EZcalcium is a fully automated toolbox for the analysis of calcium imaging data in MATLAB created by Daniel Cantu and colleagues at the David Geffen School of Medicine at UCLA.
Calcium imaging has quickly become a popular method for measuring neuronal signals both in vivo and ex vivo. Calcium imaging makes use of calcium indicators that change in fluorescence in response to neural activity, thereby acting as a proxy for neuronal firing. However, the methods needed to process fluorescent signals into usable data are multifaceted and require extensive programming experience. EZcalcium is an intuitive GUI-based software package for MATLAB that makes motion correction, segmentation, signal extraction and deconvolution (dimension reduction), analysis, and visualization of calcium imaging data easy to implement.
EZcalcium consists of three modules, each of which are well documented with step-by-step instructions for use. The first module is based on the NoRMCorre toolbox, an open source set of routines for online non-rigid motion correction, that corrects motion artifacts due to misalignment. The second module uses the CaImAn toolbox, another open source pipeline for calcium imaging data analysis, which is used for region of interest (ROI) detection. The last module is then used for refinement where parameters can be set to automatically or manually remove ROIs. The whole toolbox can also be fully automated, can do batch processing, and runs on any common desktop or laptop. EZcalcium is an excellent way to simplify your calcium imaging analysis and visualization pipeline that is user friendly and especially useful for those that do not have sufficient programming knowledge.