Microscopy Imaging Center


Open position  as Analyst / Microscopist

The Center for Microscopy and Image Analysis at the University of Zurich offers a 4 year position. Further details see here.

11 - 15 Jul 2022: MIC Workshop on Bioimage Processing

If you want to get started using the Python eco-system for your bioimaging projects this intensive one-week workshop is the right thing for you. In addition to course time, you will also have some time to work on your own projects, just getting started or continuing an existing one, and will be able to discuss them with other participants and the instructor. PhD students of the GCB profit from a reduced price. More details on the pdf below, registration here.

Whole day live demo at DBMR Bern

A Revolutionary Approach to Detect, Characterize & Screen
Confocal+ Widefield + Multimode Reading= Stunning Images+ Analysis

Join us for an overview of BioTek's new, next generation Cytation instrument, the Cytation C10 Confocal Imaging Reader.
We' ll highlight workflows to obtain phenotypic and quantitative data across its broad application range . Registration here.

Artificial intelligence methods applied to intravital microscopy of the immune system

This hyprid workshop will cover theoretical and practical aspects regarding the application of new A.I. -based methods for the analysis
of migration and interaction of immune cells captured by 4D intravital imaging. Basic knowledge in imaging is recommended.

More information and registration here.

LS2 Prestige Webinar

MIC committee member Benoit Zuber, as part of the LS2 Biophysics section, invites you to the upcoming LS2 Prestige Webinar.
Topic: “CryoEM structures of amyloid filaments from human brain” 
When: 30th March 2022, 16:00 – 17:00 (CET)
Please register here.

Join the Cutting Edge Microscopy PhD program

Interested in becoming a world-class expert in biological imaging?
The CEM PhD program currently has a few vacancies. If you are a PhD student of the GCB and you apply advanced microscopy techniques in your PHD thesis, we are looking for you. Please find more details on the flyer below and do not hesitate to contact us.

Midterm presentation

Irene Spera, student of the PhD program Cutting Edge Microscopy (CEM), will give her midterm presentation on March 9, 2022 at 11:00 online via zoom. Title: "Factors regulating the exchange of cerebrospinal fluid and interstitial fluid of the brain".

Our project investigates the perineural outflow pathways of cerebrospinal fluid (CSF) at the cribriform plate and focused on the elucidation of anatomical connections between the subarachnoid space (SAS) and the lymphatics at the exiting nerve routes. Furthermore, we want to define the anatomical spaces of the CSF flow on the brain surface and elucidate the relationship between CSF and the interstitial fluid (ISF) of the brain. To address these aims, we made use of transgenic reporter mice, fluorescence microscopy, and through skull near-infrared (NIR) in vivo imaging.

Please request acess to this online event via e-mail to Rahel Eyer. 

Join the Correlative Microscopy Symposium 

March 13 - 16, 2022

The Organization Committee and the ZEISS Microscopy Team are delighted to invite you to the 6th Joint Meeting Workshop and Symposium “From 3D Light to 3D Electron Microscopy” taking place from March 13th to 16th 2022 in cooperation with the EMBL in Heidelberg, the VIB in Ghent and the Francis Crick Institute in London.
Many prominent scientists will share their groundbreaking work on correlative microscopy in 3D and volume EM. You can also look forward to practical workshops on

  • correlative workflows
  • volume EM methods
  • sample preparation methods

and on a panel discussion of the international networking happening to promote these techniques.
This meeting will inspire you and open up the possibilities for forming new collaborative efforts to use these powerful imaging techniques to better understand the nano-world inside cells and tissues. 
Please register here.

DCI Symposium 2022

The Dubochet Centre for Imaging (DCI) Symposium 2022 will take place in Lausanne and in Geneva June 8 to 10. More details and registration here.

Image analysis expert

The Friedrich Miescher Institute für Biomedical Research (FMI), Basel, is looking for an image analysis expert.. Please submit your application by February 25, 2022.  For more details see the Job add below.

SNSF Scientific Image Competition

​​​The SNSF Scientific Image Competition encourages researchers working in Switzerland to present their works to the public and the media. Photographs, images and videos will be rated in terms of their aesthetic quality and their ability to inspire and amaze, to convey or illustrate knowledge, to tell a human story or to let us discover a new universe. Submission deadline January 31, 2022. More information here.

PhD Defense

Federico Saltarin student ot the PhD program Cutting Edge Microscopy (CEM), will give his PhD defense on December 10, 2021 at 10.30  online via Zoom.
Title: “Investigations on the extravasation of melanoma cells across the blood brain barrier”.
Please request access to this online event via e-mail to Rahel Eyer.

Our project focuses on the investigation of the extravasation of melanoma cells across the blood brain barrier in the context of brain metastasis development.
To this aim, we addressed the impact of compromised endothelial junctions at the BBB on brain metastatic melanoma cell extravasation and we developed methods and tools for the investigation of melanoma brain metastasis formation on multi-scale level.

