EZcalcium

EZcalcium analyzes calcium imaging data to extract fluorescence signals and infer neuronal and glial activity from 2-photon and head-mounted miniscope microscopy recordings.

Key Features:

• Motion correction: Performs motion correction on calcium imaging time-series to compensate for sample movement.
• Segmentation: Segments imaging data to define regions of interest (ROIs) based on pixel intensity patterns.
• Signal extraction: Extracts fluorescent signals as pixel intensity time courses from specified ROIs.
• Deconvolution: Performs deconvolution on extracted calcium fluorescence traces.
• Spike inference: Infers neuronal spiking activity from changes in pixel intensity values over time within ROIs.
• Indicator compatibility: Processes signals from genetically encoded and chemical calcium indicators.
• Imaging modality support: Supports data acquired with 2-photon excitation microscopy and head-mounted miniscopes.
• Experimental context support: Applicable to data from acute brain slices, brain organoids, and behaving animals.

Scientific Applications:

• Neuronal activity analysis: Quantifies neuronal spiking and temporal activity patterns from calcium imaging datasets.
• Glial signaling analysis: Characterizes glial calcium signaling dynamics from fluorescence recordings.
• In vivo behavioral imaging: Analyzes calcium signals collected during animal behavior using head-mounted miniscopes.
• Ex vivo and organoid studies: Applies to acute brain slice and brain organoid imaging to study cellular activity ex vivo.

Methodology:

Computational steps include motion correction, segmentation, signal extraction from ROIs, deconvolution of fluorescence traces, and inference of neuronal spiking from pixel intensity time courses.