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Minian: An Open-Source Miniscope Analysis Pipeline

Difficulty level

How to start processing the raw imaging data generated with a Miniscope, including developing a usable pipeline and demoing the Minion pipeline.

Topics covered in this lesson
  • The problem: How to get traces out of video
  • Accessible jupyter interface
  • Noises and backgrounds
  • Kernel in image filtering
  • Morphological background removal
  • Motion correction
  • Peak-to-noise ration refine
  • Minian output
  • Downstream analysis with ezTrack