Microscopy is a cornerstone of biomedical research, with a rich history of enabling scientific breakthroughs through the ages. At the same time, microscopy and image data handling are complex areas of research which necessitate significant expertise in different disciplines such as biology, chemistry, optics and informatics. The seminar series is designed to support researchers and scientists by offering a robust theoretical basis of microscopy and image data handling and discussing relevant practical considerations.

This in person seminar series will take place from 19.10 - 30.11.2026 every Monday from 14:00-17:00 in the large seminar room (SR41) at BioQuant, Heidelberg.

Throughout the seven modules, we will guide the participants through the fundamental principles of microscopy and bioimage data handling, from experimental design and sample preparation to data presentation and publication standards.

Registration is not necessary, but if you are interested in this seminar series, please fill out the short survey in the link below:

Participation interest survey

Location and time:

Monday 14:00-17:00, Large Seminar room SR41, BioQuant INF267, Heidelberg

 

Schedule: 

Date	Module	Topic
19.10.2026	00	Concepts in microscopy
26.10.2026	01	Microscopy Experiment Design and Sample Preparation
02.11.2026	02	Image Acquisition
09.11.2026	03	Image Processing
16.11.2026	04	Image Analysis and Quantification
23.11.2026	05	Image Data Management
30.11.2026	06	Image Data Presentation and Publication Standards

 

Audience: 

This seminar series is geared towards any scientist working with or planning to work with microscopy and bioimage data, from students to postdoctoral researchers and staff scientists. 

Content: 

19.10: Module 0 - General concepts in microscopy

Goal: Give a general overview about the concept of microscopy and its role in research.

Participants should gain a general framework of why microscopy is performed and how it works in general (i.e. generate an image from reality). The landscape of microscopy hotspots at the Mannheim-Heidelberg campus will also be presented. 

Speakers: Vibor Laketa

26.10. Module 1 - Microscopy experiment planning & sample preparation 

Goal: Equip participants with the skills to design robust microscopy experiments and prepare samples that maximize data quality.

The module is designed to teach people how to strategically think about microscopy experiments before they even touch a microscopy. The module should also inspire participants to employ microscopy as a method of choice when tackling complex questions in biomedical science.

Speakers: Quirin Krabichler, Diego Pastene Maldonado, Ina Schaefer

02.11. Module 2 - Image acquisition 

Goal: Provide participants with knowledge on how to choose optimal acquisition settings and avoid common acquisition pitfalls.

The module is designed to guide participants on how to acquire reproducible, high-quality images. The module will give participants a solid conceptual foundation of how images are generated in light microscopy, how acquisition parameters shape data quality, and how to recognize and avoid common pitfalls and biases. 

Speakers: Ulrike Engel, Diego Pastene Maldonado

09.11. Module 3 - Image processing 

Goal: Teach participants what image processing is, why it is needed, what operations are acceptable and how processing affects data interpretation.

ImageJ/Fiji is introduced as the reference software environment. This module will empower participants to critically evaluate image processing they see in publications, and to apply best practices in their own work. 

Speakers: Severina Klaus

16.11. Module 4 - Image Analysis & Quantification 

Goal: Teach participants how to extract reliable quantitative information from microscopy images..

Participants will learn what can be quantified, how it’s done conceptually and what pitfalls exist. 

Speakers: Alessandro Ulivi, Severina Klaus

23.11. Module 5 - Image Data Management (Short Module)

Goal: Equip participants with the knowledge and best practices to handle, organize, store and share microscopy image data in ways that ensure reproducibility, integrity, and compliance with institutional and publishing standards. 

Speakers: Alessandro Ulivi, Christian Schmidt, Victor Pérez

30.11. Module 6 - Image data presentation & publication standards 

Goal: Teach participants how to prepare microscopy images and image-derived data for publications, talks, and posters while maintaining scientific integrity, reproducibility, and compliance with publisher guidelines.

This final module gives participants the tools to present their data clearly, ethically, and in line with international standards, which not only improves their publications but also protects them from integrity issues.

Speakers: Vibor Laketa, Charlotte Kaplan