How do I extract calcium traces from images, and how do I analyze them? This 3-day workshop covers the essential concepts needed to answer these questions using Python tools like NumPy, SciPy, and Napari. Using real calcium imaging data, participants will explore how to convert continuous calcium traces into neural spikes through deconvolution, extract fluorescence estimates from Region(s) of Interest selected manually and automatically, and improve these estimates by removing contributions from the surrounding neuropil.

Learning and participation

Topics

  • Calcium Traces to Spikes: Extracting flourescence estimates from images and converting them into spikes through numpy and scipy.
  • Region(s) of Interest: Manual and automated method for selecting ROIs with napari and scikit-image.
  • Motion Correction: Correcting movement artifacts in recorded imaging data with scikit-image and CaImAn.

Intended participants

  • Researchers and students from all universities are welcome.
  • Participants of all educational backgrounds are welcome.

Certification

Students who attend at least 75% of the course will receive a participation certificate by email at the end of the course.