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DZIF Super Resolution Microscopy Workshop
Theory and Practice

Center for Integrative Infectious Disease Research (CIID), Heidelberg

27.9.2023 - 29.9.2023


We are pleased to announce a Super Resolution Microscopy workshop, to be held on 27. - 29. September 2023 at the Center for Integrative Infectious Disease Research, Heidelberg University. This workshop is organised by DZIF Infectious Diseases Imaging Platform ( and aimed at PhD students/postdocs who are interested in learning about the basics of super resolution microscopy and its applications in life sciences with the focus on host-pathogen interactions.


The workshop will cover theoretical lectures on super resolution microscopy techniques, including sample preparation and labeling, imaging, image processing and analysis, as well as advanced applications of super resolution microscopy. In addition, there will be practical, hands-on sessions where participants will have the opportunity to use state-of-the-art equipment and software to gain experience in image acquisition and analysis. There will be a limited opportunity to examine own biological samples.


Our invited speakers are experts in the field of super resolution microscopy, and they will provide comprehensive lectures and demonstrations that will enable participants to develop practical skills and learn the basic concepts as well as latest techniques in super resolution microscopy.


The course  will be 2.5days long. Due to a practical component it is limited to 6 participants (participation in theory lectures is not limited). To register, the applicants need to send a short (max. 1page) motivation letter to indicating how they plan to use microscopy in their research. Due to a limited number of participants, the applicants are encouraged to apply well in advance of the deadline as the application process will stop once all positions are filled.  Application deadline is 15.7.2023.


The workshop is free of charge.


If you have any questions or require further information, please do not hesitate to contact us at


We look forward to seeing you at the workshop.



Elisa D'Este

Elisa studied Biotechnology at the University of Trieste (Italy), where she obtained her Ph.D. working on applications of optical tweezers in neuroscience. After graduation, she joined the department of Stefan Hell at the Max Planck Institute for Biophysical Chemistry in Göttingen as a postdoctoral fellow. During these years, she specialized in the use of nanoscopy techniques to study neuronal structures, in particular the organization of the neuronal cytoskeleton. Since 2017, Elisa is PI of the collaborative research center SFB1286 (Quantitative Synaptology). In 2018 she joined the MPI for Medical Research in Heidelberg, where she conducts independent research and heads the optical microscopy facility specialized in nanoscopy techniques.


Clara Gürth

Moritz Hacke


Charlotte finished her biology diploma in Heidelberg and Toulouse (France) investigating quantitatively the cell’s chromatin structure by fluorescence microscopy. She continued afterwards with her PhD education at ETH Zurich (Switzerland) and postdoctoral research in David Drubin’s lab at UC Berkeley (USA) applying in both laboratories single-molecule localization microscopy (dSTORM) to study the role of cytoskeletal organizations in cell function. Charlotte became an application specialist of advance fluorescence light microscopy techniques over these years, with the focus on single-molecule localization microscopy and quantitative data and image analysis. In September 2022 Charlotte has started her position as a super-resolution microscopy specialist at the Cellnetworks Core Technology Platform at Heidelberg University with the current focus of implementing MINFLUX nanoscopy and supervising future super-resolution microscopy projects

Charlotte Kaplan


Severina spent the last 11 years in Heidelberg as a student, obtaining her PhD in parasitology in 2022. Since then she is splitting her time working as a research scientist in virology and working as a microscopy application specialist in the Infectious Diseases Imaging Platform (IDIP) at the Center for Integrative Infectious Disease Research (CIID) in Heidelberg.  Her work covers basic aspects of cell biology and infectiology and centers around advanced microscopy approaches with a focus on live-cell imaging, super-resolution microscopy and image analysis

Severina Klaus

Vibor obtained his PhD at the European Molecular Biology Laboratory (EMBL), Heidelberg, Germany where he worked on automated microscopy setups for high-content screening and their application in investigating diverse cellular processes. After the PhD he continued his research as a staff scientist at the EMBL where he operated at the interface between advanced light microscopy, robotics, chemical biology and cell biology. In 2013. he joined University Hospital Heidelberg and German Center for Infection Research (DZIF) to establish the microscopy infrastructure under enhanced biosafety containment (BSL2/BSL3) for infectious disease research. As head of Infectious Diseases Imaging Platform (IDIP) he is interested in all aspects of advanced microscopy applications in infectious disease research as well as development of microscopy-based assays in medical diagnostics. He has long experience in teaching various aspects of light microscopy technologies and digital image handling.

