The tools researchers actually use, in one place.
A curated, filterable grid of open-source software — pose estimation, spike sorting, calcium imaging, data standards and the computing stack underneath. Pick a domain, or just search.
AllenSDK↗
Access to Allen Institute datasets and reference atlases — mouse brain atlas, cell types, connectivity.
AlphaFold↗
Deep-learning protein-structure prediction that reshaped structural biology.
Alyx↗
Web-based electronic lab notebook and colony/experiment database for multi-lab collaborations.
anipose↗
Robust 3D pose via multi-camera triangulation, sitting downstream of DeepLabCut.
ANTs↗
Advanced Normalization Tools — high-quality image registration and segmentation for MRI/brain pipelines.
Apptainer↗
Container platform built for HPC (formerly Singularity) — reproducible, rootless environments on clusters.
Arbor↗
Modern multi-compartment simulation library that maps morphological networks onto GPUs and multicore CPUs.
B-SOiD↗
Unsupervised discovery of behavioral clusters from pose data, then a fast frame-wise classifier.
BIDS↗
Community standard for organizing neuroimaging and ephys datasets in a machine-readable layout.
Bio-Formats↗
Reads and writes hundreds of proprietary microscopy formats into a common model.
Biopython↗
Tools for computational molecular biology: sequence parsing, alignment, structure and database access.
BluePyOpt↗
Data-driven optimization of neuron model parameters using evolutionary algorithms.
BrainGlobe Atlas API↗
One programmatic interface to many reference atlases across species — the backbone of BrainGlobe.
brainreg↗
Automated 3D whole-brain registration to a reference atlas, with an optional napari plugin.
brainrender↗
3D rendering of anatomically registered neuroanatomical data, driven by the BrainGlobe Atlas API.
Brainstorm↗
GUI-first application for MEG/EEG/iEEG analysis and source imaging.
Brian2↗
Equation-oriented simulator for spiking networks — define models in plain math and run them fast.
CaImAn↗
End-to-end calcium imaging: motion correction, source extraction, deconvolution and cross-session registration.
CEBRA↗
Contrastive learning of consistent low-dimensional embeddings from joint neural and behavioral time series.
cellfinder↗
Detects and atlas-maps cells across whole-brain microscopy volumes with detection plus a deep classifier.
Cellpose↗
Generalist deep-learning cell segmentation with a human-in-the-loop GUI. Works in 2D and 3D.
CellProfiler↗
Modular, repeatable pipelines for segmentation and high-content feature extraction, runnable headless.
CloudVolume↗
Serverless client for reading and writing Neuroglancer Precomputed volumes, meshes and skeletons at petascale.
DANDI↗
CLI and archive for publishing, versioning and sharing NWB and BIDS datasets on the DANDI cloud.
DANNCE↗
Direct 3D pose estimation for freely moving rodents from synchronized multi-camera video.
Dask↗
Parallel computing that scales NumPy, pandas and scikit-learn from a laptop to a cluster.
DataJoint↗
Relational data-pipeline framework that automates neuroscience data collection and computation.
DataLad↗
Distributed data version control on Git and git-annex, tracking large files and full provenance.
DeepEthogram↗
Supervised behavior classification straight from raw video pixels — no pose step — producing full ethograms.
DeepLabCut↗
Markerless 2D/3D pose estimation for any animal or human via transfer learning — the field's most-used tracker.
DVC↗
Git for data and models — versioning, reproducible pipelines and experiment tracking.
Dynamax↗
State-space models in JAX — the modern successor to ssm, with GPU-friendly inference.
EEGLAB↗
The classic EEG analysis environment with ICA, time-frequency tools and a huge plugin ecosystem.
Elephant↗
Analysis toolkit for spike trains and signals: correlation, spectral and Granger analysis, SPADE, CSD.
EXTRACT↗
Robust automated cell extraction that suppresses contamination and crosstalk in calcium movies.
facemap↗
Tracks mouse orofacial movements and predicts neural activity from behavior via SVD of face video.
FieldTrip↗
Comprehensive toolbox for advanced MEG, EEG and invasive electrophysiology analysis.
Fiji / ImageJ↗
The public-domain workhorse of scientific image processing, with a vast ecosystem of plugins.
Galaxy↗
Web platform that makes reproducible bioinformatics accessible without writing code.
h5py↗
Pythonic interface to HDF5 — the default on-disk container behind NWB.
HDMF↗
Hierarchical Data Modeling Framework — the extensible modeling engine underneath PyNWB.
HerdingSpikes↗
Spike detection and sorting built for very large high-density MEAs, prioritizing scalability.
Ilastik↗
Interactive machine-learning for image classification and segmentation — train a classifier by painting labels.
Jupyter↗
Interactive notebooks that weave code, results and narrative — the lab notebook of computation.
Keypoint-MoSeq↗
Discovers behavioral syllables from keypoints with a generative model that separates behavior from tracking noise.
Kilosort↗
Fast spike sorting with drift correction for high-density probes like Neuropixels. KS4 uses graph clustering.
Lightning Pose↗
Semi-supervised pose estimation with Bayesian ensembling — accurate from far fewer labeled frames.
MatNWB↗
MATLAB API for NWB, generated from the schema so it stays in sync with the standard.
Mesmerize↗
Fast, memory-efficient batch management for CaImAn algorithms, designed to plug into napari.
MIN1PIPE↗
A miniscope 1-photon signal-extraction pipeline that runs end-to-end with minimal manual work.
MiniAn↗
Open analysis pipeline for one-photon miniscope imaging, built on xarray and Dask for out-of-core work.
MLflow↗
Tracks experiments, packages models and manages the ML lifecycle from prototype to deployment.
