scattering images representing tomographic slices across the breast. Figure 3 shows absorption images obtained from the right and left breast of a 48-year-old woman with a grade III carcinoma in her right breast. The high contrast produced by this lesion is primarily due to hypervascularisation. -------------------------------- Date and time: Friday 29th February 2008 at 13:00 Location: UG40, School of Computer Science Title: Mapping microstructure and connectivity of the brain with diffusion MRI Speaker: Dr Daniel Alexander (http://cmic.cs.ucl.ac.uk/staff/daniel_alexander/) Institution: University College London (http://cmic.cs.ucl.ac.uk/home/) Host: Professor Claridge -------------------------------- Date and time: Friday 7th March 2008 at 13:00 Location: UG40, School of Computer Science Title: Exploratory Data Analysis of Excitation-Emission Matrices applied to Water Quality Speaker: Professor Brunsdon (http://www.le.ac.uk/gg/staff/academic_brunsdon.html) Institution: University of Leicester (http://www.le.ac.uk/gg/index.html) Host: Professor Ela Claridge -------------------------------- Date and time: Friday 6th June 2008 at 14:00 Location: UG40, School of Computer Science Title: Image processing challenges in whole-body molecular imaging Speaker: Professor Lelieveldt (http://www.lumc.nl/1010/LKEBHome/english/research/KGB/LKEBKGBMain.html) Institution: University of Leiden, Netherlands (http://www.leiden.edu/) Host: Professor Claridge Abstract: Image processing challenges in whole-body molecular imaging With the rapid progress in molecular imaging technology, biomedical imaging is now covering a broad scale range, from the molecular level through the cellular level to the scale of the whole organism. Molecular processes can be visualized with optical, nuclear and MR imaging using targeted contrast agents, anatomical details with structural modalities (CT, MR, ultrasound), and functional information with e.g. specialized MR acquisitions. In pre-clinical research, the complementary information provided by these imaging techniques has great potential for enhanced knowledge discovery and treatment development. This presentation introduces a number of recently emerged small animal imaging modalities, and discusses specific image processing challenges inherent to these modalities. New algorithms will be discussed for fusion of optical and structural imaging, and for whole-body registration and segmentation in micro-CT follow-up studies. -------------------------------- Date and time: Friday 3rd October 2008 at 13:00 Location: UG40, School of Computer Science Title: Biophotonic Imaging and its Uses for Monitoring and Tracking Disease Events in Live Animals Speaker: Dr Kevin Francis Institution: Caliper Life Sciences Host: Professor Claridge -------------------------------- Date and time: Friday 10th October 2008 at 13:00 Location: UG40, School of Computer Science Title: Multispectral Imaging for the Detection of Retinal Diseases Speaker: Dr Iain Styles (http://www.cs.bham.ac.uk/~ibs/) Institution: University of Birmingham (http://www.bham.ac.uk/) Host: Professor Claridge Abstract: Multispectral Imaging for the Detection of Retinal Diseases Multispectral imaging combines the spatial resolution of conventional colour photography with the spectral information provided by spectroscopy. We will discuss how this imaging technique can be combined with computational models of the imaging process to yield previously unquantifiable information about the composition of retinal tissues, and how this information could be used in the clinic. We will present some of the initial findings of this work, and discuss how developments in imaging technology and computational techniques will lead to considerable improvements in the quality of the results. -------------------------------- Date and time: Friday 17th October 2008 at 13:00 Location: UG40, School of Computer Science Title: Image Analysis in Drug Discovery: Facts versus Artefacts Speaker: Dr Alison Bigley Institution: AstraZeneca Host: Professor Ela Claridge Abstract: Image Analysis in Drug Discovery: Facts versus Artefacts. Summary: The quantitative analysis of proteins, localised by immunohistochemical procedures, with respect to morphological characterisation has been singled out by the FDA as a promising tool in support of many stages of drug development, from preclinical research to clinical trials. Computerised image analysis technology is used in support of the Safety Assessment of Pathology tissue samples, by enabling the precise measurement of small changes in