The Microscopy Core Facility

Mouse Carotid Wall

The image appears to show an oblique section through an artery wall but, was in fact acquired from the outside of a live intact artery using multiphoton microscopy. The artery was not perpendicular to the lens so the left of the image shows deeper optical penetration than the right. The image is an illustration of 3 important capabilities of multiphoton microscopy; optical sectioning, penetration depth and second harmonic generation (SHG). Collagen fibres (blue) were visualised using SHG, smooth muscle cells (green) after staining with the vital dye Syto13 and endothelial cells (red) labelled with CD31 conjugated to R-phycoerythrin.


We are in the process of developing the microscopy core facility for the School of Medicine and this page will be updated as new features are added. The microscopes are available 24/7 to trained users from within the university. Access for external users can be arranged during normal working hours. 

At present there are three confocal microscopes a spinning disk confocal and two Zeiss LSM 510 confocal fluorescence microscopes both equipped with Coherent Chameleon lasers that are suitable for both confocal and multiphoton imaging. The inverted microscope on K floor is suitable for conventional cell and tissue specimens mounted under glass cover slips or in glass bottomed dishes. The upright microscope situated in the Biological Services Labs on F floor and the spinning disk confocal are available for intravital microscopy or "open dish" cell/tissue specimens since they are fitted with "dipping" lenses which need to be immersed in water/culture medium. For more detailed specifications please see the confocal pages (top left on this page).

There are three inverted widefield fluorescence microscopes, two in room DU12 and one in the Jessop laboratories. These are equipped with long working distance lenses and are ideally suited to working with tissue culture plates and dishes. They can be used for phase contrast or fluorescence imaging of either fixed or live specimens stained or expressing a range of markers. For more detailed specifications please see the widefield microscopes pages (top left on this page). 

There is a computer workstation with a full version of AIM, Zeiss confocal software, Leica LAS “browser” version, IVIS living Image and the 64bit version of ImageJ installed. This is available for use free of charge to microscopy booking system account holders.

How to gain access to the microscopes and request training

Please request an account and/or training using the microscope booking system by following this link   If you need any other help or to discuss any future requirements please contact me:

Colin Gray
Room LU104
tel 0114-2159580

Confocal/multiphoton training comes in two parts, a theory session of aproximately 2 hours and a practical of approximately 3 hours that usually takes place a day or two later. Widefield microscopy training usually takes 2 hours and covers basic operation of the microscope. Further training on more advanced features is done as required. There is a charge for training (see below for details) but further help or training (within reasonable limits) is included.  

Data Storage

Users should back up their data via the LAN or on portable devices (e.g. memory sticks, CD-ROM, DVD) at the end of imaging sessions. Data left on computer hard disks will be erased regularly for system maintenance purposes without warning. Every user is entitled to use storage space on the D or F drive (d or f:\all_users_data\) while they are acquiring images. If storage space is in short supply, you may delete data belonging to anyone without warning so remember to back up your data before you lose something important.


Please note! At the moment use of the microscopes will be charged at a heavily subsidised introductory rate. This is intended to allow time for users to gain grant funding and is a temporary measure which is not sustainable in the longer term. Charges are applied to meet microscope maintenance and external service costs and do not support other areas of the medical school. If you are thinking of applying for a grant please contact Colin Gray (details above or via link below) to discuss your requirements and obtain a quote.

A discount is available for continuous time-lapse imaging sessions >5 hours. Also discounts for heavy users (>250 hours/year) can be arranged. Reduced rates apply to Sheffield University departments. Rates for users from other academic or commercial organisations are available on request. For details contact

Training is now charged at £20 per person for widefield microscopy plus the normal access charge. From 1/11/2018) the confocal / multiphoton microscopy training charge will be £110 per person plus the normal microscope access charge for the technique used. This charge includes £60 worth of microscope time which must be used within 2 weeks of completing training. At present this is a once only charge any subsequent help/support is free (within reasonable limits). 

In order to be fair and maximize system availability these charges will apply to bookings cancelled within 24 hours of the booked time if it is not used by someone else. People doing live cell/animal work who have a good reason for an occasional late cancellation (eg the cells died), and who report this by email at the time will be allowed to re-book without charge).

Also note! You must book enough time to allow your data to be saved at the end of the session. If you inconvenience another user by over-running your allocated time you will be charged for the microscope time (minimum 1 hour) plus an extra £20 for any part of an hour which will be paid to the booked user's account as compensation.

The Histomorphometry / fluorescence Leica DMRB upright microscope, the Bioquant microscope and the Bright field and fluorescence Leica DMRB upright microscope belong to Skelet.AL and are not part of the microscopy core facility.

Other Facilities at Sheffield