BrainJ enables high-throughput analysis of serial tissue sections imaged using confocal or widefield techniques. Developed in Fiji, our approach leverages freely available tools for machine learning pixel classification for cell detection and mesoscale mapping of axons and dendrites.


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.

GuPPy, a Python toolbox for the analysis of fiber photometry data

Fiber photometry (FP) is an adaptable method for recording in vivo neural activity in freely behaving animals. It has become a popular tool in neuroscience due to its ease of use, low cost, the ability to combine FP with freely moving behavior, among other advantages.

Automated morphometric analysis with SMorph software reveals plasticity induced by antidepressant therapy in hippocampal astrocytes

Nervous system development and plasticity involves changes in cellular morphology, making morphological analysis a valuable exercise in the study of nervous system development, function and disease. Morphological analysis is a time-consuming exercise requiring meticulous manual tracing of cellular contours and extensions.

PUMA 3D Printed Open Source Microscope

PUMA is 3D printed open source portable modular microscope with augmented reality, fluorescence, phase contrast, epi-illumination, epi- and trans-polarisation and other features. You can either build it fully DIY or purchase the basic scope ready made and upgrade it as required (see below for details).

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.


WholeBrain is a software to create anatomical maps. With a code base in C/C++ with wrappers to R and JavaScript/WASM. The purpose of WholeBrain is to provide a user-friendly and efficient way for scientist with minimal knowledge of computers to create anatomical maps and integrate this information with behavioral and physiological data for sharing on the web.