Funded by the Royal Society Brian Mercer Feasibility Award


Professor Paul French and Dr James McGinty - Photonics Group, Physics Department


Molecular imaging is making a tremendous impact on biomedical research, particularly with fluorescence microscopy techniques that can exploit the ability to specifically label proteins of interest with intrinsic fluorescent labels using genetic engineering. For cell biology this enables biological outcomes of experimental interventions to be visualised in terms of specific morphological features and of changes in function, including of cell signalling networks. Basic research, preclinical studies of disease mechanisms and drug discovery have benefitted from the ability to visualise and quantify biochemical processes in a cellular context, rather than in solution. Today this trend from in vitro to in vivo is moving from the cellular scale to whole organisms since there is an increasing appreciation that the ~mono-layer cell cultures traditionally imaged in microscopes may exhibit non-physiological behaviour due to the artificially planar environment.  This has led to the increasing use of animal/embryo/engineered tissue structures, which has produced a growing need for high resolution in vivo 3-D imaging techniques that are applicable to “mesoscopic” (~0.5 - 10 mm scale) samples.  Such techniques are also valuable for developmental biology of embryos and plants and for applications in histopathology. For small (sub-mm) samples, standard fluorescence microscopy techniques such as confocal or multiphoton laser scanning microscopy (LSM) can provide the required 3-D images but these instruments are usually not suitable for imaging larger samples. This is partly because they have been designed for high resolution imaging of relatively small fields of view and partly because the focussing of light becomes more challenging with increasing depth in the sample and these techniques rely on precisely focussed light to achieve 3-D imaging.
For samples up to ~1 mm in size, an emerging technique is light sheet microscopy, which can provide a high depth resolution over larger fields of view than LSM but which still relies on precise focussing of excitation light to achieve 3-D imaging. Our project concerns the technique of optical projection tomography (OPT), which is the optical analogue of X-ray CT and can provide 3-D images of transparent samples up to cm in size. Because the 3-D image information is derived from the detected fluorescence signals (at multiple angular projections) and is independent of the excitation profile (requiring it only to be reasonably uniform) OPT scales easily from sub-mm to cm samples and is less sensitive to optical aberrations and scattering that quickly degrade the precise focussing of excitation light.
We have developed OPT instruments that range from low cost systems for rapid 3-D imaging of fixed, cleared tissue for histopathology applications such as volumetric beta cell mass assays in the pancreas to study mechanisms and potential therapies of diabetes to high resolution multichannel instruments for in vivo image of live disease models including adult zebrafish that can be used to provide readouts of cancer progression and global cell signalling responses to inflammation and infection. These include sophisticated OPT systems providing spectroscopic readouts including multispectral absorption and fluorescence imaging and fluorescence lifetime imaging (FLIM).
In this project we aim to provide upgradeable, modular OPT instruments with open source software that will enable academic researchers to access these 3-D imaging capabilities at a much lower cost than LSM or light sheet microscopy and which will find commercial application in drug discovery. We will develop an open source software platform for data acquisition, analysis, management and sharing and would enable academic users to integrate OPT workflows into their research and thus help establish markets for commercial applications, including in drug discovery (for which we can enable longitudinal studies of live disease models (c.f. figures 1(g,h)), thereby reducing the number of animals required for testing.
Specifically, we are developing two modular instruments for evaluation in biomedical laboratories.  The first prototype represents the simplest offering that would address the needs of the existing OPT community but which could be upgraded, including to imaging with higher magnification, higher resolution and advanced modalities such as multispectral and fluorescence lifetime imaging. The second prototype will employ more sophisticated illumination sources and provide imaging of both mm and cm scale samples. Both instruments would provide academic users with a complete system including open source software with data acquisition controlled by MicroManager, FBP image reconstruction using GPU enabled MatLab programmes and data management/sharing utilising OMERO.  The open source approach to software enables users to fully customise instruments for their own specific research programmes.
Prototype A will be designed to image samples up to 1 cm3 and will be applied to image fixed, cleared mouse pancreas with antibody staining, e.g. for volumetric β-cell assays in the Guy Rutter lab at Imperial. It will be optimised for 2 dye labels and background autofluorescence with excitation provided by LED sources (making it eye-safe).
Prototype B will also be designed to image samples up to 1 cm3 but will have a second 4x imaging channel for higher resolution imaging of smaller (~1 mm) samples such as zebrafish embryos. As well as imaging fixed, cleared tissue with antibody staining, it will be designed to excite CFP, GFP and RFP with automated spectral selection and will provide sufficient power to enable OPT data sets to be acquired on timescales commensurate with live samples. We anticipate that it could be applied to image zebrafish and murine tissue (including pancreas and brain) – including with the latter being cleared using CUBIC to preserve GFP/RFP emission. Multiplexed OPT would be implemented to enhance resolution and imaging speed. This prototype would be tested at the Francis Crick Institute in the Axel Behrens and Erik Sahai laboratories (currently at LRI-CRUK).