MNE-Python↗
State-of-the-art MEG/EEG processing: preprocessing, source localization, connectivity, time-frequency.
MountainSort5↗
Density-based spike sorter, rewritten for the SpikeInterface era with isosplit clustering.
napari↗
Fast n-dimensional image viewer with a deep plugin ecosystem — the Python-native canvas for imaging workflows.
natverse↗
The NeuroAnatomy Toolbox suite in R for importing, transforming and analyzing connectomes and tracings.
NAVis↗
Analyze and visualize neuron morphologies and skeletons; interoperates with CloudVolume and natverse.
NeMoS↗
GPU-accelerated GLMs for spike-train analysis, powered by JAX, with a composable basis module. Pairs with pynapple.
Nengo↗
Builds large functional brain models with the Neural Engineering Framework; targets neuromorphic hardware.
Neo↗
Shared object model plus readers for dozens of proprietary ephys formats. The I/O layer under the stack.
NEST↗
Highly scalable simulator for large networks of point neurons — millions of cells across HPC clusters.
NetPyNE↗
Declarative interface for building, simulating (via NEURON) and analyzing multiscale network models.
neuroconv↗
Converts data from dozens of acquisition and analysis formats into NWB with one uniform interface.
neuroglancer↗
WebGL viewer for enormous volumetric EM/connectomics data. The standard for cloud-scale volume viewing.
NEURON↗
Simulation of detailed biophysical neurons with complex morphology and ion channels.
Nextflow↗
Dataflow workflow engine for scalable, portable pipelines — the backbone of the nf-core community.
NumPy↗
The foundational n-dimensional array library nearly every scientific Python tool builds on.
NWB Widgets↗
Interactive Jupyter widgets that let you browse and plot the full contents of any NWB file.
nwbinspector↗
Checks NWB files against best practices and schema compliance before you publish or archive.
ONE↗
Open Neurophysiology Environment — a lightweight standard and API to search and load data across labs.
Open Ephys GUI↗
Free plugin-based system to acquire, process, record and visualize multichannel ephys. Includes an NWB engine.
OpenNeuro↗
Free archive for sharing BIDS-formatted neuroimaging datasets — hundreds of studies.
pandas↗
Fast, expressive data structures for tabular and time-series data.
papermill↗
Parameterize and execute Jupyter notebooks programmatically for reproducible, scheduled reporting.
Phy↗
GPU-accelerated GUI for manual curation — merge, split, label — of large-scale sorted ephys.
PyalData↗
Analysis of trial-based population data in a tidy trial_data structure ported from MATLAB TrialData.
pyGLMnet↗
Elastic-net-regularized GLMs with a scikit-learn-style API, including Poisson GLMs for spike counts.
pymdp↗
Active inference and POMDP agents — simulate perception, learning and action under the free-energy principle.
pynapple↗
Lightweight time-series and interval toolkit — tuning curves, correlograms, decoding, filtering. GPU via pynajax.
pynaviz↗
Visualization companion to pynapple — interactive views of time series, intervals, tuning curves and spectrograms.
PyNWB↗
Reference Python API for reading and writing Neurodata Without Borders files.
pytest↗
The standard testing framework — what turns research code into software people can trust.
Rastermap↗
Nonlinear embedding that sorts neurons by activity similarity to reveal structure in huge population recordings.
samtools↗
Standard utilities for manipulating SAM/BAM/CRAM alignments — sorting, indexing, pileups.
Scanpy↗
Scalable single-cell RNA-seq analysis — preprocessing, clustering, trajectory inference — on AnnData.
scikit-image↗
Image-processing algorithms on NumPy arrays — filtering, segmentation, morphology.
scikit-learn↗
General-purpose machine learning — classification, regression, clustering, model selection.
SciPy↗
Fundamental algorithms for scientific computing — optimization, signal processing, statistics.
scvi-tools↗
Probabilistic deep-generative models for single-cell omics — integration, label transfer, DE.
Seurat↗
The standard R toolkit for single-cell genomics: QC, integration, clustering and differential expression.
SimBA↗
GUI pipeline for building supervised behavioral classifiers from pose keypoints, focused on social behavior.
SLEAP↗
Deep-learning system for fast multi-animal 2D pose tracking with a choice of network backbones.
Snakemake↗
Python-like workflow manager for reproducible pipelines that scale from laptop to cluster to cloud.
SpikeGLX↗
High-channel-count acquisition GUI for Neuropixels with synchronized NI-DAQ. Read directly by SpikeInterface.
SpikeInterface↗
Unified API wrapping 15+ sorters plus preprocessing, metrics, curation and comparison — the hub of the ephys stack.
SpyKING CIRCUS↗
Fast, scalable template-matching spike sorter that handles dense arrays across CPUs and clusters.
ssm↗
Bayesian learning and inference for state-space models — HMMs, linear dynamical systems, recurrent SLDS.
StarDist↗
Segments nuclei and other star-convex objects with high accuracy, even in crowded fields.
Suite2p↗
Registration, ROI detection and neuropil correction for two-photon imaging. Scales past 10,000 neurons.
Tridesclous↗
Transparent, GUI-driven spike sorting emphasizing visualization of every step.
VAME↗
Clusters behavior into motifs using a variational autoencoder over aligned pose sequences.
WaveClus↗
Unsupervised spike detection and sorting via wavelets and superparamagnetic clustering.
xarray↗
Labeled n-dimensional arrays for multi-dimensional scientific data; integrates with Dask and Zarr.
Zarr↗
Chunked, compressed n-dimensional arrays for parallel and cloud computing. An optional NWB backend.