Autor: Mateusz Kostecki

This practical workshop will guide you step by step through the process of pose estimation with DeepLabCut and an introduction to its output data structure and analysis of kinematics. Many researchers use pose estimation tools but struggle to get consistent, high-quality results or move beyond tracking into real behavioural insights. This workshop is designed to close that gap.

The workshop is intended for young researchers, including Master’s and PhD students, as well as postdocs and established scientists who want to sharpen their practical understanding of state-of-the-art behavioral analysis tools.

Prior experience with experimental data and a basic understanding of Python are required to benefit from the workshop, especially the data analysis part of it.

What will you learn?

By the end of this course, you will be able to:

• Confidently navigate the DeepLabCut workflow (via GUI and code)
• Annotate data properly, select the right model backbone, train your model, and evaluate its performance
• Analyze your videos and tune tracking in multi-animal projects
• Preprocess and structure your data for advanced behavioral analysis

We encourage participants to bring video recordings from their own experiments—these can be used during practical sessions to kickstart your own analysis projects.

Requirements: Basic Python knowledge, laptop.

Instructors:

• Konrad Danelewski, Nencki Institute

The workshop will take place on Nov 20-21st, 9:45 AM -5 PM at COS, Heidelberg. Institute. Please find the application form here. The workshop is free of charge and is held in a stationary form only!

Many experiments require us to synchronize multiple data streams – from cameras, sensors, microscopes – precisely deliver stimuli, and, quite often, to do everything in a closed-loop setting. The fact that different devices use different software doesn’t make this task easier.

One of the best – and open – solutions to those challenges is Bonsai, a reactive programming language that allows you to collect data from multiple systems, from calcium imaging, through sound recordings to sensors and control output devices – such as feeders, motors, or stimulus delivery systems and build close-loop paradigms. It is easy to learn and implement and robust.

During our workshop, we will introduce basic logic of Bonsai, cover loading and saving data, working with camera to track animals and basics of closed-loop experiments. We will also cover using Arduino alongside Bonsai to control experimental equipment and save the data from your sensors

Requirements: Windows computer, webcam

Instructors:

• Mateusz Kostecki, Heidelberg University
• Jagoda Nawrocka, University of Warsaw

The workshop will take place on Oct 17th, 9:45 AM -5 PM at COS, Heidelberg. Institute. Please find the application form here. The workshop is free of charge!

The workshop is held in stationary form only!

Arduino is an easy-to-learn and easy-to-use microcontroller platform that gives almost infinite possibilities. It allows you to make devices that can improve and automatize your research or hobbyist projects – you can build

During the workshop, you will learn basics of Arduino; you will work with different types of sensors, diodes, motors, and other elements. The workshop will give you the knowledge and skills necessary to make useful lab devices by yourself. No previous knowledge of electronics or programming is required!

The workshop will take place on May 28th, 9:45 AM -12:45 PM at COS, Heidelberg. Institute. Please find the application form here. The workshop is free of charge!

We are happy to announce the next Heidelberg Open Lab Workshop – Spectral Analysis of Experimental Data – that will be conducted by Axel Hutt (INRIA).

The spectral analysis of experimental time series—for example, those obtained from biological systems—requires a fundamental understanding of basic principles. This course aims to minimize the use of mathematical formalism and instead explain the core concepts through numerous examples. Naturally, questions are warmly welcome.

The course is intended for young researchers, including Master’s and PhD students, as well as Postdocs and established scientists who wish to fill potential gaps in their understanding. Topics to be discussed include:

• Sampling Theory
• Fourier Analysis
• Spectral Filters
• Time-Frequency Analysis (wavelets, Short-Time Fourier Transform)
• The concept of analytical signals (e.g. Hilbert Transform)
• Synchronisation (coherence, phase synchronisation)
• Statistical inference of spectral power

Prerequisites: The participant should already have worked with experimental data and should  have a basic knowledge of applied mathematics.

Lecturer

Axel Hutt studied Physics at the University of Stuttgart and worked on his PhD at the Max Planck Institute for Cognitive Neuroscience in Leipzig. He won a Schloessmann Fellowship of the Max Planck Society and was awarded an ERC Starting Grant in 2010. His research interests are the stochastic dynamics of neural systems in theory and experimental data with a recent strong focus on neuromodulation in the clinical context.

Details

The workshop will be organized locally (we do not provide online streaming) on May 23rd 2025, 10AM – 5 PM at the Centre for Organismal Studies, Heidelberg. Please find the application form HERE. The deadline for the application is May 16th. The workshop is free of charge.

We are happy to announce our first Heidelberg Open Lab workshop!

Organizing scientific events—workshops, summer schools, conferences, symposia—can seem like a daunting task. You need to design the event structure, secure funding, invite guests, promote it, handle payments, and communicate with participants. On top of that, there are logistics to manage: catering, flights, hotels, and scheduling.

It’s a lot, but with the right approach, some key knowledge—and the right people around you—you can successfully organize an event, even with limited resources.

During our workshop, you will learn how to navigate these challenges efficiently, streamline the planning process, and make your event a success.

During our workshop you will learn how:

• design your event, select its target and set goals
• secure funding: find sponsors, write grant applications
• promote your event on social media and mailing groups
• how to approach graphic design
• how to contact guests and prepare invitations
• how to proceed funding: event fees, grants, sponsors money
• how to ensure good atmosphere
• what to do afterwards

And much more!

The event will take place on Monday, April 7th at COS, Heidelberg at 16:45. Please find the application form HERE.

We are happy to invite you to the first meeting of Heidelberg Open Lab!

Heidelberg Open Lab will be a node of the Nencki Open Lab project. It is a grassroots initiative aiming to create local scientific communities that exchange skills and knowledge between neuroscientists – but also scientists from other fields of biology – by organizing workshops, courses, summer schools, seminars, and symposia on topics ranging from programming, data analysis, trough electronics, 3D printing, optics – and much more.

Join us if you want to create a community of life scientists, organize workshops, courses, symposia, and more!

During the kick-off meeting, we will introduce the idea of the project, show you what we have done before, and discuss with you what we can do here – and how you can get engaged!

Please fill out the short registration form HERE.

The meeting will take place on Tuesday, March 18th at 5:30 PM in room 00.001 (ground floor) in the Center for Organismal Studies,  Im Neuenheimer Feld 230, Heidelberg.

Everyone can join (affiliation and your academic level don’t matter!).

You can find more information about us on our webpage and on the webpage of the Nencki Open Lab initiative. You can follow our initiatives on social media: Bluesky, Twitter, Instagram and Facebook!

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