Autumn school on single particle cryo-EM: from sample to 3D reconstruction 

General Info

The EMBL Imaging Centre in collaboration with the Heidelberg University is offering a 5-day autumn school covering all aspects of the single particle cryo-EM workflow. The autumn school will focus on basics of the workflow aimed at PhD students and early career researchers with no or limited experience in single particle cryo-EM.

Content of the course:

• Theoretical background and practicals delivered by experts in the field
• Sample preparation, grid screening and high-end data collection
• Image processing and data analysis

External Speakers

Daniel Bollschweiler

Max Planck Institute of Biochemistry, Munich-Martinsried

Tillman Schäfer

Max Planck Institute of Biochemistry, Munich-Martinsried

Lecture/Practical Content

Lectures:

1. Dirk Flemming (Heidelberg University): Sample and grid preparation for single particle cryo-EM. This lecture will discuss general considerations about suitable samples for single particle cryo-EM as well as grid preparation.
2. Cristina Paulino (Heidelberg University): The transmission electron microscope. This lecture will cover basics about the instrument itself with a focus on relevant aspects for its use in single particle cryo-EM data acquisition.
3. Sebastian Unger (EMBL): Single particle data acquisition. General workflow of single particle data acquisition with a focus on practical considerations for microscope operations.
4. Simon Fromm (EMBL): Single particle data analysis. General workflow and concepts of single particle data processing and introduction to the processing software used in the practical.
5. Daniel Bollschweiler/Tillman Schäfer (external speakers, MPI of Biochemistry, Munich-Martinsried): Title to be determined. The lecture will present real-world examples overcoming challenges along the SPA workflow.

Practicals:

Trainers: Joe Bartho (EMBL), Rafal Zdanowicz (EMBL), Sebastian Unger (EMBL), Simon Fromm (EMBL), Jan Rheinberger (Heidelberg University)

Practical 1: Sample preparation (Plunge freezing)

To collect single particle cryo-EM data on a cryo-TEM, the biochemically pure sample needs to be embedded into a thin layer of vitrified buffer solution. This is achieved by rapidly plunge freezing the sample after it has been applied onto a support called EM grid.

For this process, different instruments, instrument settings and sample supports (EM grids) can be used to optimize the result. In the practical, different test samples will be vitrified demonstrating the effect of varying those parameters.

The participants will have the opportunity to use:

• Vitrobot Mark 4 (Thermo Fischer Scientific), plunge freezer generating a gradient of ice thickness
• EM GP2 (Leica Microsystems), plunge freezer for single-side blotting

Practical 2: Sample loading and screening with a 200 kV cryo-TEM

After sample vitrification the EM grid is introduced into the cryo-TEM to evaluate the grid preparation. As it is impossible to predict ideal grid preparation settings, it is important to screen differently prepared grids. Modern cryo-TEMs with a so-called autoloader can take up to 12 grids which can then be screened consecutively without need to manually change the sample. For this, grids prepared in the first practical have to be made ready for loading into the autoloader, a process called clipping.

The participants will have the opportunity to use:

• Clipping of EM grids into cartridges
• Loading the clipped grids into 200 kV cryo-TEMs equipped with an autoloader (ThermoScientific Glacios and Talos Arctica microscopes) 
• Operation of microscopes to collect screening images using SerialEM software

Practical 3: High-end single particle data collection on a 300 kV cryo-TEM

Once a grid suitable for high-end data collection is identified (practical 2), it is transferred into a different cryo-TEM for high-end data collection. The participants will setup automated data collection to collect a data set suitable for image analysis.

The participants will have the opportunity to use:

• ThermoScientific Titan Krios (300 kV cryo-TEM)
• Monitor on-the fly image processing, which serves to asses data quality and eventually optimize data collection

Practical 4: Single particle data analysis

In this concluding practical, participants will analyze the single particle cryo-EM data collected in practical 3 to reconstruct a 3D volume of the molecule of interest, which was used in practical 1 for EM grid preparation.

The participants will have the opportunity to use:

• cryoSPARC software installed on a high-performance computing environment

Programme

Practical Information

The course is limited to 8 participants. For selection purposes, please note that your application will not be considered without CV and a letter of motivation, stating your background and how this course would be beneficial for your future work.

Deadline for registration is September 13th 2026.

There is no registration fee. Travel and accommodation need to be organized and covered by the participants.

Selection Info

Selected participants will be announced on September 21st 2026. For selection purposes, please note that your application will not be considered without CV and a letter of motivation, stating your scientific background, how this course would be beneficial for your future work.

The participants are selected based on EMBL’s course and conferences inclusive criteria (which can be found on the course and conference homepage) and are summarized below:

• Selection of candidates is based on there being a good match between the learning objectives of the course and the stated needs of the candidate, as well as accessibility to the instruments/workflows to the candidate after the course.
• Depending on the applicants, the course will not welcome more than 25% of participants from the same institution’s host country. Same institutions have to be avoided in order to ensure a broader geographical distribution of the knowledge learned during the course.
• Aim for gender balance when selecting the final participants (at least 30% of the minority gender). 
• Applications from organisers, speakers, or trainer laboratories are not prioritised.