Welcome to mesmerize-core’s documentation!#


mesmerize-core interfaces CaImAn algorithms, helps with parameter optimization, and data organization. It is a collection of “pandas extensions”, which are functions that operate on pandas DataFrames. It essentially creates a user-friendly “psuedo-database” of your calcium imaging data and CaImAn generated output files. This makes it easier to work with the results of the various CaImAn algorithms to assess the outputs and create visualizations.


For installation please see the instructions on the README on GitHub:



We’re open to contributions! If you think there’s a useful extension that can be added, or any other functionality, post an issue on the repo with your idea and then take a look at the Contribution Guide.

You can also look at our “Milestones” for future versions to give you an idea of what we plan to implement in the future: https://github.com/nel-lab/mesmerize-core/milestones

Old Mesmerize Desktop application#

mesmerize-core in combination with fastplotlib basically replaces the Mesmerize desktop application which is now treated as legacy software. We strongly recommend mesmerize-core over the old desktop application, but if you really want to use the old desktop application you can access it here: http://mesmerize.readthedocs.io/

Indices and tables#