CALIMA

CALIMA analyzes calcium imaging data to detect regions of interest, identify calcium spikes, and reconstruct neuronal networks for studies of neuronal communication and network dynamics.

Key Features:

• Cell Detection: Uses the difference of Gaussians algorithm to detect regions of interest (ROIs) corresponding to cells in calcium imaging data.
• Calcium Spike Analysis: Applies a z-scoring algorithm to set spike-detection criteria and identify calcium transients from ROI signals.
• Network Reconstruction: Infers network structure by computing cross-correlations between cellular activity traces and combining ROI activity with positional information to infer inter-cell connections.

Scientific Applications:

• Neuronal communication and network dynamics: Provides cell-level activity and inferred connectivity measures for studies of neuronal communication and network dynamics.
• Cultured primary rat cortical neurons: Applicable to calcium imaging datasets from cultured primary rat cortical neurons.
• SH-SY5Y neuroblastoma cultures: Applicable to calcium imaging datasets from SH-SY5Y neuroblastoma cultures.
• Synchronous firing detection: Facilitates detection and analysis of synchronous neuron firing in neuronal cultures.

Methodology:

Implements difference of Gaussians for ROI detection, z-scoring for spike detection, and cross-correlation analysis for network inference while combining ROI activity with positional information; evaluated on known example datasets and new videographic in vitro brain cell footage with reported average cell-detection sensitivity of 82% across datasets and up to 96% spike-detection sensitivity with optimal parameters, compared to other software and manual analyses.