Confocal and Advanced Light Microscopy (CALM) Facility

User guidelines and rules

This page gives a detailed description of all facility guidelines and rules.

CALM Facility User Guidelines

The following guidelines should be read and acknowledged by filling in and submitting the CALM user registration form as part of the registration with our Pasteur Platform Management System (PPMS) (secured).  These guidelines are in place to guarantee optimal use of the facility, to avoid damage to the equipment and to ensure that imaging is carried out in a safe working environment.


Overview over the guidelines and rules as detailed below:

  • Location of facility
  • Management
  • Access
  • Training and User Registration
  • Booking
  • Charging and cancellation
  • Data transfer and storage
  • Out-of-hours working
  • Health and Safety
  • Imaging Live samples at CALM
  • Waste Disposal
  • Lens care and use of immersion oil
  • Use of gases in the CALM facility
  • General user guidelines for equipment use



The CALM imaging facility is located on level 2 (rooms C2.38 and C2.39) and in the basement/level 0 (room E0.17) of the QMRI. The facility office is on level 1 in room E1.21 (tel - 0131 242 9155).



CALM is a facility of the Centre for Inflammation Research, in the QMRI; it is used by researches from within and outwith the QMRI.  Day-to-day management and operation of the facility is under the responsibility of the CALM facility manager.  The Head of CALM provides guidance with regard to the overall management and strategic planning of the imaging facility.



Access to the facility for novice/newly trained, inexperienced users is from 10am to 4pm Monday to Friday, trained users can access the facility at all times, but out-of-hours access will apply to working before 08:00 and after 19:00, Mon-Fri and after 13:00 on Saturday and all Public Holidays.  Facility access is restricted to authorised/trained users via the PPMS login pages and will be in part protected by swipe card. 

Please note that continued access to the facility is subject to approval of the facility staff.


Training and User Registration

All users need to register with CALM by requesting an account on the PPMS. Requests can be placed via the following link: PPMS registration (secured). The registration requires charging details and approval from their respective PI to access the facility.

Before using any of the microscope systems independently, training is required.  New facility users who are already proficient in imaging or have used other light microscope facilities will still need a short induction to make sure they are aware of local rules and any special requirements and that they can work within the health and safety rules of the facility. Permission to use any of the equipment will be managed via PPMS.

Training is provided on a one-to-one basis.  Most users require an initial training session of 2 hours; this may need to be followed by a further 2-4 hours of assisted imaging or application training.  In addition CALM runs an imaging course of lectures and practical demonstrations and users are encouraged to attend this course (Beyond Pretty Pictures’).

Please contact the CALM facility manager to arrange a training session.



The microscopes can be booked through PPMS by registered, trained novice and experienced users. Alternatively, an assisted session can be booked for users who have not been trained.

Users can make bookings up to 2 weeks in advance; booking of required time slots is compulsory.  The PPMS booking system is also the basis for the charging system and equipment usage is monitored electronically on each of the microscopes and computers.  It is therefore important that each user logs out of PPMS after using the equipment. Not doing so might lead to incorrect charges and is eventually the responsibility of the user. Please note that unsupervised use of the any of the confocals is not permitted by users that have not been fully trained and registered with the facility.

During peak times of usage booking may be limited to a maximum number of hours per user per day.

Please note that if you are swapping a session with another user you must change the booking details.


Charging and cancellation

The facility works on a cost recovery basis and therefore an hourly charge for all services is levied.  The appropriate charges are due for every booked session.  To avoid idle capacity by unused but booked time slots, users will still be charged for their booking unless the session is cancelled within an appropriate time scale.  If you need to cancel a booking at short notice due to the poor condition of samples, because cells have become infected or because of experiments that have unexpectedly not worked, please contact the CALM facility manager as soon as you realise you will not be using the booking (

If you cannot attend a booked session please email the CALM facility manager so that the session can be cleared to allow other users access.  A charge might apply for bookings cancelled late, which is to discourage users from extensively block-booking resources.

You will find a detailed list of charges and booking rules at this link.


Data transfer and storage

CALM users are responsible for the storage and archiving of their data and no responsibility is taken by the CALM facility at any stage.

We recommend you to primarily use the University’s data management platforms DataSync and DataStore. However, the CALM facility has an on-line data transfer partition for temporary data transfer, in case you generate image data sets that cannot be easily transferred (e.g. data sets larger than 10 GB).  This server partition is only for the transfer of microscopy-related data from the CALM microscopes to your own image data storage solution.  Processed data can also be uploaded from the CALM image analysis computers.  Please observe the following guidelines:

  • The CALM server space is to be used as a scratch disk i.e. only for copying, and not for storing data.
  • It is backed up daily, but no guarantee is given of the security or integrity of any data on this ECDF server.  
  • Any data on the server will be removed within two months of upload.  
  • Files not related to microscopy must not be uploaded and if they are they will be removed.  Please put all your data into a folder with your name also stating the date.
  • It is the responsibility of the user to ensure that their data is removed from the transfer partition and stored on their own computer/data storage facility, as soon as this is feasible. 
  • CALM users can rent online partitions for long-term storage through the University’s ECDF, which you have to pay for.