Selected OPT publications

Optical Projection Tomography as a Tool for 3D Microscopy and Gene Expression Studies, J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sorensen, R. Baldock and D. Davidson, Science 296 (2002) 541-545

Fluorescence Lifetime Optical Projection Tomography, J. McGinty, K. B. Tahir, R. Laine, C. B. Talbot, C. Dunsby, M. A. A. Neil, L. Quintana Rio, J.  Swoger, J. Sharp and P. M. W. French, J Biophotonics 1 (2008) 390-394

Ablation of AMP-activated protein kinase alpha 1 and alpha 2 from mouse pancreatic beta cells and RIP2.Cre neurons suppresses insulin release in vivo, G. Sun, A. I. Tarasov, J. McGinty, A. McDonald, G. D. Xavier, T. Gorman, A. Marley, P. M. French, H. Parker, F. Gribble, F. Reimann, O. Prendiville, R. Carzaniga, B. Viollet, I. Leclerc, and G. A. Rutter, Diabetologia 53, 924-936 (2010)

In vivo fluorescence lifetime optical projection tomography, J. McGinty, H. B. Taylor, L. Chen, L. Bugeon, J. R. Lamb, M. J. Dallman, and Paul M. W. French, Biomed. Opt. Expr. 2 (2011) 1340-1350

Simultaneous angular multiplexing optical projection tomography at shifted focal planes, L. Chen. J. McGinty and P. M. W. French, Opt Lett 38, (2013) 851

Accelerated Optical Projection Tomography Applied to In Vivo Imaging of Zebrafish”, T. Correia 1, N. Lockwood, S. Kumar, J. Yin, M-C Ramel, N. Andrews, M. Katan, L. Bugeon, M J Dallman, J McGinty*, P. Frankel*, P. M W French* and S. Arridge*, PLoS ONE 10(8): e0136213, doi:10.1371/journal.pone.0136213

Visualising apoptosis in live zebrafish using fluorescence lifetime imaging with optical projection tomography to map FRET biosensor activity in space and time, N. Andrews, M-C Ramel, S. Kumar, Y. Alexandrov, D. J. Kelly, S. C. Warren, L. Kerry, N. Lockwood, A. Frolov, P. Frankel, L. Bugeon, J. McGinty, M. J. Dallman* and P. M. W. French*, Early view J. Biophotonics 1–11 (2016) / DOI 10.1002/jbio.201500258

Quantitative in vivo optical tomography of cancer progression & vasculature development in adult zebrafish, Sunil Kumar, Nicola Lockwood, Marie-Christine Ramel, Teresa Correia, Matthew Ellis, Yuriy Alexandrov, Natalie Andrews, Rachel Patel, Laurence Bugeon, Margaret J. Dallman, Sebastian Brandner, Simon Arridge, Matilda Katan, James McGinty,*, Paul Frankel,*, Paul M. W. French*, To be published in Oncotarget.