An open-source method for analysis of confocal calcium imaging with sparse cells

Research within the neuroscience field has evolved to use complex imaging and computational tools to extract comprehensive information from data sets. Many laboratories struggle to adopt computational methods when updating protocols to meet modern standards. Difficulties arise due to the lack of computational knowledge and paywalls for software. Calcium imaging is a widely used technique that requires sophisticated software to get precise and reproducible results. However, it is often analyzed manually even though manual analysis is a time-consuming process that introduces operator bias and is prone to error. To bridge this gap, we propose a calcium imaging analysis method using TrackMate, an open-source Fiji plugin, to track neurons, detect the region of interest, and extract the intensity of fluorescence. This method can be done without coding or be combined with Python or Jupyter Notebook scripts to accelerate the analysis. In addition, this method is compatible with standard laptop and/or desktop computers.