LINdoscope 2023: Neuroimaging and data analysis is a two-week EMBO Practical Course, organised by

• Alessio Attardo (Leibniz Institute for Neurobiology),
• Oliver Barnstedt (Leibniz Institute for Neurobiology),
• Sanja Mikulovic (Leibniz Institute for Neurobiology),
• Janelle Pakan (Otto-von-Guericke University Magdeburg),
• Anne Petzold (University Hospital Cologne), and
• Matthias Prigge (Leibniz Institute for Neurobiology),

held from 4-15 September 2023 at the Leibniz Institute for Neurobiology (LIN) and the German Center for Neurodegenerative Diseases (DZNE) in Magdeburg.

This repository contains code and notebooks to help teach students basic concepts and practical steps of Python-based analysis of calcium imaging data combined with behavioural tracking in behaving mice.

Contributors:

• Oliver Barnstedt (LIN Magdeburg, DE)
• Eric Thomson (Flatiron Institute, US)
• Mackenzie Mathis (EPFL, CH)
• Felix Kuhn (LIN Magdeburg, DE)
• Alisa Bakhareva (UK Cologne, DE)
• Arjun Putcha (UNC, US)
• Charitha Omprakash (LIN Magdeburg, DE)
• Csilla Novak (LIN Magdeburg, DE)

Main packages used:

• CaImAn: Giovannucci et al., 2019
• DeepLabCut: Mathis et al., 2018
• MouseFlow
• VAME: Luxem et al., 2022
• 🦓 CEBRA: Schneider, Lee, Mathis, 2023

Raw data:

All course participants have received access to relevant sample data used for these notebooks. Access can be requested by email to [email protected].