Cryo-EM Workshop

NCCR TransCure Single Particle Cryo-EM Workshop 2018 at C-CINA

The NCCR TransCure Single Particle Cryo-EM workshop took place at C-CINA, Mattenstrasse 26, 4058 Basel, Switzerland, starting Wednesday, August 22 until Friday, August 24, 2018.

The workshop introduced all aspects of the single particle cryo-EM pipeline. This includes sample preparation, electron microscopy hardware, electron microscopy data collection schemes, image processing algorithms, estimation and correction of electron microscopy parameters during images processing, particle picking, 3D protein reconstruction, resolution estimation, data handling, and model building. Morning lectures will introduce the theoretical aspects of cryo-EM. Afternoon practicals on provided or own computers introduced single particle image processing. The workshop targeted PhD students and PostDocs that have some basics knowledge of structural biology and/or electron microscopy.

Group Photo of the Workshop Participants

Click on the image to zoom


Registration is now closed.


Please note that the travel and lodging are not covered in the workshop registration fee and participants will have to arrange it by themselves. We recommend the following hostels:

  • BaselBackPack -
  • Youth Hostel Basel -


The workshop will take place in C-CINA of the Biozentrum of the University of Basel. This is NOT in the Biozentrum, but in the northern part of Basel, in Mattenstrasse 26, 4058 Basel. Practical lectures will be held in the Misrock Seminar Room in the ground floor of the building.

Lunch vouchers are valid in the canteen of the Rosenthal campus (close to C-CINA)

A demo on the C-CINA electron microscopes is part of the workshop.

A computer hands-on practical will take place in the Biozentrum in Klingelbergstrasse 70, in Room U1075.

Organizers and Lecturers

The workshop is organized by

Henning Stahlberg, C-CINA, Biozentrum, University of Basel
Kaspar Locher, ETH Zürich
Karen Bergmann, C-CINA, Biozentrum, University of Basel. 

Lectures will be given by 

Ariane Fecteau-LeFebvre, C-CINA
Carola Alampi, BioEM Lab, C-CINA
Dongchun Ni, C-CINA
Henning Stahlberg, C-CINA
Ioannis Manolaridis, ETH Zürich
Julia Kowal, ETH Zürich
Kaspar Locher, ETH Zürich
Lubomir Kovalczik, C-CINA
Mohamed Chami, BioEM Lab, C-CINA
Paula Navarro, C-CINA
Philippe Ringler, C-CINA
Ricardo Adaixo, C-CINA
Ricardo Guerrero, C-CINA
Ricardo Righetto, C-CINA
Stefan Albiez, C-CINA


The workshop is supported by

NCCR TransCure

Biozentrum of the University of Basel

C-CINA of the Biozentrum of the University of Basel




Wednesday, August 22, 2018
9:00 Registration, Coffee C-CINA, Mattenstrasse 26, 4058 Basel
10:00 Welcome Locher and Stahlberg C-CINA, Misrock
10:15 Lecture Overview of Cryo-EM Henning Stahlberg C-CINA, Misrock
11:00 Lecture Sample Preparation Philippe Ringler C-CINA, Misrock
11:45 Lecture Grid Freezing Mohamed Chami C-CINA, Misrock
12:30 Lunch Rosental SV Cantine
14:00 Lecture EM Hardware Ariane Fecteau-LeFebvre C-CINA, Misrock
15:00 Demos at Electron Microscopes. Groups rotate:
  • neg. stain and cryo grid preparation
  • T12 negative stain grid screening
  • Talos 200kV cryo-EM grid screening
  • Titan 300kV cryo-EM automated data collection
  • Spirit 120kV

  • Philippe Ringler
    Carola Alampi
    Mohamed Chami
    Lubomir Kovaczik
    Ricardo Guerrero
    C-CINA Basement
    18:45 Dinner C-CINA, Science Lounge, 7th floor
    19:00 Selected talks by students (during dinner in Science lounge) C-CINA, Science Lounge, 7th floor

    Thursday, August 23, 2018
    9:15 Welcome, Coffee C-CINA, Mattenstrasse 26, 4058 Basel
    10:00 Lecture Overview data processing algorithms Henning Stahlberg C-CINA, Misrock
    10:45 Lecture Online Processing during data collection Henning Stahlberg C-CINA, Misrock
    11:30 Lecture Drift correction, CTF Fitting, Particle picking Ricardo Adaixo C-CINA, Misrock
    12:20 Group Photo taking
    12:30 Lunch
    14:00 Lecture Single particle cryo-EM reconstruction with cisTEM Ricardo Righetto C-CINA, Misrock
    14:45 Transfer to Biozentrum (Klingelbergstr. 70, Basel)
    15:00 Hands-on Practical, cryo-EM image processing with cisTEM.
    10 groups of 2 students each.
    Ricardo Righetto
    Dongchun Ni
    Ricardo Adaixo
    Stefan Albiez
    Computer room U1075, Pharmazentrum
    18:00 Free time
    19:00 Dinner downtown Italian Restaurant "Centro"
    Streitgasse 20, Basel (GoolgeMaps Link)

    Friday, August 24, 2018
    8:30 Welcome, Coffee C-CINA, Mattenstrasse 26, 4058 Basel
    9:00 Lecture Introduction to Data Processing with cryoSPARC Ricardo Adaixo C-CINA, Misrock
    10:00 Lecture Resolution Analysis: FSC, ResMap, local resolution filtration, visualization Ricardo Righetto C-CINA, Misrock
    11:00 Lecture on Different Geometries for Single Particle Processing: 2D crystals and helical samples Henning Stahlberg C-CINA, Misrock
    11:30 Lecture on Electron Tomography Sub-Volume Averaging Paula Navarro C-CINA, Misrock
    12:00 Lunch
    13:30 Lecture Model Building Julia Kowal C-CINA, Misrock
    14:15 Lecture Specific Application Case: ABC transporters Ioannis Manolaridis C-CINA, Misrock
    14:45 Lecture The Role of Cryo-EM in Membrane Protein Research Kaspar Locher C-CINA, Misrock
    15:30 Workshop Summary, Snacks, and departure. Locher and Stahlberg C-CINA, Misrock