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DZIF Super Resolution Microscopy Workshop
Theory and Practice

Center for Integrative Infectious Disease Research (CIID), Heidelberg

10.4.2024 - 12.4.2024


We are pleased to announce a Super Resolution Microscopy workshop, scheduled for April 10th to 12th, 2024, at the Center for Integrative Infectious Disease Research, Heidelberg University. Organized by the DZIF Infectious Diseases Imaging Platform (, this workshop is tailored for PhD students and postdocs keen on learning fundamentals of super resolution microscopy and its applications in life sciences with a special emphasis on host-pathogen interactions. 


Key Workshop Highlights: 

  • Theoretical lectures covering super resolution microscopy techniques, sample preparation, labeling, imaging, and image processing. 

  • Hands-on sessions providing participants with practical experience using cutting-edge equipment and software for image acquisition and analysis. 

  • limited opportunity to examine own biological samples 

  • expert speakers 


Workshop Details:  


Duration: 2.5days 

Participation: Practical component of the workshop is limited to 6 participants (Theory lectures open to 30 participants). 


Registration: individuals interested in attending both the theory and the practical parts are required to submit a concise (max. 1 page) motivation letter to, outlining how they plan to integrate microscopy into their research. Individuals interested only in the theory part don’t need to send a motivation letter but an email with the basic contact information (name, position, group, institute). Early application is encouraged due to limited slots. The application deadline is March 25, 2024. 

Costs: The workshop is free of charge. 

Contact: For any inquiries or additional information, please feel free to reach out to 


We look forward to seeing you at the workshop, fostering collaboration and knowledge exchange in the dynamic field of super resolution microscopy. 


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.


Elisa D'Este

Ulrike is a cell- and developmental biologist educated in Basel, Frankurt and Darmstadt. During a post-doc at Harvard Medical School, Boston, she found her interest in imaging polarized cells on the move. There she started using high spatial and temporal imaging to detect how signaling to the cytoskeleton drives cell protrusions. 2005 she came to Heidelberg University at COS to built and lead the Nikon Imaging Center at Heidelberg University. This light microscope facility offers a wide range of techniques from nano to mm-scale, to support researchers across Campus in their research. Ulrike’s expertise in microscopy is wide spread, with a focus on live imaging and subcellular structures. While TIRF has been one of her favorites, a recent addition to the facility is a STORM setup, complementing the super-resolution portfolio on Campus. Ulrike has been teaching courses in light microscopy and handling of digital images the last 15 years.


Ulrike Engel

Clara studied Biotechnology in Senftenberg and Heidelberg and obtained her PhD in Göttingen and Heidelberg in the department of Stefan Hell. During her PhD she worked with Elisa D’Este with a focus on nanoscopy methods in synaptology. After her PhD she joined the company Abberior Instruments as an application specialist for STED and MINFLUX applications.


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


Aleks did his diploma thesis in Biology (Neuroscience) at Belgrade University. After this he had moved to Heidelberg to do his PhD thesis on mechanisms of neurodegeneration under noninflammatory conditions using various in vivo/in situ imaging techniques. In 2020 he had started his postdoc in the lab of Prof. Thomas Kuner at the Department of Functional Neuroanatomy. His main research focus is studying the nanoarchitecture of neuronal synapses using various super-resolution microscopy techniques (dSTORM, DNA-PAINT, MINFLUX).  

Aleksandar Stojic


Wednesday (April 10.)

9:00 - 9:10 Welcome, course 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 - 10:45 Overview of super resolution techniques - pixel reassignment super-resolution approach  - Vibor Laketa / Sylvia Olberg, CIID, Heidelberg

10:45 - 10:55 break

10:55 - 11:40 Expansion microscopy - Severina Klaus, CIID, Heidelberg

11:45 - 12:30 Introduction to the STED and MINFLUX instruments (overview of the Abberior technologies used in their STED and MINFLUX systems) - Clara Gürth, Abberior Instruments

12:30 - 14:00 Lunch break

14:00 - 18:00 Practicals - two groups (Airyscan and STED microscopy, Severina Klaus / Sylvia Olberg, CIID, Heidelberg)

18:00 - 18:15 debrief




Thursday (April 11.)

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

10:00 - 10:10 break

10:10 - 11:00 Introduction to MINFLUX and STORM nanoscopy:  how to choose the right application for my experiment? - Charlotte Kaplan, Bioquant, Heidelberg

11:00 - 11:10 break

11:10 - 11:35 Multicolor STED and DNA paint microscopy in HIV research - Moritz Hacke, CIID, Heidelberg

11:35 - 12:00 Super-resolution imaging of synaptic nanoarhitecture - Aleksandar Stojic, UKHD, Heidelberg

12:00 - 13:30 Lunch break

13:30 - 18:00 Practicals - two groups (MINFLUX and STORM microscopy, Charlotte Kaplan / Ulrike Engel, Bioquant, Heidelberg)

18:00 - 18:15 debrief



Friday (April 12.)


Image visualisation and analysis practicals

9:00 - 9:30 Deconvolution of the STED data in Huygens - Severina Klaus, CIID, Heidelberg

9:30 - 10:15 AI-based image segmentation in ilastik (two groups) - Severina Klaus / Vibor Laketa, CIID, Heidelberg


10:15-10:30 break


10.30-11:00 STED data visualisation and analysis in Imaris - Vibor Laketa, CIID, Heidelberg

11:00 - 11:30 Comparison of the Airyscan and STED data in FIJI - Sylvia Olberg / Vibor Laketa, CIID, Heidelberg

11:30 - 12:00 Visualization of the MINFLUX data in Paraview and pyMINFLUX - Charlotte Kaplan, Bioquant, Heidelberg


12:00-12:30 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 25.3.2024.


The workshop is free of charge.


Participation in the theory lectures is limited to 30 participants. 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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