MIC Symposium 2021

Finally, after a missing year 2020 due to covid pandemic, the traditional MIC Symposium took place in UniS on November 19, 2021. The topic of this year was 3D electron microscopy.  The scientific committee represented by Wanda Kukulski, Michael Stoffel, Benoît Zuber (University of Bern) and Dimitri Vanhecke (University of Fribourg), prepared an interesting program, which attracted more than 110 participants. More details see here.


LS2 Intersection Microscopy 

The LS2 Intersection Microscopy together with the Swiss Society for Optics and Microscopy (SSOM) was founded in February 2019. During the past years, microscopy techniques as well as image analysis capabilities have developed at incredible pace. Today, microscopy based research is becoming increasingly important in all fields of life sciences. The LS2  microscopy intersection aims for a better and intensified knowledge transfer between the microscopy community and life scientists in Switzerland and thus intends to promote the faster introduction of new and cutting-edge microscopy techniques in Switzerland. Also, high-end microscopy techniques should become even better known as well as the core facilities providing them.

Apply for the LSmembership here and select "Microscopy" in the online application form.

PhD Defense

Martin Liptay student ot the PhD program Cutting Edge Microscopy (CEM), will give his PhD defense on October 1, 2021 at 15:00  online via Zoom.
Title: “Replication fork remodeling and PARP inhibitor resistance in Brca1/2-mutated mouse mammary tumors”.
Please request access to this online event via e-mail to Rahel Eyer.

Poly (ADP-ribose) polymerase inhibitors (PARPi) are a class of targeted therapeutics that recently entered the clinic for the treatment of patients suffering from BRCA1/2-mutated breast and ovarian cancer. Unfortunately, similar to other anticancer therapeutics, their efficacy in tumor eradication is frequently limited by acquired drug resistance. By employing a variety of molecular biology and imaging techniques, we identified novel, non-canonical functions of DNA repair proteins H2AX and MDC1 in the metabolism of replication forks and in mediating PARPi response in BRCA1/2-deficient mammary tumors.

Zietschmann-Preuss-Award 2021

The 2021 Zietzschmann-Preuss Award presented by the World Association of Veterinary Anatomists goes to Christina Alexandra Kalenberg, Department of Clinical Veterinary Science, University of Bern, post-graduate student of MIC Board member Michael Stoffel. We congratulate her on this success!

DOI: 10.1111/ahe.12525

Communication training for students of the PhD program Cutting Edge Microscopy (CEM)

The communication training for CEM students took place on 6 and 8 September 2021 in Berne. During two interesting and varied days, the participants had the opportunity to work on impactful speaking techniques, exercices for voice warming and were able to improve their personal skills under instruction of  Michael Berndonner, external public speaking and communication trainer.

PhD Defense

Eleonora Lupi, student ot the PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on September 29, 2021 at 15:30  online via Zoom.
Title: “Establishment of a zebrafish screening assay for the identification of compounds affecting proepicardial and epicardial formation”.
Please request access to this online event via e-mail to Rahel Eyer.

Description: the epicardium is the most external layer of the heart that has been demonstrated to have an important role during heart formation and regeneration. Despite the increasing interesting on this tissue, some mechanisms leading its formation remain still unknown. With this project we aimed to study the effect of epigenetic modulators on the proepicardial and epicardial formation in zebrafish model, to better understand the epigenetic role in this process. A drug screening was performed and zebrafish embryos were imaged using an Acquifer imaging machine. We were able to implement an automatic pipeline to quantify the number of the epicardial cells and determine the effect of the drugs on the epicardium.

PhD Defense

Alberto Mattei, student ot the PhD program Cutting Edge Microscopy (CEM), will give his PhD defense on September 1, 2021 at 10.00 am online via Zoom
Title: "Exploring Signaling Mechanisms regulating genetic and non-genetic Drug Resistance in Melanoma"
Please request access to this online event via e-mail to Rahel Eyer.

"Metastatic melanoma is a very aggressive type of cancer that in over 50% of cases carries a BRAFV600E mutation. The mutated BRAF drives aberrant MAPK-ERK pathway activation and tumor progression. Selective BRAFV600E inhibitors have been on the market since 2011, but drug resistance almost invariably develops and patient relapse in the clinic. We explored mechanisms that regulate genetic and non-genetic drug resistance in melanoma."

Congratulations to new publication!

Congratulations to Yury Belyaev, Federico Saltarin, Ruth Lyck and Paolo Favaro from University of Bern and their collaborators to their new publication on "Learning to Reconstruct Confocal Microscopy Stacks From Single Light Field Images" published in IEEE Transactions on Computational Imaging in July 2021, DOI.

Swiss Microscopy Core Facility Day 2021

Registration for the 2021 Swiss Microscopy Core Facility Day at the new Biozentrum in Basel is open.
Link to registration here.

LS2 Webinar Series

The LS2 Microscopy Intersection is happy to organise the LS2 Microscopy Webinar Series. One Tuesday each month, a speaker will share their exciting work on imaging methods and their applications in science or industry.

The next LS2 Microscopy Webinar will take place on the 20th July 2021 at 17:00 (~30min plus Q&A time). Register here.

