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Advanced Bioimaging

Training and courses

Hands-on training

Training to use the Advanced Bioimaging equipment is provided one-on-one, using the users’ own samples and subject to the usual charges. In my experience, the process runs more smoothly if not too much time elapses between sessions, so it works best if you know you will have plenty of samples to look at in the first couple of months of training. If you don’t use the equipment for six months, the first session will be “supervised” again, just to make sure you remember how everything works.

  1. Email Saskia to register your interest - she will get you access to the Moodle
  2. Complete the moodle for electron microscopy (provided by the EM RTP in Physics) at:

  3. After you’ve completed the Moodle, please contact me for your first training session. Because of the variety of projects we do, I always train people on their own samples. This also gets you data more quickly. We will cover sample prep/staining in the first session if you have not done this before. You will have at least two training sessions in person to be signed off for supervised use.

  4. During supervised use, you will only be able to use the microscope while Ian Hands-Portman or myself are in the building in case of issues. After two sessions of supervised use with minimal intervention, you can be signed off for independent use and be trained on starting up and shutting down the microscope.

  5. When you are signed off for independent use, you will get a certificate to add to your training records. You can now book any time without checking if there’s anyone around.

For any additional techniques (tomography, cryo, cryo-tomography, diffraction, 2200 use) the same procedure applies, with training and supervised use first, before being signed off to use it independently. If you need any of those, we can start that once you’re signed off for the 2100Plus at room temperature.

An annual (autumn) single-particle cryo-EM workshop is run by the Leicester Institute for Structural Cellular Biology (LISCB), please contact Saskia if you are interested in attending this course.

Software for Image Processing

Relion is the most commonly used software for high-resolution structures. However, it is quite demanding of the computer system. If you are processing negative stain data, EMAN2Link opens in a new window might be sufficient and will run on a Macbook or desktop computer.

If you do need Relion, we are working with the Scientific Computing RTP to get this working. A limited number of users with smaller datasets can use a dedicated workstation, please contact Saskia for details of this. If you have data from the Krios at Leicester, please use the Leicester computing facilities in the first instance. If you are planning to run Relion on a regular basis, we can advise on suitable computer setups for this.

For tomogram processing or montage stitching, you'll need IMOD, which should run on a Macbook or linux machine. A dedicated machine for this will soon* be available in the imaging suite.

For people new to Linux (or command line on their Macbook), please work through this Unix introduction from Surrey UniversityLink opens in a new window.

Theoretical background

The Cryo-EM lectures by Grant Jensen from CalTech are an excellent way to improve your background knowledge and learn about how the electron microscope works. Not all sections may be relevant to you, but I recommend watching all the lectures in part 1 to 4 and either part 5 (tomography) or 6 (single particle analysis) depending on what you're doing.