Calcium Imaging Analysis Guide

What problem does it solve?

Calcium imaging data analysis is technically demanding; this guide encodes domain-validated pipeline knowledge for preprocessing, ROI detection, neuropil correction, dF/F computation, deconvolution, and quality metrics to enable robust neural signal extraction from calcium signals.

Core Features & Use Cases

• Domain-specific decisions for 2P, 1P, and fiber photometry calcium imaging; provides recommended parameter values and pitfalls for accurate spike inference; supports researchers designing and analyzing experiments.
• Use Case: For a mouse cortex two-photon dataset, follow the recommended motion correction, ROI detection, neuropil correction, and deconvolution steps to estimate spike trains and QC metrics.
• Use Case: Compare indicators GCaMP6s vs jGCaMP8 in a mixed dataset and choose tau and baseline methods accordingly.

Quick Start

Load your calcium imaging dataset and follow the step-by-step pipeline to obtain deconvolved spike estimates and QC metrics.