Data Analysis

Open Source Brain

Open Source Brain, a platform for sharing, viewing, analyzing, and simulating standardized models from different brain regions and species. Model structure and parameters can be automatically visualized and their dynamical properties explored through browser-based simulations.

MorphoPy: A python package for feature extraction of neural morphologies

MorphoPy is an open software package written in Python3 that allows for visualization and processing of morphological reconstructions of neural data. It has been created to facilitate the translation from morphology graphs into descriptive features like density maps, morphometric statistics, and persistence diagrams for down-stream exploration and statistical analysis.


OpenCitations is an independent infrastructure organization for open scholarship dedicated to the publication of open bibliographic and citation data by the use of Semantic Web (Linked Data) technologies. It is also engaged in advocacy for open citations, particularly by organizing the Workshops for Open Citations and Scholarly Metadata, and in its role as a key founding member of the Initiative for Open Citations (I4OC) and the Initiative for Open Abstracts (I4OA).


DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.

BrainGlobe atlas API

Many excellent brain atlases exist for different species. Some of them have an API (application programming interface) to allow users to interact with the data programmatically (e.g. the excellent Allen Mouse Brain Atlas), but many do not, and there is no consistent way to process data from multiple sources.


brainrender is a python package for the visualization of three dimensional neuro-anatomical data. It can be used to render data from publicly available data set (e.g. Allen Brain atlas) as well as user generated experimental data.


JASP is a cross-platform statistical software program with a state-of-the-art graphical user interface. The JASP interface allows you to conduct statistical analyses in seconds, and without having to learn programming or risking a programming mistake.

Neuroimaging Informatics Tools and Resources Collaboratory (NITRC)

NeuroImaging Tools & Resources Collaboratory is an award-winning free web-based resource that offers comprehensive information on an ever expanding scope of neuroinformatics software and data. Since debuting in 2007, NITRC has helped the neuroscience community make further discoveries using software and data produced from research that used to end up lost or disregarded.

ReproNim: A Center for Reproducible Neuroimaging Computation

ReproNim’s goal is to improve the reproducibility of neuroimaging science and extend the value of our national investment in neuroimaging research, while making the process easier and more efficient for investigators.

Simple Behavioral Analysis (SimBA)

Several excellent computational frameworks exist that enable high-throughput and consistent tracking of freely moving unmarked animals. SimBA introduce and distribute a plug-and play pipeline that enables users to use these pose-estimation approaches in combination with behavioral annotation for the generation of supervised machine-learning behavioral predictive classifiers.