Analysis pipelines for calcium imaging data.

Calcium imaging is a popular tool among neuroscientists because of its capability to monitor in vivo large neural populations across weeks with single neuron and single spike resolution. Before any downstream analysis, the data needs to be pre-processed to extract the location and activity of the neurons and processes in the observed field of view. The ever increasing size of calcium imaging datasets necessitates scalable analysis pipelines that are reproducible and fully automated. This review focuses on recent methods for addressing the pre-processing problems that arise in calcium imaging data analysis, and available software tools for high throughput analysis pipelines.