The pages within this section contain some major rules and guidelines for working in the FILM facility.
To use the facility you will need to register on PPMS
General enquiries to firstname.lastname@example.org.
Expand each of the subsections below for further information
- The facility is open to all college staff and students
- Usage for people from outside the college is possible (subject to availability). If interested, please get in contact
- Usage of any microscope in the facility is only allowed after personal training (see training page for more details). First-time users, please get in contact with facility staff to arrange the training
- Usage is logged by time, and hourly charges apply for all microscopes
Important ! - the booking system from the 1st May will change to PPMS
if you have not registered you will not be able to book the microscopes and software
Facility usage regulations
The facility is very popular, with well over 100 active users every year. To guarantee the smooth running and safety of all users, it is very important that all users read and respect the following guidelines:
• usage of any microscope in the facility is only allowed after personal training (needed for each microscope)
• facility staff can give training for use of FILM microscopes only!
To maximise access and to keep usage charges affordable, it is essential that users are cooperative and disciplined with bookings. In detail, the following rules apply:
- every usage must be booked in advance online
- whenever a change to the booking is needed, please do so as soon as possible to allow other people to use the equipment.
- Bookings can be amended up to 1h before the session. After that, cancellations are only possible by emailing FILM staff at email@example.com with a legitimate reason.
- If a user doesn’t show up at the booked time within 30 minutes from start, any other user can use the microscope.
- any instrument can only be booked maximally 2 weeks in advance (day on day); longer advance bookings are only possible through facility staff if justified by specific experimental requirements.
- Booking during peak hours (9-17h) is restricted to a maximum of 8h; there is a weekly booking limit of 16h during peak time per user, so as to allow others to gain access to the instrument. The booking restriction is lifted if the microscope is not booked 24h beforehand.
There is no limits to booking outside peak hours (if you have autonomous user rights).
- any break within a booking (e.g lunch break) must be at least 1 hours to allow another user to use the time.
- If a microscope is not functional, please report this to facility staff and leave a note in the online booking - you won’t be charged if the equipment is not functional.
- The online booking system is also used for recharging. Therefore, the booking time must correspond to the actual usage time, i.e. if usage is longer than expected, the booking must be updated accordingly to make the change visible to other users.
Rules before 1st May 2017
- Every usage must be booked online on the FILM Sharepoint Site (see below for details).
- Any instrument can be booked maximally two weeks in advance and no more than three sessions in advance. If your experiments require longer planning, facility staff can make the booking for you.
- Please only book time slots, not 'all day'.
- Please complete any changes to your booking as soon as possible and notify other users through the 'Sharepoint/messages' newsgroup. Failure to do so will mean you will be charged for the original booking.
- Bookings cannot be deleted. Instead, make the end time and start time the same to nullify the booking. However, please do everything you can to avoid booking a microscope and not using it.
- Please note: If you don't arrive at your booked time, the entire booking becomes invalid after 30 minutes.
FILM Sharepoint website
When you register for the facility, you will automatically be added to the 'FILM Facility Users group', and after training will allow you to book microscopes, send messages to other microscope users and get email alerts.
Booking a microscope in Sharepoint
The Sharepoint site only works well with Internet Explorer, Firefox and Safari (not with Chrome).
1. Go to the FILM Sharepoint site under 'lists' (navigation bar on the left) and choose the microscope you want to book
2. Go to 'new/new item' or click on the 'plus' symbol in the top right.
3. Fill in the booking form as follows:
- Name of User - your actual name (usernames are hard to interpret)
- User E-Mail - just write your college username, the rest is completed automatically
- Start time / end time - fill in date and time
- Contact phone number - helps other people to contact you if things change at short notice.
- Journal number - Leave this empty.
- Troubles - anything going wrong with the booking, for example, lasers not coming on or software crashing. Please write everything down as this will assist us in solving these problems. Important - If you can't use the microscope due to a technical fault, please write "Didn't work because..." describing the fault. You won't be charged for this session, but we need to know the reason for any problems or failures.
- Attention: the booking system allows double bookings, so be careful what you book.
Booking additional hardware
The microscopes cannot be continually fitted with every option, so some configurations have to be requested prior to the session. This might be a special objective or filter set. these usually will be identified during the training session. The additional hardware option can be requested through hardware request web page in Sharepoint.
