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CaPTure: Calcium PeakToolbox for analysis of in vitro calcium imaging data
Madhavi Tippani1, Elizabeth A Pattie1, Brittany A Davis1
1Lieber Institute for Brain Development, Johns Hopkins Medical Campus, 855 North Wolfe Street, Suite 300, Baltimore, MD, 21205, USA.
Background:
Calcium imaging is a powerful technique for recording cellular activity across large populations of neurons. However, analysis methods capable of single-cell resolution in cultured neurons, especially for cultures derived from human induced pluripotent stem cells (hiPSCs), are lacking. Existing methods lack scalability to accommodate high-throughput comparisons between multiple lines, across developmental timepoints, or across pharmacological manipulations.
Results:
To address this need we developed CaPTure, a scalable, automated Ca2+ imaging analysis pipeline ( https://github.com/LieberInstitute/CaPTure ). CaPTuredetects neurons, classifies and quantifies spontaneous activity, quantifies synchrony metrics, and generates cell- and network-specific metrics that facilitate phenotypic discovery. The method is compatible with parallel processing on computing clusters without requiring significant user input or parameter modification.
Conclusion:
CaPTure allows for rapid assessment of neuronal activity in cultured cells at cellular resolution, rendering it amenable to high-throughput screening and phenotypic discovery. The platform can be applied to both human- and rodent-derived neurons and is compatible with many imaging systems.
