International Brain Laboratory ORG

Main repository for IBL rig code

IBL core shared libraries

Unified environment and Issue tracker for all IBL

pyqt5 dependent applications for IBL sessions

Open Neurophysiology Environment

Extraction code for IBL satellite projects eg. U19 / personal projects

Multichannel time series lossless compression in pure Python based on NumPy and zlib

IBL AI Agent helps you use a coding agent such as OpenAI Codex to analyze International Brain Laboratory (IBL) data.

Code related to the brainwide map paper

Resources for the IBL portion of the UCL Neuropixels Course 2024

DataJoint pipeline for IBL project

Collection of tools to handle Neuropixel 1.0 and 2.0 data

The International Brain Laboratory et al. (2020) A standardized and reproducible method to measure decision-making in mice. bioRxiv, 909838

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Brain flatmaps generation

Initial repo for behavioral analyses

Interactive visualization tool for multiple volumes, meshes and points based on VTK. The app can be controlled with Python scripts (optionally headless), with a Qt UI & dynamic statistics or with Jupyter.

Train ANN-RNNs to perform the IBL task and then dissect them.

Spike Sorting Utilities

Video analysis for the IBL dataset

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Toolbox for change-point detection and ideal-observer analyses of IBL task data

Python package for elastix-based registration of tissues to atlases; with mouse brain registration to the Allen CCFv3 built-in.

Project seeking to localize encoding of the task prior in the brain

Neuropixel raw data viewer

A modern Python interface for Bpod Finite State Machines.

Materials for NeuroMatchAcademy workshop for IBL data pipeline access

Deployment scripts for ibl

IBL atlas module

Ephys alignment tool

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Urai AE, Aguillon-Rodriguez V, Laranjeira IC, Cazettes F, The International Brain Laboratory, Mainen ZF & Churchland AK (2021) Citric Acid water as an alternative to water restriction for high-yield mouse behavior. eNeuro, 8(1). doi: 10.1523/ENEURO.0230-20.2020

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Gallery of visualizations and associated code

IBL set of Matlab tools and functions

Tools for electrophysiology analysis

A Python-based module for creating flexible and robust spike sorting pipelines.

Repository containing courses on data usage

IBL Spikesorting pipeline implented using Spikeinterface

default mode network manifold analysis

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Mostly a fork of the pybpod without the git submodule structure.

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IBL API for atlas web

Style guidelines for IBL papers

An implementation of demixed Principal Component Analysis (a supervised linear dimensionality reduction technique)

examples of scripts how to use IBL-BWM dataset

WIP code for analyzing outputs of spike sorters

brain-wide-bench neural model benchmarking platform

Cluster jobs for SDSC Popeye

Multi-Photon Calcium Imaging preprocessing

LFP compression for Neuropixels recordings

Utilities to run processing on AWS Cloud

A repository to plan the extracellular electrophysiology course for OSSS 2026

IBL Software Reliability Engineering

A repository to plan the extracellular electrophysiology course for OSSS 2026

A registry of publicly available datasets on AWS

Tools to build reveal web-based presentations for scientific visualisations

A collection of methods and tools for experimental photometry data

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IBL core shared libraries

extension for the NWB format with IBL specific metadata

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Code related to mesosocope experiments and analysis

IBL visualisations using datoviz

NeuroPyxels (npyx) is a python library built for electrophysiologists using Neuropixels electrodes. This package stems from the need of a pythonist who really did not want to transition to MATLAB to work with Neuropixels: it features a suite of core utility functions for loading, processing and plotting Neuropixels data.

Conversion of IBL data to NWB format.

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Python library for accessing Bpod modules used at IBL

Software to control and record from multiple cameras

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A collection of extensions to the Qt framework.

Apply Zoe's model to get engagement score for all BWM trials

Small utilities with minimal dependencies

Public website prototype

PCB files for the Adafruit Qualia Driver

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IBL governance policies and documents

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Create NWB files by converting and combining neural data in proprietary formats and adding essential metadata.

A Python wrapper for tycmd

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The HTML Presentation Framework

phy: interactive visualization and manual spike sorting of large-scale ephys data

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Firmware for Bpod HiFi Module

A singleton wrapping pyserial's Serial class

Example notebooks for the Dandy Hub archive

clusterless decoding of neural data using a mixture of Gaussians (MoG)

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DataJoint deployments for IBL's kubernetes cluster. Codebase for IBL Navigator located in: https://github.com/datajoint-company/ibl-navigator.

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Real-time behaviour measurement software

Set of functions and properties to allow the manipulation of a PyBpod GUI project using code

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Repository meant to easily find compatible versions of useful python packages with heavy reliance on Github Actions CI

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YASS: Yet Another Spike Sorter

A light version of IBL pipeline that allows users to access datajoint tables.

Collection of spike sorters Docker files

Community Detection for spike data

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DataJoint Tutorial for IBL pipeline

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