Also, please read our PDF guide regarding hardware requests - Booking additional hardware (PDF)
Changing or deleting a booking
- Click on your booking
- Select 'edit item' from the top menu
- Adjust your booking
- In 'discussions/microscope messages' send a message to other users to notify them of the change
- You cannot delete a booking - instead make the end time the same as the start time, resulting in '0 hours' of usage.
- Please leave the start time unchanged, and make sure you don't set the end time before the start time - that would result in negative usage time and cause problems with the booking system.
Staying informed: messages ('discussions' on the website)
These allow users to inform each other of changes to their booking, and facility staff to inform users of any technical issues affecting their experiments.
- To set up an alert, go to 'FILM <microscope> messages', and click on 'actions/alert me'.
- You can change or delete the alert at any point
- You can also be alerted whenever someone else changes or deletes a booking on a specific microscope (do the same on the booking page)
Training for the use of facility microscopes
Usage of any facility microscope is only allowed after personal training, no matter how experienced you are. This includes not just technical training, but also an introduction to facility rules, health and safety, and other important issues, and therefore is strictly compulsory.
Microscope training is for FILM users only. Our training has become popular, and people using their own lab microscopes have asked for it - unfortunately we don't have sufficient staff to respond to this surplus demand at the moment. To guarantee the best use of staff time, people not using FILM microscopes after training will be charged for microscope and staff time (see charges for further details).
Ordered steps to follow for training
- Send an email to a member of FILM staff with a short description of your planned experiment.
- We will confer with you to arrange a time and date. FILM staff can help in planning the experiment and choosing the correct equipment.
- The required microscope is then booked for at least three hours (see below). Unless you have your own lab or grant, please make sure your supervisor is ready to cover the usage charges - when using the microscope you must provide a grant code for payment.
- Then you prepare your samples because the training will be done with your own samples on the correct microscope. The next time you utilise the facilities, you can just continue where you have started before.
- Eventually, for the training, you will get a short introduction into the facility, and then exact explanations how to set everything up specifically for your own sample. This will take around two hours, depending on your previous experience, after which you can go on imaging on your own and get used to the equipment.
This process makes the training much more efficient, ensuring that you are confident the next time you do imaging on your own.
Health and safety
The Imperial emergency number is 4444 (security will organise an ambulance or any other help needed). In case of a laser emergency, contact security (4444) to arrange immediate transport to the Western Eye Hospital in Marylebone Road (NW1 5QH).
First aid boxes are placed in rooms SAFB-408 and SAFB-527.
Please report all incidents to FILM staff.
All microscope rooms at present are classified as laboratories of the lowest biosafety level, containment level 1, so only qualify for low-risk cell lines and organisms. It is each user's responsibility to make sure their samples fall into this category.
If you are planning experiments requiring a higher safety level, please get in contact. Some basic information on regulations for usage of organisms with special safety requirements in FILM, see the document FILM Health and safety SOP (PDF).
For more information on biological safety and containment levels, see the Approved List of Biological Agents (including classification) on the Health and Safety Executive (HSE) website. Some information is also on Imperial's Biological Safety website.
All users should be aware of the fact that even fixed samples are still biological material with a residual risk, and also several of the chemicals used for sample preparation are carcinogenic or otherwise unhealthy, like formaldehyde, all nuclear stains, sodium azide, amongst others. Therefore, as in any lab, all equipment should be regarded as potentially contaminated. No eating or drinking is allowed in the facility.
Lasers are generally enclosed and don't pose a special hazard to users unless reflected from the sample. Nevertheless, a laser safety training course is always advisable.
The two multiphoton microscopes CF3 and CF4, and the laser tweezers on CF2 all use very powerful class 4 infrared lasers which are invisible and potentially hazardous. Therefore, people using those microscopes need special training - for information please get in contact.
More information about laser safety can be found on Imperial's laser safety website. See also their 'Introduction to laser safety' (Powerpoint file) used in the laser safety training.
Data and network
Network policy and virus protection
To avoid data loss and downtime of the microscopes, users are asked to do everything to avoid infection of the microscope computers with viruses, malware, and trojans.
