BlueCelluLab
BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)
https://github.com/bluebrain/bioexplorer
The Blue Brain BioExplorer (BBBE) is a tool for data visualization experts and scientists to extract and analyze scientific data from visualization and interactive exploration
nat
NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.
https://github.com/bluebrain/morphio
A python and C++ library for reading and writing neuronal morphologies
https://github.com/bluebrain/bluepyemodel
Blue Brain Python Electrical Modeling Pipeline
https://github.com/bluebrain/bluenaas-brainareaexperiment
BlueNaaS Brain Area Experiment
https://github.com/csinva/biophysical-threshold-simulations
Simulations for characterizing stochastic threshold in biophysical neurons.
https://github.com/bluebrain/coreneuron
Simulator optimized for large scale neural network simulations.
xolotl
A MATLAB neuron simulator. Very fast (written in C++). Flexible (fully object oriented). Immediate (live manipulation in MATLAB). Comes with a powerful parameter optimizer. Get started ➡️
https://github.com/bluebrain/emodel-generalisation
Generalisation of electrical models of neurons with MCMC
https://github.com/bluebrain/ultraliser
Reconstruction of watertight meshes, annotated volumes and center line skeletons of neuroscience spatial structures from non-watertight inputs, segmented masks, skeletons of NGV morphologies and volumes.
gutanalysistoolbox
Analysis and characterisation of cells within the gut wall using deep learning models. The current focus is on studying enteric neurons and enteric glia.
pyoelectricity
Source code for the associated publication: Schlötter Moritz, Maret Georg, Kleineidam Christoph J (2023) Annihilation of action potentials induces electrical coupling between neurons eLife 12:RP88335