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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
  • The new problem
  • Accessible jupyter interface
  • Minian has low memory demand
  • Noises and backgrounds
  • Kernel in image filtering
  • Effect of different kernel size
  • Denoise with median filter
  • Visualization of denoise
  • Morphological background removal
  • Motion correction
  • CNMF formulation
  • Seeds generation
  • Peak-to-noise ration refine
  • Noise frequency
  • Results of initialization
  • Spatial update
  • Temporal update
  • Minian output
  • Downstream analysis with ezTrack