The Aaron Klug Centre for Imaging and Analysis

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General notes for users of the EM unit


Although Electron Microscopes are high tension, water-cooled pieces of equipment, potentially capable of emitting penetrating and dangerous X-rays, they have been installed in strict conformity with all regulations for such equipment. The emission of radiation from the column is prevented not only by lead screens specially fitted for the purpose but also by apertures and other removable components normally present in the column during standard modes of use. Thus most electron microscopes are extremely well shielded and do not produce exposure rates greater than background.

When operating an electron microscope, note:

  • Users must adhere to the techniques in which they have been trained.
  • The instrument must not be operated when partially dismantled or before all covers and components normally present have been correctly replaced (for instance when servicing or maintenance has just been carried out).
  • No structural alterations or modifications to the instrument may be made without expert advice and subsequent checks must be made to confirm that hazards have not been introduced by such modifications.
  • All accidents, malfunctions, or suspected faults must be reported to a responsible person. Only trained technical staff may attempt to trace, or rectify, electrical or mechanical faults.

The 2010 TEM (and eventually the 1200) uses SF6 gas for insulation of the high tension (HT) tank. The gauge on the HT tank should read between 0.1-0.2. If it drops below 0.1, there may be a leak. If there is a significant leak of this gas, the oxygen monitor in the room will beep, the microscope should be switched off and the room evacuated. This gas is heavier than air, and will therefore displace oxygen from floor level up. A liquid N2 spill could also activate the alarm.

If the alarm goes off: Switch off the microscope, leave the room and shut the door, and put up a notice prohibiting others from entering. The attendant on duty at the front desk (x6031) should be notified of the reason for the alarm. Access to the room must be prohibited until the gas has been cleared by the air circulation system (½-1 hr), and JEOL must be notified in the case of an SF6 leak. Once it disperses, the alarm can be stopped with the red reset button, and if it doesn't restart, it is safe to stay in the room.

All users must be shown the alarm system. The EM rooms must be labelled "authorized personnel only", and the O2 monitors should have a notice with this procedure.

General Laboratory Safety

  • The EM Users form must be completed and signed before any work can be done in the EM laboratories. This form is kept outside the inquiries office
  • Handle all dangerous chemicals in the fume cupboards, wearing gloves, these are provided by the Unit. Be careful with the stains used for Negative Stain microscopy.

Osmium Tetroxide

  • Handle ampoules with disposable gloves.
  • Use double bottles and seal with parafilm.
  • Open only in a fume hood, and in a well-ventilated room.
  • Do not hold your breath when using OsO4. Your nose is a very sensitive detector of dangerous fumes.

Aldehydes and Buffers

  • Handle in fume hood.
  • Some buffers (e.g. Cacodylate and Veronal) contain toxic components, and must be handled with caution. Use gloves at all times.

Embedding Resins

  • Most embedding resins may cause dermatitis.
  • When preparing the mixtures and during embedding procedures, ALWAYS use disposable gloves.
  • Cover working areas with paper towel and wipe spills immediately with alcohol.
  • Do not use alcohol to remove resins from your skin, it increases penetration. Use soap & water.
  • Get medical attention for any suspicious skin rash.
  • Harden all waste resin before disposal, wrap discarded containers, beakers, vials, pipettes, etc. carefully.
  • Never pour any plastic containing solutions (e.g., propylene oxide-epon mixture) down the drain. They will harden.
  • All chemical waste should be placed in the waste bottles in the fume cupboard. These bottles are clearly labelled so please dispose of your hazardous waste properly. Glass and sharp objects can be placed in the specially marked plastic bins in the lab.

Liquid nitrogen and cryogenic liquid handling

  • When handling liquid N2, particularly at the 1200 EX, remember to open the curtain and doors to avoid oxygen depletion. Oxygen depletion is the main danger from the use of liquid nitrogen - make sure you are in a well ventilated room.
  • Leather gloves and eye protection must be worn whenever handling cryogenic liquids


  • The preparation of liquid ethane for cryo work must only be done behind the shield in the fume hood. Use low flow rates of ethane to prevent splashing.
  • Gloves must be worn.
  • Ethane is flammable and potentially explosive. Do not use in the presence of flames and use only in a vented area. Once the ethane cylinder is open do not switch anything on or off in the fume hood, including the light. Do not create any static.

Critical Point dryer

  • Critical Point Dryers are potentially lethal. Do not observe them in use unless you understand the danger. The critical point dryer in the E.M.Unit is operated only by a trained technician. Do not attempt to operate it yourself.