CALM is a multi-user facility and the microscope computers are purely for image acquisition and are not equipped for data storage.  As soon as you have transferred data to your own server or hard drive, please delete your data from the microscope hard drive.  Facility hard drives are routinely cleaned every 3-4 weeks to ensure that microscope software runs smoothly, and data that has been left on the microscope hard drives will be deleted without giving notice.

For instructions on how to access the ECDF services please see the following link

ECDF storage facilities

The use of external hard drives and USB drives for data transfer  is only permitted under special circumstances, on demand and on an individual basis.  This is to minimise the risk of viral infection of the microscope computers. 


Out-of-hours working

Trained users can use the CALM equipment outwith the normal working hours of 09:00  – 17:00 and also during weekends.  However, working in the facility outside normal working hours is subject to the Institute’s Health and Safety regulations. 

Any out-of-hours working in the CALM facility must be covered by the local H&S policy and certified by an appropriate training record.  The guidelines for out-of-hours working can be found at  LINK  - QMRI late-and-lonely working guidelines


Acknowledgement of support

If you have used the CALM facility for producing results for publication, we ask that you acknowledge this.  Quantification of the input of the CALM facility is vital in applications for future funding to maintain and develop the imaging modalities provided by the facility. We therefore ask you to report to us all your publications, which include data or services generated in the CALM Facility.

If you have used the facility with minimal input from CALM staff, we would suggest the following sentence in the acknowledgements section: "light microscopy was carried out in the CALM Imaging Facility at the University of Edinburgh".

Where specific members of staff have provided advice or technical expertise, we would ask that they are acknowledged by name, for example: "we thank ******* from the CALM Imaging facility at the University of Edinburgh for assistance with microscopy …"

Where a member of staff has contributed significantly to a publication, for example by providing strategic planning, experimental design, acquired images or analysed data that has been used in a research paper, or have contributed to the writing of a research paper, please include them as a co-author.

For more detailed guidance, see the following recommendations:

RMS Core Facilities Publication Policy


Health and Safety

All users are responsible for guaranteeing health and safety of their experiments and are expected to have completed a Risk Assessment and/or COSHH form, where applicable, for all samples brought into the CALM facility for imaging. 

Please note that the risk assessments and standard operating procedures for CALM cover only the equipment and its operation.  In this regard all users are responsible for the safe handling and disposal of their samples and should plan and bring with them the necessary PPE to contain any hazards. 

The CALM facility is a multi-user facility and therefore health and safety regulations must be adhered to ensure the safety of all users.  Where the samples include materials that have been genetically modified, the GM risk assessment must be approved by the School GM Safety Committee in advance of any work proceeding.

Please note: to avoid cross-contamination to other users, the wearing of gloves while using the microscopes is not permitted.

1. Risk Assessments, Safe System of Work and COSH forms

Please make sure that you have read, understood and signed all the CALM risk assessments, COSHH and Safe system of Work (previously: Standard Operating Procedures) before you use any of the CALM resources as a trained user.  These can be found in appropriate folders in each microscope room.

2. Laser Safety

Both the Leica SP5, Leica SP8 and Andor Revolution microscope systems utilise built-in class 3B lasers.  These are medium-power lasers with an output of up to 200 mW and a wavelength range of 400-700 nm, and are classed as a moderate risk, because they are fully enclosed and secured in each of the systems.  Viewing the direct beam and specular reflection of the laser beams can be hazardous.  However, if the confocal systems are used correctly, due to the inherent engineering safety controls the user can operate the system without being exposed to the laser beam, and the systems have therefore been down-classified to Laser Safety Class 1M.

Near infra-red (NIR) laser use:

The NIR-lasers housed in the CALM facility are class 4 lasers.  These are high-power lasers with an output of up to 5 W, and a wavelength range of 690-1400nm.  By definition, a class-4 laser can burn the skin, in addition to inflicting potentially devastating and permanent eye damage as a result of direct or diffuse beam viewing.  These lasers may ignite combustible materials, and thus may represent a fire risk.  All NIR laser users must have completed the University’s Laser Safety Course and be registered as UoE laser user. Three levels of MP laser use have been identified.  Level 1 users are not permitted to switch on, off or tune the MP laser: this must be done by a level2/3 user or the CALM facility manager.  Level 2 users can switch on, off and tune the MP lasers, but they must have completed the UoE Laser Safety Course, be registered on the UoE Laser register, be fully trained in tuning the MP laser and be entered on the IMPACT MP authorised user register.  Level 3 users can work with an open beam path for laser re-alignment and cleaning/maintenance of the mirrors within the NIR laser cavity, if they have been adequately trained for this.  Level 3 use is restricted to named UofE personnel and Coherent/LaVision Biotec engineers.


Imaging live specimens at CALM

For intra-vital, whole animal imaging please read the information provided at the live specimen imaging section (LINK). For live-cell imaging, full details of the specimen/type of cells you are working with, decontamination procedures for spills and waste disposal specific for your particular sample should be provided by filling in the ‘Live-cell Imaging Experiment Form’ prior to your imaging session.  Due to the nature of the imaging experiments carried out at CALM, only specimens designated as biological hazard class 1 can be brought into the facility.

