Command Line Tools

This directory contains documentation for the various command-line interface (CLI) tools available in CLAH Image Analysis.

CLI Categories

tifStackFunc

Core tools for processing raw imaging data:

• Motion correction of calcium imaging movies
• Segmentation of cells using CNMF
• Generation of segmented dictionaries (segDict)
• Output includes motion-corrected movies, component evaluations, and spatial maps

Unit Analysis

Tools for analyzing individual units and their responses (set up mostly for 2P experiments currently):

• Quick Tuning: Analysis of cell responses to behavioral cues
• Multi-session Structure Wrapper: Combines data across sessions
• Post Cell Registrar Cue Cell Finder: Identifies cells responding to specific cues

Cell Registration

Tools for registering cells across sessions:

• Cell Registrar with ROICaT: Aligns cells across multiple sessions
• Cluster Info Collater: Aggregates and analyzes registration results