ZEISS Microscopy Image Contest 2021 

We are thrilled to announce the ZEISS Microscopy Image Contest 2021. Do you take stunning microscopy images? Submit your best image now!  The contest is open to all microscopy enthusiasts and professionals in any application field. Images can be taken with any ZEISS microscope (light, X-ray or electron microscope). Deadline for entry is July 31, 2021.

All participants will receive a copy of the ZEISS Microscopy Calendar 2022. On top of that, the three winners will receive the following prizes:

  • 1st Prize: ZEISS Primostar 3
  • 2nd Prize: ZEISS Victory Pocket 10x25
  • 3rd Prize: ZEISS Terra 10x42

To submit your image and read all FAQs and rules, visit our contest web page

New position in microscopy at Wyss Center, Geneva


The position is conceived to focus on transversal activities among the different microscopes and image analysis systems with technical roles on maintenance, assistance and quality control of the microscopes and integration of image analysis pipelines. The person will also be involved in the run of Wyss Center driven research projects.

Deadline 23th of July, with possibility of extension.

Exciting publication of Professor Olivier Pertz

We congratulate MIC committee member Oliver Pertz and his team to their exciting new study “Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival” published in Developmental Cell in June 2021.

QUAREP-LiMi WG 10 Image Quality Talk from Alan C. Bovik

"On Picture Quality Prediction"

Alan Bovik is a faculty member in the Department of Electrical and Computer Engineering, the Wireless Networking and Communication Group (WNCG), and the Institute for Neuroscience. His research interests include digital television, digital photography, visual perception, social media, and image and video processing. To recieve the Zoom link to this talk, please contact Yury Belyaev.

15th EXCITE Zurich Summer School

Registration is now open for the 15th EXCITE Zurich Summer School on Biomedical Imaging that will take place in Zurich, Switzerland, from 6 - 17 September 2021. Application deadline: Monday, 3 May 2021 (Notification of acceptance: 1 June 2021).


PhD Defense

Coralie Dessauges, student ot the PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on May 3, 2021, at 1.00 pm. Title: An optogenetic actuator/biosensor circuit for large scale interrogation of MAPK signaling dynamics
Please request access to this online event via e-mail to Rahel Eyer.

In this work, we developed a set of optogenetic circuits to activate the MAPK/ERK pathway with light from different levels of the MAPK network and measure the corresponding ERK activity with a high temporal resolution. Together with automated imaging and image-analysis pipelines, our systems enable us to image and stimulate ERK signaling in hundreds of cells in a highly automated and dynamic fashion. Taking advantage of this throughput, we conducted an RNAi perturbation screen to investigate the role of 50 proteins of the MAPK network in ERK signaling regulation.

PhD Defense

Nora Ruef, student ot the PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on March 26, 2021, at 4.00 pm. Please request access to this online event via e-mail to Rahel Eyer.

"In this thesis we investigated the unique migration mode of submandibular salivary gland tissue resident memory CD8+ T cells and how memory CD8+ T cells perform homeostatic surveillance of a complex organ with mixed epithelial – connective tissue composition."

PhD Defense

Julia Bruggisser, student of he PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on March 25, 2021, at 3.00 pm. Please request access to this online event via e-mail to Rahel Eyer.

Title: Clostridium Perfringens β-Toxin: Receptor Identification and Oligomer Structure

Self-evaluation of the Microscopy Imaging Center (MIC)

Please complete the survey of the MIC here until March 16, 2021. This survey is designed to evaluate the performance of the MIC with respect to teaching and services. Your participation will help to implement improvements exactly there where you requested them most

New instrument at ARTORG

02.02.2021 - The newly acquired EVOS M7000 microscope from Thermo Fisher is a widefield fluorescence microscope, suitable for.... continue reading

White Paper of QUAREP-LiMi is online

29.01.2021 – Read the White Paper «QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy» here.

Virtual Seminar Invitation - ImageXpress Pico

02.03.2020 - When size doesn't matter: meet ImageXpress Pico, the miniature but mighty microscope. Continue reading

DBMR Hyperion Imaging System

02.11.20 – New MIC Instruments

Location: INO-F608A
Type: Imaging mass cytometer
Site: UniBE-Insel Read more

DBMR Helios Mass Cytometer

07.10.20 – New MIC Instruments

Location: INO-F608A
Type: Mass Cytometer
Site: UniBE-Insel Read more

DBMR Hyperion Imaging System

05.10.20 – New MIC Instruments

Location: INO-F608A
Type: Imaging mass cytometer
Site: UniBE-Insel Read more

LHEP Keyence VHX-7000

05.10.20 – New MIC Instruments

Location: Gebäude der exakten Wissenschaften (ExWi)
Type: Widefield Microscope
Site: UniBE-ExWi Read more

IZB Nanolive 3D Cell Explorer

10.08.20 – New MIC Instruments

Location: Institute of Cell Biology, Baltzerstrasse 4, 3012 Bern
Type: Widefield Microscope
Site: UniBE-Muesmatt Read more

IRM ThermoFisher Phenom XL Scanning EM (Bob)

02.11.20 – New MIC Instruments

Location: Institute of Forensic Medicine, Bühlstrasse 20, 3012 Bern
Type: Electron Microscope
Site: UniBE-Muesmatt Read more