Calcium Imaging Analysis Guide

Purpose

This skill encodes expert methodological knowledge for analyzing calcium imaging data from fluorescent genetically encoded calcium indicators (GECIs). It covers the domain-specific decisions that a general-purpose programmer or data scientist would get wrong without specialized training in optical neurophysiology: choosing deconvolution parameters based on indicator kinetics, correcting neuropil contamination, handling modality-specific preprocessing, and interpreting fluorescence signals as neural activity.

When to Use This Skill

• Designing an analysis pipeline for two-photon, one-photon/miniscope, or fiber photometry data
• Choosing motion correction strategy for awake behaving animal recordings
• Selecting ROI detection method for your preparation density and imaging modality
• Setting deconvolution parameters matched to your calcium indicator
• Evaluating whether extracted signals reflect genuine single-neuron activity
• Troubleshooting common artifacts: photobleaching, neuropil contamination, motion

Research Planning Protocol

Before executing the domain-specific steps below, you MUST: