Calcium Imaging

DataJoint Core

DataJoint Core is an open-source toolkit for defining and operating computational data pipelines (i.e., sequences of steps for data acquisition, processing, and transformation). Pipelines built in DataJoint Core offer: Efficient design with intuitive queries Automated, reproducible computation with full referential integrity Coordination of multiple human and computer workers Flexibility to adapt and change DataJoint Core includes libraries for Python and MATLAB, a REST API, and GUI tools for data entry and visualizations.


MINI2P is an open-source miniature 2-photon microscope brain explorer for fast high-resolution calcium imaging in freely-moving mice. In brief Development of a miniature 2-photon miniscope for large-scale calcium imaging in freely moving mice allows stable simultaneous recording of more than a thousand cells across multiple planes of densely active cortical regions in a wide spectrum of behavioral tasks without impediment of the animal’s behavior.


Mesmerize is a platform for the annotation and analysis of neuronal calcium imaging data. Mesmerize encompasses the entire process of calcium imaging analysis from raw data to interactive visualizations. Mesmerize allows you to create FAIR-functionally linked datasets that are easy to share.

Mesmerize Core

A batch management system for calcium imaging analysis using the CaImAn library. It contains pandas.DataFrame and pandas.Series extensions that interface with CaImAn for running the various algorithms and organizing input & output data.

CaImAn: open source scalable algorithms for calcium and voltage imaging data

Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets generated over the course of months.

CASCADE: Calibrated inference of spiking from calcium ΔF/F data using deep networks

CASCADE translates calcium imaging ΔF/F traces into spiking probabilities or discrete spikes. CASCADE is based on deep networks and runs on Python (Linux/Windows/Mac); it can be used either as a web application (Colaboratory notebook), or locally on a CPU or GPU.

The Open-Source UCLA Miniscope Project

One of the biggest challenges in neuroscience is to understand how neural circuits in the brain process, encode, store, and retrieve information. Meeting this challenge requires tools capable of recording and manipulating the activity of intact neural networks in freely behaving animals.


Stalefish is a tool to analyse gene expression from ISH or other histology slice images. From your 2D brain slice images you can build a 3D expression surface from a brain structure such as the isocortex or the hippocampus.

Non-Telecentric 2P microscopy for 3D random access mesoscale imaging (nTCscope)

Ultra-low-cost, easily implemented and flexible two-photon scanning microscopy modification offering a several-fold expanded three-dimensional field of view that also maintains single-cell resolution. Application of our system for imaging neuronal activity has been demonstrated on mice, zebrafish and fruit flies

An open-source experimental framework for automation of high-throughput cell biology experiments

Modern Biology methods require a large number of high quality experiments to be conducted, which requires a high degree of automation. Our solution is an open-source hardware that allows for automatic high-throughput generation of large amounts of cell biology data.