MNE-LSL
MNE-LSL: Real-time framework integrated with MNE-Python for online neuroscience research through LSL-compatible devices. - Published in JOSS (2025)
Reducing the efforts to create reproducible analysis code with FieldTrip
Reducing the efforts to create reproducible analysis code with FieldTrip - Published in JOSS (2024)
Connectome Mapper 3
Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)
BlueCelluLab
BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)
NeuroAnalyzer
NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data - Published in JOSS (2025)
BrainGlobe Atlas API
BrainGlobe Atlas API: a common interface for neuroanatomical atlases - Published in JOSS (2020)
fsbrain
R library for structural neuroimaging. Provides high-level functions to access (read and write) and visualize surface-based brain morphometry data for individuals and groups.
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
freesurferformats
GNU R package for reading and writing neuroimaging file formats. Not limited to FreeSurfer anymore, despite its name.
https://github.com/bluebrain/brayns
Visualizer for large-scale and interactive ray-tracing of neurons
https://github.com/brainglobe/brainreg-napari
Automated 3D brain registration in napari with support for multiple species and atlases.
fafbseg
Tools to work with the FlyWire connectome. Fully interoperable with navis.
syncopy
Systems Neuroscience Computing in Python: user-friendly analysis of large-scale electrophysiology data
organize-oasis
Organize the entire OASIS1 dataset based on the group name (AD, MCI, CN) locally
mrisharingguide
We developed a guide for researchers in the Netherlands who want to share brain MRI data to help them get started.
https://github.com/connectomicslab/cmtklib-data
Datalad dataset that stores all data resources of the cmtklib module of Connectome Mapper 3 (https://github.com/connectomicslab/connectomemapper3).
brainreg
Automated 3D brain registration with support for multiple species and atlases.
SPM 25
SPM 25: open source neuroimaging analysis software - Published in JOSS (2025)
https://github.com/bids-standard/pybids-reports
A subpackage of pyBIDS, implementing automatic report generation from BIDS datasets.
organize-adni
Organize the entire ADNI dataset based on the group name (AD, MCI, CN) locally
https://github.com/bluebrain/neurodamus
A BBP Simulation Control application for NEURON
https://github.com/brainlesion/preprocessing
preprocessing tools for multi-modal 3D brain imaging
https://github.com/antsx/antsr
R interface to the ANTs biomedical image processing library
https://github.com/brainlesion/deep_quality_estimation
Quality estimation for BraTS glioma segmentation models
