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    450 repositories

    • deep_ccf_registration

      Public
      Arbitrary modality registration to CCFv3 using deep learning
      deep-learningimage-registrationcommon-coordinate-framwork
      Jupyter Notebook
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •9•30•270•12•Updated Dec 9, 2025Dec 9, 2025

    • neuron-proofreader

      Public
      NeuronProofreader is a Python library for automated proofreading of split and merge mistakes in neuron reconstructions.
      Python
      •
      MIT License
      •0•6•0•0•Updated Dec 9, 2025Dec 9, 2025

    • biofile-finder

      Public
      An open-use web application created for easy access, collaboration, and sharing of datasets through rich metadata search, filter, sort, and direct viewing in common industry applications or in our web-based 3D Volume Viewer.
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •3•15•72•3•Updated Dec 8, 2025Dec 8, 2025

    • spatial_compare

      Public
      package for comparing spatial transcriptomics datasets
      Jupyter Notebook
      •
      Other
      •8•6•11•7•Updated Dec 6, 2025Dec 6, 2025

    • HMBA_BasalGanglia_Consensus_Taxonomy

      Public
      SCSS
      •
      Creative Commons Zero v1.0 Universal
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • Spatial-Transcriptomics-Processing-Pipeline

      Public
      Nextflow
      •
      Other
      •0•0•0•0•Updated Dec 4, 2025Dec 4, 2025

    • cell_type_mapper

      Public
      Repository for storing prototype functionality implementations for the BKP
      Python
      •
      Other
      •7•38•5•2•Updated Dec 4, 2025Dec 4, 2025

    • npc_lims

      Public
      Tools to fetch and update paths, metadata and state for Mindscope Neuropixels sessions, in the cloud.
      Python
      •
      MIT License
      •1•0•3•0•Updated Dec 4, 2025Dec 4, 2025

    • HebbsVision

      Public
      Jupyter Notebook
      •
      Other
      •0•2•0•0•Updated Dec 3, 2025Dec 3, 2025

    • render-python

      Public
      A python interface for render
      Python
      •
      BSD 2-Clause "Simplified" License
      •11•7•15•1•Updated Dec 2, 2025Dec 2, 2025

    • jem

      Public
      Repository containing JEM (JSON Electrophysiology Metadata), a web-form for logging metadata during slice electrophysiology experiments.
      HTML
      •
      Other
      •4•5•0•0•Updated Dec 2, 2025Dec 2, 2025

    • vis

      Public
      Typescript packages for building big-data visualization tools & components, with examples for a variety of common data types & formats
      visualizationwebglbig-datatoolkit
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•6•11•7•Updated Dec 2, 2025Dec 2, 2025

    • pytic

      Public
      PyTic - An Object-Oriented Python Wrapper for Pololu Tic Stepper Drivers
      Python
      •
      Other
      •8•12•6•1•Updated Dec 1, 2025Dec 1, 2025

    • bmtk

      Public
      Brain Modeling Toolkit
      pythonsimulationmodelingneuroscienceneural-networksneuroinformaticsneuron
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •96•311•63•9•Updated Dec 1, 2025Dec 1, 2025

    • neuroglancer

      Public
      WebGL-based viewer for volumetric data
      TypeScript
      •
      Apache License 2.0
      •335•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • IPNWB

      Public
      IGOR Pro
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•5•1•Updated Nov 27, 2025Nov 27, 2025

    • lamination_station

      Public
      Bayesian detection of lamination and structures from labeled spatial points
      Python
      •0•1•0•0•Updated Nov 26, 2025Nov 26, 2025

    • microns_tutorial

      Public
      MICrONS databook and analysis tutorials
      HTML
      •2•7•2•0•Updated Nov 26, 2025Nov 26, 2025

    • acq4

      Public
      Data acquisition for patch clamp ephys / optogenetics / imaging experiments
      Python
      •
      MIT License
      •53•1•0•0•Updated Nov 26, 2025Nov 26, 2025

    • aibs-informatics-cdk-lib

      Public
      Library for AWS CDK Constructs related to AIBS Informatics Services
      aibs-informatics
      Python
      •
      Other
      •0•1•0•1•Updated Nov 26, 2025Nov 26, 2025

    • exc_vis_manuscript

      Public
      Analysis and figure code for mouse excitatory visual cortex Patch-seq and whole neuron morphology manuscript
      Python
      •
      Other
      •1•0•0•0•Updated Nov 25, 2025Nov 25, 2025

    • sonata

      Public
      Collaboration between BBP and AIBS
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •38•59•32•9•Updated Nov 24, 2025Nov 24, 2025

    • abc_atlas_access

      Public
      Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
      Jupyter Notebook
      •
      Other
      •31•91•19•5•Updated Nov 24, 2025Nov 24, 2025

    • human_patchseq_excitatory

      Public
      BSD 2-Clause "Simplified" License
      •0•0•0•0•Updated Nov 24, 2025Nov 24, 2025

    • npc_sessions

      Public
      Tools for accessing and packaging data from behavior and epyhys sessions from the Mindscope Neuropixels team, in the cloud.
      Python
      •1•2•53•0•Updated Nov 21, 2025Nov 21, 2025

    • dynamic_routing_analysis

      Public
      Tools for accessing, processing and presenting data from Dynamic Routing experiments.
      Jupyter Notebook
      •0•2•0•0•Updated Nov 21, 2025Nov 21, 2025

    • ZeroMQ-XOP

      Public
      The ZeroMQ XOP enables Igor Pro to interface over the network using a ZeroMQ messaging layer and JSON as message format
      C
      •
      BSD 3-Clause "New" or "Revised" License
      •8•9•10•0•Updated Nov 21, 2025Nov 21, 2025

    • aibs-informatics-aws-utils

      Public
      Library of generic Python AWS utils used by the AIBS Informatics "Marmot" team
      pythonawsaibs-informatics
      Python
      •
      Other
      •0•1•2•0•Updated Nov 20, 2025Nov 20, 2025

    • CCF-MAP

      Public
      Primer and examples for using templates and atlases in HMBA/BICAN
      HTML
      •0•0•0•0•Updated Nov 17, 2025Nov 17, 2025