structure and function with respect to treatment and time. The processes used for the production and staining of samples for such analysis and the systems employed to evaluate structural and/or functional changes contain inherent problems, resulting in both deterministic and stochastic artefacts. These factors need to be taken into consideration when embarking on computer-assisted analysis of light microscopical images for regulatory submission. A range of processing, optical and system fundamentals will be discussed in order to highlight how artefacts may hinder the production of robust and accurate quantitative data. -------------------------------- Date and time: Friday 6th March 2009 at 13:00 Location: UG40, School of Computer Science Title: Demonstration of an Optical Coherence Tomography (OCT) Imaging System Speaker: Dr Jon Holmes (http://www.md-ltd.co.uk/our-team.html#holmes) Institution: Michelson Diagnostics Ltd. (http://www.md-ltd.co.uk/) Host: Professor Claridge Abstract: Demonstration of an Optical Coherence Tomography (OCT) imaging system A state-of-the-art commercial multi-beam Optical Coherence Tomography (OCT)imaging system will be demonstrated, showing the capability of the instrument to provide high resolution (< 10 µm) images of tissue in real time, revealing details of tissue microstructure. We will discuss aspects ofthe physics and technology of OCT that require study that may enable further improvements in diagnostic image quality. -------------------------------- Date and time: Friday 20th March 2009 at 13:00 Location: UG40, School of Computer Science Title: Time-resolved fluorescence imaging Speaker: Professor Hemmila Ilkka (ilkka.hemmila@perkinelmer.com.) Institution: Perkin-Elmer Life Sciences (http://las.perkinelmer.com/) Host: Professor Claridge Abstract: Time-resolved fluorescence imaging Time-resolution with long decay-time probes has gained established position as a tool in diagnostics and drug discovery to enable both highly sensitive assays (DELFIA) or simple homogeneous assays (TR-FRET). The potential of TR detection has created interest also in the attempt to gain the same improvements in gated imaging on cells and tissues by means of eliminating all ambient interferences through temporal filtering. In imaging decay times can be exploited in different ways. In lifetime imaging (FLIM) regular fluorescent probes are used and decay times or decay time changes are employed as the assay response. Lanthanide chelates, having millisecond decay times, allow the use of very simple millisecond time-domain gating and complete temporal discrimination of autofluorescence background. This allows robust background-free images of stained tissues or fixed cellular samples having normally very high autofluorescence interference. This has been achieved through highly fluorescent, stable and biocompatible lanthanide chelates. Lanthanide chelates, due to their exceptional Stoke´s shift, are also perfect for various signal amplification technologies, such as nanobeads, clusters or enzymatic amplifications (tyramine reaction). Lack of inner-filter quenching allows efficient and queantitative signal amplification The applications published so far are mostly based on fluorescent europium chelates as the labels and image acquisition taken after appropriate delay with CCD camera. The overall goal, improving sensitivity, is not achieved in all applications, mainly due to the slow photon production rate of lanthanides making their use slow and cumbersome in confocal imaging system requiring very high resolution. On the other hand, lanthanides have provided clear advantages in imaging applications where accurate quantification is needed (lack of inner filter quenching), samples and conditions where background is problematic (fixed cells, and samples with environmental contaminants), and applications where multiple colors are needed (e.g. multi-label differential cell counting). -------------------------------- Date and time: Friday 27th March 2009 at 13:00 Location: UG40, School of Computer Science Title: Luminescent Lanthanide Complexes for Imaging at the Nanoscale: from DNA labels to nanoparticles Speaker: Dr Zoe Pikramenou, School of Chemistry (http://www.chem.bham.ac.uk/staff/pikramenou.shtml) Institution: University of Birmingham (http://www.bham.ac.uk/) Host: Professor Ela Claridge -------------------------------- Date and time: Friday 8th May 2009 at 13:00 Location: UG40, School of Computer Science Title: Inverse Problems in Biomedical Photoacoustic Imaging Speaker: Dr Ben Cox (http://www.medphys.ucl.ac.uk/~bencox/) Institution: University College London (http://www.ucl.ac.uk) Host: Professor Ela Claridge Abstract: Inverse Problems in Biomedical Photoacoustic Imaging Biomedical photoacoustic imaging uses laser-generated ultrasonic pulses to image soft tissue with sub-100 micron spatial resolution. One of its successes to date has been in imaging the microvasculature within optically-scattering tissue, such as around small animal brains and in human skin. The experimental photoacoustic scanner used at UCL, and photoacoustic images obtained using it will be shown. Also, the physical principles behind the technique, and some of the inverse problems associated with it will be discussed, including quantitative imaging, and how image reconstruction relates to wave chaos. -------------------------------- Date and time: Friday 15th May 2009 at 13:00 Location: UG40, School of Computer Science Title: Functional- and molecular- tomography of glowing mice and blushing brains Speaker: Dr Joseph Culver (http://orl.wustl.edu/people/joe.htm) Institution: Washington University School of Medicine (http://medschool.wustl.edu/) Host: Professor Ela Claridge Abstract: Functional- and molecular- tomography of glowing mice and blushing brains Our lab explores ways of leveraging non-invasive optical measurements for both functional- and molecular- biological imaging. Optical approaches to small animal in vivo molecular imaging provide high sensitivity, stable non-radioactive probes, and an extensive array of functional reporting strategies. For example optical methods can report on large variety of protein activities, and reveal cancer progression by imaging events such as angiogenesis and metastases. However, quantitative whole body assays in live intact animals remain elusive. While bioluminescence and fluorescence reflectance planar imagers provide quick assessments, quantitative localization is lacking due to strong depth dependence in sensitivity, masking of buried targets by superficial tissues, and poor resolution. We are developing a small animal fluorescence tomography (FT) platform to address these imaging challenges. With a fast scanning FT prototype we have begun tackling the practical challenges of providing flexible- and dense- spatial sampling, whole body field-of-view and reasonable scan times (minutes). Currently we are extending our FT platform into the ultrafast time domain (~1ns) to improve a number of image quality metrics and further expand our biological reporting strategies. For application in humans we are developing a portable device for functional neuroimaging. Diffuse optical tomography (DOT) is well-suited for several novel situations including studies of human child development that would benefit from enriched ecological environments for a wider range of behavioral paradigms. However, successful DOT in humans is challenging due to the concurrent requirements of high-dynamic range, low crosstalk, high channel counts, and sufficient temporal resolution. Hence, most optical imaging of human brain activity is performed using a topography approach with relatively sparse imaging arrays. Tomographic approaches offer benefits including volumetric localization and better discrimination of the functional brain signals from the background that are crucial to establishing DOT as a standard brain-mapping tool. We have developed new instrumentation with improved performance characteristics that permits use of high-density DOT arrays. Current studies in the adult visual cortex demonstrate the capability to distinguish activation sites separated by ~ 1cm. Our goal is to develop DOT for mapping activity throughout the outer surface of the brain with sub-centimeter resolution. -------------------------------- Date and time: Friday 12th June 2009 at 13:00 Location: UG40, School of Computer Science Title: Demonstration of an Optical Coherence Tomography (OCT) Imaging System Speaker: Dr Jon Holmes (http://www.octnews.org/entity/profile/jon-holmes/) Institution: Michelson Diagnostics Ltd (http://www.md-ltd.co.uk/) Host: Professor Ela Claridge Abstract: Demonstration of an Optical Coherence Tomography (OCT) imaging system A state-of-the-art commercial multi-beam Optical Coherence Tomography (OCT) imaging system will be demonstrated, showing the capability of the instrument to provide high resolution (< 10 µm) images of tissue in real time, revealing details of tissue microstructure. We will discuss aspects of the physics and technology of OCT that require study that may enable further improvements in diagnostic image quality.