Containment methods for your experiment should be known; you should know and be able to provide any available documentation concerning safe methods for managing any biohazardous, genetically modified or infectious agent associated with your live sample in the lab environment before using the microscope.

All preparation procedures using the POC live cell chamber should be completed in a lab of the appropriate level for the risk posed by the live cell culture/ sample.  Once the chamber is assembled, carry it to the imaging room in a securely closed container. 

Gloves should be worn when handling the live-cell chamber and mounting the chamber in its holder on the microscope stage.  Once the chamber is mounted and has been disinfected on the outside, gloves should be removed and at no time should gloves be used when operating the microscope.

It is the responsibility of the user to bring appropriate material for disinfection and clearance of any spills.  Any spills must be dealt with immediately; the CALM facility manager should be notified if there is a spill. 

Waste from live-cell experiments should not be disposed of in the CALM facility; all waste must be taken back (transported appropriately) to the lab of origin and disposed of according to the correct procedures for the type of risk associated with the sample.


Waste Disposal

Bins for lens tissue, waste tips and sharps bins are provided in the imaging rooms, glass material (slides or cover slips) containing non-hazardous samples may be discarded in the designated bins for sharps.  No other waste should be disposed of in the CALM facility.  Please take all other waste (solid/liquid non-hazardous and hazardous) back to the lab where the samples were prepared and where appropriate disinfection and disposal routes are in place and dispose of it appropriately. (LINK CIR H&S)


Lens care and use of immersion oil

Do not change or remove any objective lenses unless you have been trained and authorised to do so.  Once removed, objective lenses should be stored in the appropriate objective container (make surely the objective is securely screwed into the lid of the container, but do not over-tighten) and stored securely.  If you remove an objective from the turret, cover the empty socket with an appropriate protective cap (check all caps are in position before switching on the lasers).

Take care not to contaminate any water, silicone oil or air lenses with immersion oil.  If this accidentally happens, please remove the oil with the provided ethanol/isopropanol cleaning solution and lens-cleaning tissue immediately and inform CALM facility staff.

Once you have used oil on a slide you cannot return to using the 5x, 10x, or 20x air objectives before thoroughly removing the oil from the slide to avoid contamination of any other type of lens.  Any accidental spill of oil running down the barrel of the objective lens must be cleaned up immediately to prevent oil penetrating the thread of the nose-piece.

Oil must be cleaned from the oil immersion objectives after uses using the lens paper and ethanol/isopropanol mix provided.  Lenses should be cleaned using the protocol demonstrated during confocal training to prevent the objective lens from being scratched.  If you are unsure of the correct protocol for cleaning oil from an objective please ask for assistance. 

Use only the correct immersion oil for each microscope system, as contamination of the lenses with other immersion oils may change the refractive index of the oil applied to the lens.  To prevent oil contaminations from previous use of slides (e.g. on other microscopes), please thoroughly clean all your slides before use.


Use of gases in the CALM facility

Most of the microscopes in the facility are equipped with gas supply lines to use carbon dioxide, nitrogen or oxygen for live-specimen experiments. Before you use any of these, ask facility staff for the mandatory induction. Do not move cylinders, disconnect gas tubing or similar if you are not authorised to do so. If you discover any disconnected lines or tubing at any point, please report to facility staff immediately.


General user guidelines for equipment use

The general responsibilities of each user are as follows:


  • Book the required time slot and only use booked time
  • Before starting your session ensure that the equipment is undamaged and clean, and the nose-piece in the position carrying the lowest magnification lens.
  • Log in using your PPMS credentials to access any of the booked equipment


During your session:

  • Ensure that the objective lenses come into contact only with the correct immersion medium and only use reasonable amounts of immersion media (one drop of oil or water is usually enough)
  • Ensure a safe distance between the objective and the specimen
  • Please clean up any spills immediately, to prevent liquid soaking into inaccessible spaces.  Please notify the CALM facility staff of any spills that you are unable to remove immediately
  • Equipment failure, software errors or any other problems with the microscope systems should be brought to the attention of the CALM facility staff immediately.  They should also be noted in the equipment log sheet for future reference.

After each session:

  • Clean immersion lenses after use, with lens tissue and 90% ethanol/10% iso-propanol mix. If you are unsure of the correct protocol for cleaning oil from an objective please ask for assistance. 
  • Please leave the lowest-power objective in the active position for the next user and move the nosepiece to lowest Z-position on the inverted systems.
  • If there is another booking within 1 hour leave the Argon laser on standby and any other gas laser (HeNe on Leica SP5) on. 
  • Turn off the LED light sources.
  • If no one is booked on the system within the next hour turn off all lasers.
  • Remember to fill in the log sheet and please note any problems encountered.
  • Turn-off any CO2 or other gas supply that you have used.
  • Clean the microscope as instructed.

Last user of the day:

  • The last user of the day should make sure that the system has been shut down properly.  If you are the last user and you cancel your booking, please inform the user before you that they now have the responsibility of shutting down the system.

Please treat the microscopes and objectives with the respect they deserve!