BioImaging Facility - John Innes Centre

The JIC Bioimaging facility is a well-equipped light and electron microscopy unit. Its dedicated team has many decades of imaging experience. This accessible expertise enables a fast-track consultative approach to experimental design/method development, thus maximising the chances of early success and optimising results quality. Although the primary research focus at JIC is plant science related, the team welcomes enquiries from anyone interested in using the imaging facilities.


Imaging Platforms

Keywords - Light Microscopy: Confocal microscopy | Superresolution microscopy | Widefield microscopy | TIRF | Live cell imaging | PALM | STORM | FCS/FCCS | Structured Illumination Microsocpy
Keywords - Electron Microscopy: Transmission EM | Scanning Transmission EM | Electron tomography | Scanning EM (FEG) | Cryo-SEM

The JIC Bioimaging facility has a super-resolution system (Zeiss Elyra PS1), two spinning disk confocals (Andor Revolution XD and VisiTech) and two point-scanning confocals (Zeiss LSM 780 and Leica SP5) plus a good range of other wide-field and stereo light microscopes, all with digital cameras. A range of inverted and upright systems will cover most requirements. Image analysis workstations are also available.

There is also a transmission electron microscope (FEI Tecnai 20) and two field-emission scanning electron microscopes (FEI Nova NanoSEM 450 and Zeiss Supra 55 VP) plus a variety of specialist sample preparation equipment for EM such as coaters, a high-pressure freezer, embedding machines and ultramicrotomes. Both SEMs have Gatan cryo-systems with high and low vacuum capabilities. ETD, TLD (In lens), BSE, STEM and EDS detectors are all available.


Keywords – Biological: Cell Biology | Developmental Biology | Plant Biology | Microbiology | Bio-materials | Food
Keywords - Physical Sciences: Bioengineering and biomaterials | Nanomaterials (nanoparticles, 2D nanomaterials, nanowires and nanotubes) | Polymers and organic electronics

Whilst our expertise is particularly strong in the two areas of high-resolution cryo-SEM and live-cell imaging using GFP technology, we support a wide range of specialist imaging techniques and can accommodate various types of samples, from whole tissues to nano-structure imaging.

All our confocal systems are equipped with multiple lasers (to excite most available dyes) and highly sensitive detectors. This, together with the rapid acquisition using our spinning disc confocals, enables detailed analysis of living cells. Using our in-house designed perfusion chambers, long-duration time-lapse observations can be performed over several days, to study developmentally regulated dynamic events.

Other advanced imaging techniques are available including super-resolution (STORM, PALM and SIM) and FCS. We also routinely prepare and image resin-embedded material, negative-stained viruses and nano-particles in the TEM.

Sample Preparation

Keywords - Biological: Resin embedding | Ultrathin sectioning | Serial sectioning | Immunolabelling | Plunge Freezing | High Pressure Freezing | Freeze substitution | Critical Point Drying | Freeze fracture | Metal coating | Negative stain | Photoconversion | PLT | Immunofluorescence | Cryostat sectioning | Vibrating microtome | Enzyme histochemistry | Live Cell

Samples can be prepared by a variety of techniques for TEM such as high-pressure freezing and freeze-substitution or by chemical fixation and resin embedding, including the PLT method. Negative staining and other techniques such as PATAg staining and immuno-gold labelling are also available. The 200kV TEM has a LaB6 electron source and two CCD cameras (side and bottom mounted) and can perform electron tomography with high and dual tilt holders. For SEM, cryo-techniques are a speciality at JIC but critical point drying is also routinely used. We offer plunge freezing as a routine cryo-SEM method, but high-pressure freezing or impact freezing for high resolution freeze-fracture work is also available. We have sputter coaters, carbon coaters and a glow discharge machine. In addition to ultrathin resin sectioning for EM, we can also cut semi-thin resin sections or wax, vibratome or cryostat sections for light microscopy.

Data Analysis

Keywords - Software: ImageJ | FIJI | Amira | Matlab | AutoQuant | Metamorph | AxioVision

Image data can be analysed in-house using dedicated workstations. Commercial software from Leica, Zeiss, Molecular Devices and Media Cybernetics are available offline. There is a dedicated workstation for super resolution (SIM / PALM / STORM) image processing. For 3D visualisation and analysis we use either FEI Amira or open source VolViewer.

Shared Access

The Bioimaging facility at the John Innes Centre (JIC) is one of a number of research facilities within JIC and across the partner institutions that comprise the Norwich Research Park (NRP). Many of these facilities (including Bioimaging) are available for use by NRP institutions as well as the wider community external to the NRP.

In common with all of the NRP shared facilities, the Bioimaging facility at JIC uses an FEC model to help recover costs. An on-line booking system is available for internal use but external clients should contact the facility manager to discuss their needs. Comprehensive training is provided for those people wishing to use specific Bioimaging equipment without supervision.

Although JIC’s primary research focus and reputation concerns plant and microbial sciences, the Bioimaging team has been involved with an increasing number of applications outside the scope of such research. The team welcomes enquiries from anyone interested in using the imaging facility.


The majority of the JIC’s funding is won in open competition from funding agencies worldwide, with more than 50% coming from UK government sources. BBSRC provides a large proportion of the JIC’s funding in the form of responsive mode funding and strategic funding for the Institute Strategic Programmes.

The JIC also holds grants from the European Research Council and charitable sources such as The Bill & Melinda Gates Foundation.

Share this