This documentation is for the older Mesmerize legacy desktop application. Please see the home page or GitHub repo for information on the latest packages.


Mesmerize is a platform for the annotation and analysis of neuronal calcium imaging data. It encompasses the entire process of calcium imaging analysis from raw data to semi-final publication figures that are interactive, and aids in the creation of FAIR-functionally linked datasets. It is applicable for a broad range of experiments and is intended to be used by users with and without a programming background.

Welcome Window

Share your analysis pipelines and figures along with your publication


The Viewer

Explore image sequences, and use various modules for pre-processing and signal-extraction. Annotate regions of interest with any relevant information. Map stimuli/behavior periods.


CaImAn modules

Mesmerize contains front-end GUI modules for the CaImAn library. This makes it very easy for users without a programming background to use the library.

CaImAn Elastic Motion Correction




Batch Manager

Computationally intense procedures performed can be organized with the Mesmerize Batch Manager.


Project Organization

Explore project data and create experimental groups.


Data analysis - pyqtgraph programmable flowcharts.

Build your own analysis piplines using flowcharts.


Interactive Plots

Create shareable interactive plots where the analysis history of every datapoint is traceable. Explore information associated with a datapoint, such as the spatial localization of its parent ROI and raw data.

Interactive Heatmaps


Interactive Cross-correlation analysis


Other types of plots: Beeswarm, Violins, KShape, Proportions, Scatter