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#3 Hands-On Analysis Tutorial

Difficulty level

This lesson will go through how to extract cells from video that has been cleaned of background noise and motion.

Topics covered in this lesson
  • Pre-processing and motion correction
  • Compute a max projection
  • Parameters
  • Max window
  • Cutoff frequency
  • Threshold of this peak to noise ratio
  • Over merging
  • Spatial matrix initialization
  • Initial spatial footprint
  • Update background
  • Size threshold
  • Spatial update
  • General visualization of the result
  • Temporal update
  • Visualization of the dropped cells
  • Reproducibility