Specifically, users are required to stick strictly to the following policy:
- Users are not allowed to install any software without permission
- You can browse the internet to look up microscopy-relevant information, scientific publications, news and radio programs, but do not browse or download files from any suspicious websites
Facility users are solely responsible for their own data, but FILM tries to make data handling for users as easy as possible. At acquisition, all data are stored on local microscope hard drives. To make movement, save storage and processing as efficient as possible, FILM offers a FILM file server to be used as a scratch disk, to copy data between microscopes and other computers in the college
Rules for using the file server
The facility has a file server to copy image files between microscopes, personal computers and analysis workstations. The server is available for free to all users of the facility. If you want to use it you have to provide your network username and CID in the facility user registration form.
- The server is only to be used as a scratch disk to transfer data, not for data storage
- Be aware that all data are accessible to all users, so anybody can see (or could mistakingly delete) your data
- Server space is shared between all users; to keep it available, files can be deleted at any time without notice, whenever the server fills up
Access to the file server (scratch)
To access the FILM file server space ('scratch' disk for temporary file transfer):
- open 'My computer'
- in the menu, select 'tools > map network drives'
- select a free drive letter (e.g. "X:")
- for folder location use "\\film-nas.med.ic.ac.uk\scratch" (some computers refuse to connect, if this happens, try "\\188.8.131.52\scratch" instead)
- tick the box 'Reconnect at logon' and click 'OK'
- type in your username and password (use 'ic\username' instead of just your username on microscope computers)
For Apple Macintosh
- in the desktop menu, go to 'connect to server'
- type in "smb://film-nas.med.ic.ac.uk/scratch" (some computers refuse to connect, if this happens, try "smb://184.108.40.206/scratch" instead)
- in the upcoming window type:
- Workgroup: 'IC'
- Name: your normal IC 'username'
- Password: your normal IC 'password'
If your computer for whatever reason refuses to connect to our server (for instance, wrong system clocks are known to cause problems), you can always use the college's FileExchange Server to transfer data (https://fileexchange.imperial.ac.uk/). It is advised to zip everything into a single file before upload.
Access the FILM documentation drive
The documentation drive has some of the software packages for downloading:
Connect as described above, using a different drive letter (eg. "W:") and '\\film-nas.med.ic.ac.uk\documentation' as the folder address.
Additional Central servers
FILM also offers the following infrastructure.
- a central storage server maintained in cooperation with the Bioinformatics Support Service. All FILM users have a basic space allocation included in the usage charges, additional storage space can be rented from BSS (don't forget to include the costs in your grant applications).
- two central processing servers, for management and high-performance processing and analysis of data produced by FILM microscopes:
- a server running the OMEROimage database (which allows import of original microscopy files from all microscopes, annotation and visualisation and data sharing; for more information or access requests, see BSS website / Data Management), Huygens Deconvolution and Definiens for high-level image analysis.
- a server running Zeiss ZEN for analysis of super-resolution data (and any other Zeiss data).
Data workflow (recommended)
See also overview of FILM data flow (PDF)
- At acquisition, data are stored on the local hard drive of the microscope computer
- After acquisition, the user copies the data to the central image data server
- For smaller processing, analysis and visualisation steps, the user can open data from their local desktop or copy them out for analysis
- For large-scale processing, the central high-performance servers are used: all processing servers have direct high-speed connections to the central storage space, so this is the most efficient and fastest way to handle the data
A basic allocation of backed-up storage space on the central server is included in the FILM usage charges. For larger data, users have to plan in advance, adding the costs to grant applications (which is required by all funding bodies anyway). For details see BSS website / Data Management.
Acknowledging FILM in publications
FILM is funded from a variety of sources (Research Councils, College etc.) to which we are accountable. They all require acknowledgement of their funding in publications. This means that all internal users paying the subsidised rate (much lower than the full economic costs) are required to acknowledge FILM usage in their publications.
An example sentence would be:
“The Facility for Imaging by Light Microscopy (FILM) at Imperial College London is part-supported by funding from the Wellcome Trust (grant 104931/Z/14/Z) and BBSRC (grant BB/L015129/1)”
- If you have used the Elyra PS1 super-resolution microscope, please acknowledge specifically the BBSRC funding (grant BB/L015129/1).
- If you have used FILM CF3 or Nikon High-Content microscopes, please acknowledge the Wellcome Trust funding (grant 104931/Z/14/Z).
We also ask that you consider how much use you have made of FILM staff time. We don't charge for any staff time, but if this goes beyond basic training and support please consider whether to acknowledge the staff member(s) or even include them as (a) co-author(s) as appropriate.
Please use Report a Publication in the PPMS homepage as soon as possible – its very easy (using PMID), and a big help, thanks