Blizard Institute

BALM Home menu


In BALM our vision is to provide a state of the art imaging facility pioneering novel techniques and making cutting edge discoveries. To ensure this can be realised we have set up the facility to allow for multi-user access and polyvalent functionality of the equipment. We do our best to adapt systems to accommodate everybody's experiments and are open for users to bring in custom adaptations.

  • All experiments carried out in the BALM facility are important. To ensure that you, the user have secure access to the microscopes we provide personal logins and private user space. This means you have your own settings which are modified only by you personally.
  • To facilitate and ease the use of the facility for everyone we have user guidelines. Before using the facility please familarise yourself with them.
  • Microscopes are expensive and fragile pieces of equipment. To ensure we keep our equipment in cutting edge condition we have to charge a small fee for usage. Our tariffs can be found on the BALM site homepage.
  • We have a variety of techniques available and are always keen to develop more. If you have an idea for a project please get in touch.
  • We are aiming to provide protocols and user guides for the more commonly used techniques here.
  • We have a small shop of fluorescent dyes and antibodies which you are very welcome to purchase to test if your experimental conditions work. The list of what is available is here.
  • Answers to the more frequently asked questions are in our FAQ section.

BALM has policies and guidelines for the imaging facility to help everyone get the best out of their experience here.

To continue the good work of the BALM facility all users must adhere to these guidelines, which have been agreed by the imaging steering committee.

Anyone who either has an interest in the work of the Imaging facility or uses the imaging facility microscopes should register with BALM by contacting the facility manager. This will allow you to be updated with news about the facility and developments in light microscopy. All users must supply an active grant code prior to facility usage.

Usage of any facility microscope is only allowed after personal training coordinated only through the imaging facility - no matter how experienced you are. This includes not just technical training, but also an introduction into facility rules, health & safety and other important issues, and therefore is compulsory. You are liable for any costs associated with damage or repair to equipment if you use BALM equipment untrained and may be barred from use of the facility.

Standard Operating Procedures for use of the machines are printed and posted above each microscope, these must be adhered to. They were written to ensure everyone has an equal opportunity to benefit fully from the equipment

All uses of BALM Microscopes must be booked on the Quartzy booking site. Please respect each other's bookings. Once booked, a person has the right to use the microscope uninterrupted. When cancelling a booking, please make every effort to contact the people booked before and after you. They might be happy to take over your time slot. – In extraordinary circumstances the BALM facility staff reserve the right to cancel bookings at short notice.

If you arrive more than 30 minutes late for a microscope session your booking is void. You will be charged for 1 hour or for the amount of time you have booked for the equipment, whichever is greater. If you cancel a session without using the equipment after the session has finished you will be liable for the cost of the whole imaging session unless you have discussed this with the BALM staff. This is to prevent people block booking busy equipment, not turning up and preventing others from using it.

Please discuss block bookings of equipment of longer than 3 hours a day with the BALM manager at the beginning of the project. The facility has over 200 users at present and everyone's experiments are equally important.

Please keep the facility safe, clean and tidy. There are clinical waste bins in every room, please use them. 

Each user has an allocated user area as well as a personal profile. It is up to you to make sure there is enough space in your user area for your experiment. Please don't stop other people from doing experiments by leaving large quantities of your data on imaging facility computers.

The imaging facility cannot store your data long term. Please save your data in the location given at training. Data found on the C drive of computers, or older than 1 week on any computer attached to a microscope may be deleted if space is needed. Data on the networked mass storage server will be kept for a minimum of 1 month. After this, it will be overwritten with new data.

BALM staff are happy to advise and collaborate with projects, technical time is charged at £30 per hour. Research students and Postdocs are advised to discuss any technical work needing to be done with their PIs prior to starting a project. If there is going to be substantial technical work carried out this needs to be discussed in a meeting with both the PI and the BALM facility manager present, (at a minimum) prior to starting work.

It isn't possible for you to install personal software on any imaging facility machines.

Here is a selection of very useful links for anyone interested in microscopy:

If you've just started microscopyread this guide [PDF 1KB]about how to keep the microscope clean and working well.

Instructions about what to put in Materials and Methods about core facility microscopes are here [PDF 1KB]. You can find out more about the equipment on the equipment pages.

This list of techiques is not exhaustive. Please come and discuss with us if you want to do an experiment not listed here. We are happy to develop new methodologies or refer you elsewhere in the university.



Brief overview and link

Epifluorescent Microscopy

Leica - Epi, MMLeica, TES

Fluorescence microscopy is a simple way of seeing where your protein of choice is located in your sample. More info here l

Confocal microscopy

Confocal Zeiss 710 Z2, Confocal 510 Meta inverted, Spinning disk

Confocal microscopy offers several advantages including a shallow depth of field, removal of out-of-focus glare, and the ability to collect serial optical sections from thick specimens. More info here

Image Analysis See Image analysis page Making measurements of your data for statistical analysis.

Colour imaging of cells

Leica - Epi, Sterology Microscope

To image histology and pathological specimens More info here

Differential Interference contrast Microscopy (DIC)



DIC is a mechanism for rendering contrast in transparent specimens. More info here

Live cell imaging

Confocal 510 Meta inverted, TES, Spinning disk

These microscopes will allow you to find out what’s happening in real time on your microscope

Time-lapse microscopy long term


This microscope has a large environmental control chamber specifically for experiments lasting over 3 hours

3 dimensional cell imaging and reconstruction

Confocal 510 Meta inverted, Confocal Zeiss 710 Z2, Spinning disk, Imaris

Using a automatically motorised z stage its possible to images sections of your sample and reconstruct it in three dimensions

Real time calcium imaging

TES, Spinning disk.


To quantify in real time how calcium signaling is changing

Small scale screening

TES, Spinning Disk

An automatic x,y,z stage makes it possible to visit each well of a 96 well dish and image it.

FRAP -Fluorescence recover after photobleaching

Confocal 510 Meta inverted, Confocal Zeiss 710 Z2, Spinning disk

FRAP measures the ability of a molecule to move around over time. Find out more here

FRET - Forster resonance energy transfer

Confocal 510 Meta inverted, Confocal Zeiss 710 Z2, Spinning disk

FRET is a mechanism describing energy transfer between two chromophores. More info here



Stereology is a standard methodology for quantitative histology used in biomedical research. provides a good, comprehensive overview of unbiased stereology. 

Laser ablation microdissection


Laser ablation microdissection allows the removal of very small sections of tissues or cells

Below are a list of useful protocols for microscopy. This page is continuously updated so do check back.

Sample Prep

Protocols: Microscopy

Protocols: Image Analysis

Once you have acquired your images there is still plenty which can be done with them. Images can be used to make measurements or really draw out the point you need to make.

BALM offers tutorials on image analysis. You can watch these here:

Return to top