Coaters and glow discharge unit

  • This equipment in the E.M.Unit is only operated by trained technicians. Please ask for help to get your samples coated or your grids glow-discharged. Never observe metal evaporation without goggles the intense brightness can burn your retina.

Handling of delicate equipment

The EM equipment is expensive and delicate, and should NOT be used unsupervised by anyone not FULLY familiar with the correct procedures. We do not have the funds to replace the expensive items listed below.

Turbo pumps must not be run at air pressure - this will damage the blades and cost several thousand pounds to repair. There are turbo pumps on the carbon coater and for pumping down the cryo stages.

EM specimen holders (normal and cryo) and goniometers are also delicate, high precision items. They must never be handled roughly or put under mechanical strain. (£20,000+).

CCD cameras on the TEMs (£25,000 each) will be damaged by a focussed beam, and should never be used in electron diffraction mode. They should be put in standby mode when changing magnification or other conditions. The camera on the 1200 MUST be put in standby mode whenever there is no illumination falling on the camera - ie at all times except when the screen is up and there is a spread beam. Otherwise the image intensifier will be damaged by trying to amplify a zero signal. The camera on the 2010 has an extra circuit which protects it when the screen is lowered, but must still be protected from the focussed beam and magnification changes. Both cameras can be misaligned by knocking them with your knees or feet - don't touch them (they are inside the cylinders under the main console).

Filaments: the tungsten filament on the 1200 must always be turned up gently and NEVER beyond the set saturation point. It is not expensive to replace but costs at least 24 hours. The LaB6 filament on the 2010 can only be turned up under computer control, because it needs very slow heating - 10 min the first time each day, and 6 min thereafter. It costs £1000 and several days to replace. A LaB6 should last 6 months - 1 year. The filament heating knob must NEVER be touched on the 2010. Turning the microscope directly up to maximum voltage can also blow the filament - start from 80kV when cold.

The ion getter pump on the 2010 (also very expensive) is damaged by water vapour. NEVER let the anticontaminator warm up with the ion pump on - it is automatically switched off when the ACD heat button is activated and comes back on again when the heating cycle is over and the water is removed, so that the column vacuum will be ready for the next user. For the same reason, the cryo stage must not be left to warm up in the microscope. Also, the tip of the cryo stage must be pumped to high vacuum just before insertion into the 2010 to avoid vacuum problems and cumulative damage to the ion pump.

Film handling

ALL exposed plates must be reloaded with films to top up the current film box to 50 for dessication. Each user is responsible for leaving the microscope loaded with a full box of dessicated films - otherwise the next cryo session would be delayed. Make sure the films and cassettes are loaded correctly in the metal boxes - otherwise you will cause a film jam and mess up a subsequent user's session. You must also ensure that the full number of films are loaded - unexpectedly missing films will also waste someone else's work. Do not leave small numbers of empty cassettes, and if you do not develop your films at the end of your session, take them away with you wrapped in a cardboard film box. Do not leave them in the darkroom. Label newly loaded microscope film boxes with the date and number of films. When replacing films in the microsope, do not leave the camera chamber open longer than necessary, and also take the dessicated films quickly to the microscope - they rehydrate quickly when taken out of the dessicator. The dry N2 gas line must be open and taps correctly switched when opening the camera chamber, and the gas cylinder should be closed with the spanner when finished. Newly loaded films must be fully pumped down in the camera chamber before pressing ACD heat. This is indicated when valve V2 is lit, or when the lower scale (camera) is in the green area.

Development: D19 developer full strength. low dose - 12 min; normal dose - 3.75 min at 21°C (see wall chart for temperature dependence). Films should be agitated during development to avoid uneven developing. Users must replace developer and fixer solutions when they get too old or have processed too many films, and write the date of replacement and user initials on the list.

General duties: Users should help the EM technicians with replacement of gas cylinders when necessary, in addition to the regular liquid N2 rota. Spares for EM equipment are stocked by the EM technicians, but users are responsible for ordering their own experimental supplies. Office supplies should not be taken from the EM unit. Please leave the equipment clean and ready for the next user. It is not the job of the EM technicians to clean up after users - they have much more important things to do. Cryo tools etc must be left in the correct places, otherwise the next user's session can be messed up. If items need replacing, please let the EM technicians know. Please use the microscope log books to report faults or changes needed.