Advanced Imaging Resource

The Advanced Imaging Resource (AIR) provides equipment, training and support for all aspects of advanced light microscopy. We support imaging ranging from model organisms through to sub-cellular structures utilising cutting-edge imaging tools and technologies. We also offer practical workshops, seminars and demonstrations of new equipment. To keep up to date please see our SharePoint page: Scientific Facilities and Technical Services.

The facility office is located at CG:05/7 on the ground floor of the IGC Central Building and on the ground and first floor of the IGC South building at the Institute of Genetics and Cancer, Western General Hospital Campus. 

The facility supports four Zeiss upright systems for epifluorescent microscopy including a system dedicated to deconvolution microscopy. There are two Nikon inverted epifluorescent systems capable of live imaging. One system is specified for conditional imaging of multiwell plates and tiling, using the Nikon Jobs platform. All systems are equipped with objectives between 10x – 60x magnification and can image using 405, 458, 488, 514, 568, 594 and 640nm light with other objectives available upon request. For technical information please contact us.

The facility supports four confocal imaging systems, all of which are inverted in configuration and are equipped for live imaging:

• The Leica Stellaris is equipped with a white light laser and spectral detection, it has additional capabilities for FCS, FRAP, FLIM and FRET methods through the FALCON unit.
• The Andor Dragonfly is a new generation spinning disk confocal specified for imaging cells, live super-resolution and model organoids and organisms. It is equipped with laser lines at 405, 458, 488, 514, 560, 594, 640 and 680nm. It is capable of FRAP and Photoactivation utilising a Mosiac system. The SRRF software upgrade enables short live super-resolution experiments in 2D. The system has specialist lenses available upon request.
• The Nikon AX confocal is a point scanner equipped with 6 laser lines at 405, 458, 488, 514, 561 and 640nm.
• The Olympus FV3000 is located in the IGC South building. It is equipped with 6 laser lines at 405, 458, 488, 514, 561 and 640nm.
• The Olympus SpinR is a specialist system designed for high content imaging of individual Microscopy plates. This system comprises a Yokagawa spinning disk, 6 laser lines at 405, 458, 488, 514, 561 and 640nm and bespoke software for intuitive data processing from 96 or 384 well plates.

Our ESRIC centre of excellence hosts two systems at present. A Nikon SoRa equipped with at 405, 488, 514, 561 and 640nm lasers. This system doubles the Abbe resolution in x,y, and z dimensions and is suitable for cell and tissue samples. The Nikon N-STORM can carry out an array of single molecule localisation microscopy (SMLM) including, but not limited, to dSTORM, PALM and PAINT.

With the Histology core facility we offer equipment for scanning both colour brightfield and fluorescent slides. We also host a laser capture microdissection system. The Histology facility can offer support with sample preparation for laser capture. Together with the Mass Spectrometry facility, we are able to offer support for single cell proteomics.

• Fluorescent and Brightfield slide scanning – Zeiss Axioscan Z1, 4x, 10x, 20x, 40x objectives, DAPI, FITC, Texas Red, TRITC, Cy5 + BF scanning channels, can scan up to 100 slides.
• Brightfield slide scanning –  Hamamatsu Nanozoomer, 4x, 10x, 20x, 40x objectives, can scan up to 360 slides (from July 2025).
• Laser Capture – Leica Laser Capture Microdissection system, 4x, 10x, 20x, 40x, 63x objectives.

We provide a full range of image analysis support for research studies within the Institute of Genetics and Cancer. We can support your project from inception all the way to publication. Bioimage analysis is included within the hourly recharge for all AIR equipment (*). We support four powerful workstations which can be accessed in person or remotely. 

Software available includes: Fiji / ImageJ, CellProfiler, Imaris, QuPath, Napari and offline software for all our acquisition systems. 

(*) Please note – we reserve the right to either charge additionally or refuse projects involving imaging not carried out on equipment within AIR. Please contact the AIR manager to discuss any Bioimage analysis projects using data collected outwith the AIR facility. 

Specialist systems are available for supported imaging. Please contact Martin Lee at: martin.lee@ed.ac.uk for more details.

Multiphoton Microscope

Our bespoke multiphoton microscope features an APE PicoEmerald S laser coupled with an Olympus FV1000 inverted microscope. Utilizing two lasers (700-1031 nm) and five detectors, this flexible platform supports various imaging modalities, including:

• Two-Photon Fluorescence: Enables deeper imaging in thick samples using infrared light.
• Second Harmonic Generation: Provides label-free imaging of structured collagen.
• Coherent Raman: Offers chemically specific imaging of tissues using endogenous biomolecules such as lipids and proteins.
• Intravital Imaging: Facilitates long-term live imaging in mice through optical windows.

Oblique Plane Microscope

Oblique Plane Microscopy (OPM) is a form of light-sheet fluorescence microscopy that employs a single microscope objective to produce the illumination light sheet and detect resulting fluorescence. It is compatible with conventional sample mounting techniques, including 96- and 384-well plates, enabling high-throughput 3D screening.

Our bespoke multiphoton microscope features an APE PicoEmerald S laser coupled with an Olympus FV1000 inverted microscope. Utilising two lasers (700-1031 nm) and five detectors, this flexible platform supports various imaging modalities, including:

• Two-Photon Fluorescence: Enables deeper imaging in thick samples using infrared light.
• Second Harmonic Generation: Provides label-free imaging of structured collagen.
• Coherent Raman: Offers chemically-specific imaging of tissues using endogenous biomolecules such as lipids and proteins.
• Intravital Imaging: Facilitates long-term live imaging in mice through optical windows.

Oblique Plane Microscopy (OPM) is a form of light-sheet fluorescence microscopy that employs a single microscope objective to produce the illumination light sheet and detect resulting fluorescence. It is compatible with conventional sample mounting techniques, including 96- and 384-well plates, enabling high-throughput 3D screening.

The facility is supported by an experienced team of technical staff. As well as three expert technicians, the facility also has a dedicated bioimage analyst. We work closely with Histology, supporting digital pathology. In addition, the facility has a network of super-users who are available to discuss application of imaging techniques to molecular cell biology research. We also have a steering committee which meets annually and comprises of academics who utilise bioimaging significantly in their research, ECRs and Postdocs.

We are a sub-node of  BioimagingUK and the EuroBioimaging project. We work closely with other Bioimaging core facilities in Edinburgh through Edinburgh Bioimaging.

The AIR is part of a cross-disciplinary, cross-institutional collaborative consortium for super-resolution imaging - ESRIC. ESRIC is a national open access facility hosting state-of-the-art super-resolution microscopy equipment. ESRIC shares expertise through a prestigious international specialist supported by the Royal Microscopical Society. To celebrate the work of ESRIC and to develop our network, an annual symposium is hosted at the IGC.

Please visit the ESRIC website for more information.