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This repository contains notebooks and resources for the workshop taking place in March 2024 at the Leibniz Institute for Neurobiology in Magdeburg.

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Behavior and Calcium Imaging Analysis Workshop

This repository contains notebooks and resources for the workshop taking place in March 2024 at the Leibniz Institute for Neurobiology in Magdeburg.

Overview

This workshop focuses on behaviour analysis and calcium imaging. Participants will learn about data preprocessing, analysis, and visualization using Python and popular libraries such as DeepLabCut and CaImAn.

Notebooks

  1. DeepLabCut Tutorial: This notebook provides a hands-on introduction to DeepLabCut, a toolbox for markerless pose estimation. Participants will learn how to train a network, evaluate performance, and analyze videos using DeepLabCut. Adapted from the demo notebooks from DeepLabCut repository.

  2. CaImAn Tutorial: In this notebook, participants will explore calcium imaging data analysis using the CaImAn library. They will learn about preprocessing steps, component extraction, and interpretation of results. Adapted from the demo notebooks from CaImAn repository.

Running the Notebooks

You can run the notebooks directly in your browser using Google Colab. Follow these steps to open the notebooks:

  1. Go to Google Colab.
  2. Click on the "File" menu, then select "Open notebook".
  3. In the "GitHub" tab, enter "CogEmLab" in the search box.
  4. Find and select the desired notebook from the search results.
  5. The notebook will open in Colab, and you can start running the code.

Data Availability

Data for this workshop will be available on a shared Google Drive. The link to the Google Drive will be shared directly with participants.

About

This repository contains notebooks and resources for the workshop taking place in March 2024 at the Leibniz Institute for Neurobiology in Magdeburg.

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