Welcome to CaliAli Documentation

Introduction

• About CaliAli

  • Key Features
  • Version History
  • License
  • Questions about CaliAli?

• Installation and system requirements

  • System Requirement
    • Hardware
    • Others
  • Installation

Pipeline step-by-step

Note

Already familiar with the documentation? Get a quick overview of the functions you need to run in the TL;DR section.

• Getting Started

  • CaliAli processing steps

• Downsampling and Motion Correction

  • Downsampling and Conversion to .h5 Format
  • Motion Correction

• Inter-Session Alignment

  • Evaluate Alignment Performance
  • Processing Sessions without Concatenation

• Calcium Signal Extraction with CaliAli

  • Select Extraction Parameters
  • Adjusting PNR and Corr. Thresholds
  • Extracting Calcium Signals

• Post-processing

  • Monitoring Extracted Components
  • Sort spatial Components
  • Deleting and Merging Components
  • Picking Neurons from Residual

Others

• Utilities

  • Reproducing Video Data in .h5 Format
  • Monitoring Extracted Calcium Transients
  • Separate Data from Different Sessions
  • Other Functions

• TL;DR