Vibor Laketa

Holger Lorenz


Holger is a cell and molecular biologist educated at the Universities of Göttingen and Munich (LMU), Germany. He did his postdoc research at the National Institutes of Health, NIH, USA, in Dr. Jennifer Lippincott-Schwartz’s lab with a focus on advanced light microscopy of subcellular processes. After having spent a couple of years in the optical industry, he joined in 2008 the Center of Molecular Biology (ZMBH) at the University of Heidelberg to set up a core facility for advanced imaging. He serves as head of the core facility to support researchers with light microscopy - ranging from basic to superresolution/nanoscopy - and image analysis/processing applications. Holger has been active in developing microscopy applications to determine protein topologies and sub-locations, and he has a long track record of teaching digital image analysis to under- and postgraduates. His courses cover all aspects of image processing including the ethically- and quantitatively-correct use of existing analysis tools and goal-oriented software programming.

Sylvia studied Biochemistry in Berlin and obtained her PhD in cell biology at the Pasteur Institute in Paris working on host pathogen interactions. Already during her PhD she was fascinated by microscopy and worked as an associated scientist at the imaging platform of the Pasteur Institute. Following, she joined the lab of Freddy Frischknecht at the University Hospital in Heidelberg to investigate cell motility of malaria parasites using live cell imaging as well as TIRF and traction force microscopy. During this postdoc she decided to stay in the microscopy community and joined Carl Zeiss Microscopy GmbH to work as widefield and super resolution specialist in the European demo center of Carl Zeiss in Munich. She decided to come back to the academic setting and after briefly working in the imaging facility in Freiburg, she joined Infectious Diseases Imaging Platform (IDIP) at the University Hospital Heidelberg as the imaging specialist.

Sylvia Olberg


Wednesday (September 27.)

9:00-9:10 Welcome, course introduction, participant introduction (Vibor Laketa, CIID, Heidelberg)

9:10-9:55 Introduction to super resolution microscopy (what is resolution, why is it limited and why does it matter - Holger Lorenz, ZMBH, Heidelberg)

9:55-10:05 break

10:05-11:00 Overview of super resolution techniques (different super resolution approaches, pros and cons, applications in infection disease research)  - Vibor Laketa / Sylvia Olberg, CIID, Heidelberg)

11:00-11:15 break

11:15-11:55 Introduction to the STED and MINFLUX instruments (overview of the Abberior technologies used in their STED and MINFLUX systems) - Clara Gürth, Abberior Instruments

12:00-13:30 Lunch break

13:30-14:00 IDIP tour, introduction of the participants involved in the practical part

14:00-18:00 Practicals - two groups (Airyscan and STED microscopy)

18:00-18:15 debrief




Thursday (September 28.)

9:15-10:00 Sample preparation considerations in super resolution microscopy (Elisa D'Este, MPI, Heidelberg)

10:00-10:15 break

10:15-11:00 Introduction to MINFLUX microscopy (Charlotte Kaplan, Bioquant, Heidelberg)

11:00-11:15 break

11:15-12:00 Multicolor STED and DNA paint microscopy in HIV research (Moritz Hacke, CIID, Heidelberg)

12:00-13:30 Lunch break

13:30-18:00 Practicals - two groups (MINFLUX and 3D STED/DyMIN microscopy)

18:00-18:15 debrief



Friday (September 29.)


09:15-10:00 Expansion microscopy (Severina Klaus, CIID, Heidelberg)


10:00-10:15 break


10.15-12:30 Data analysis (handling super resolution images in FIJI, figure preparation for visualization and presentation/publication, AI for segmentation)


Optional: STED/Airyscan imaging of samples brought by participants with final (10min) presentation of obtained data


12:30-13:00 Final discussion and feedback


Theory + Practicals

Due to a practical component the workshop is limited to 6 participants. To register, the applicants need to send a short (max. 1page) motivation letter to indicating how they plan to use microscopy in their research. Due to a limited number of participants, the applicants are encouraged to apply well in advance of the deadline as the application process will stop once all positions are filled.  Application deadline is 15.7.2023.


The workshop is free of charge.


Participation in the theory lectures is not limited. To register simply send an email to with the subject line "SR workshop registration" and a short text indicating your name, position and affiliation. 


The workshop is free of charge.

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