Computational Neuroscience

INCF NeuroStars

Neurostars is an open source question and answer site that serves the INCF network and the global neuroscience community as a forum for knowledge exchange between neuroscience researchers at all levels of expertise, software developers, and infrastructure providers.

INCF TrainingSpace

TrainingSpace is an online hub that aims to make neuroscience educational materials more accessible to the global neuroscience community developed by the Training and Education Committee composed of members from the INCF network, HBP, SfN, FENS, IBRO, IEEE, BD2K, and iNeuro Initiative.

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.

DIPY

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.

NeuroFedora

NeuroFedora is an initiative to provide a ready to use Fedora Linux based Free/Open source software platform for neuroscience. We believe that similar to Free software, science should be free for all to use, share, modify, and study.

DataJoint

DataJoint is an open-source library for managing and sharing scientific data pipelines in Python and Matlab. DataJoint allows creating and sharing computational data pipelines, which are defined as databases and analysis code for executing steps of activities for data collection and analysis.

Heuristic Spike Sorting Tuner (HSST), a framework to determine optimal parameter selection for a generic spike sorting algorithm

Extracellular microelectrodes frequently record neural activity from more than one neuron in the vicinity of the electrode. The process of labeling each recorded spike waveform with the identity of its source neuron is called spike sorting and is often approached from an abstracted statistical perspective.

BossDB

BossDB is a volumetric database that lives in the AWS cloud. Hundreds of terabytes of electron microscopy, light microscopy, and x-ray tomography data are available for free download and study.