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    478 repositories

    • deep_ccf_registration

      Public
      Tissue slice registration to the CCF using deep learning
      deep-learningimage-registrationcommon-coordinate-framwork
      deep-learningimage-registrationcommon-coordinate-framwork
      Jupyter Notebook
      •0•2•0•0•Updated May 3, 2026May 3, 2026

    • MultiTaskMPN

      Public
      Jupyter Notebook
      •1•2•0•0•Updated May 3, 2026May 3, 2026

    • 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 co…
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •6•17•74•11•Updated May 2, 2026May 2, 2026

    • visual_behavior_analysis

      Public
      Python package for analyzing behavioral data for Brain Observatory: Visual Behavior
      pythonbehaviorneuroscience
      pythonbehaviorneurosciencepsychologypsychophysics
      Jupyter Notebook
      •
      Other
      •7•26•65•6•Updated May 2, 2026May 2, 2026

    • xenium_analysis_tools

      Public
      Jupyter Notebook
      •
      MIT License
      •0•5•0•3•Updated May 1, 2026May 1, 2026

    • CHARGE

      Public
      Cell HierARchy Gene Explorer (CHARGE) is an interactive tool for identifying genes of potential biological interest in a cell type taxonomy.
      R
      •
      Other
      •0•0•0•0•Updated May 1, 2026May 1, 2026

    • openscope_databook

      Public
      OpenScope databook: a collaborative, versioned, data-centric collection of foundational analyses for reproducible systems neuroscience 🐁🧠🔬🖥️📈
      visualizationpythonreproducible-research
      visualizationpythonreproducible-researchdata-visualizationdata-analysisnwbdandi-archive
      Python
      •
      Other
      •31•75•8•0•Updated May 1, 2026May 1, 2026

    • ConnectsCommonConnectivity

      Public
      A repository to organize data models and code for creating a pilot common connectiivty matrix for BRAIN CONNECTS
      Jupyter Notebook
      •
      MIT License
      •1•1•0•1•Updated May 1, 2026May 1, 2026

    • vis

      Public
      Typescript packages for building big-data visualization tools & components, with examples for a variety of common data types & formats
      visualizationwebglbig-data
      visualizationwebglbig-datatoolkit
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•7•12•13•Updated May 1, 2026May 1, 2026

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •9•29•280•9•Updated May 1, 2026May 1, 2026

    • abc_atlas_access

      Public
      Documentation and examples demonstrating how to access data from the Allen Brain Cell Atlas
      Jupyter Notebook
      •
      Other
      •37•103•21•6•Updated May 1, 2026May 1, 2026

    • EducationAndEngagement

      Public
      Jupyter Notebook
      •
      MIT License
      •0•6•1•0•Updated May 1, 2026May 1, 2026

    • neuron-proofreader

      Public
      NeuronProofreader is a Python library for automated proofreading of split and merge mistakes in neuron reconstructions.
      Python
      •
      MIT License
      •0•8•0•2•Updated Apr 30, 2026Apr 30, 2026

    • OCS-Submission-Capsule-API

      Public
      Python
      •0•0•0•0•Updated Apr 30, 2026Apr 30, 2026

    • IPNWB

      Public
      IGOR Pro
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•5•0•Updated Apr 30, 2026Apr 30, 2026

    • openscope_upload

      Public
      Code to process and then upload openscope files to code ocean
      Python
      •0•1•1•1•Updated Apr 29, 2026Apr 29, 2026

    • scrattch.taxonomy

      Public
      Allen Institute Taxonomy building R package
      HTML
      •1•4•10•0•Updated Apr 29, 2026Apr 29, 2026

    • spots-in-space

      Public
      spatial transcriptomics analysis
      Python
      •
      Other
      •0•3•15•3•Updated Apr 29, 2026Apr 29, 2026

    • 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•55•0•Updated Apr 28, 2026Apr 28, 2026

    • CCF-MAP

      Public
      Primer and examples for using templates and atlases in HMBA/BICAN
      HTML
      •0•0•0•0•Updated Apr 27, 2026Apr 27, 2026

    • 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 Apr 27, 2026Apr 27, 2026

    • pytorch-CycleGAN-and-pix2pix

      Public
      Image-to-Image Translation in PyTorch
      Python
      •
      Other
      •6.6k•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • mtrain_regimens

      Public
      Repository to track training stages and regimens for visual behavior
      Python
      •
      Other
      •4•3•14•0•Updated Apr 23, 2026Apr 23, 2026

    • AllenInstituteTaxonomy

      Public
      R
      •1•4•6•0•Updated Apr 22, 2026Apr 22, 2026

    • FISHsim

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • ephys-analysis-tools

      Public
      Code base generating formatted data tables that streamlines data analysis process for ephys production metadata.
      Jupyter Notebook
      •0•1•0•0•Updated Apr 22, 2026Apr 22, 2026

    • dynamic_routing_analysis

      Public
      Tools for accessing, processing and presenting data from Dynamic Routing experiments.
      Jupyter Notebook
      •0•2•0•0•Updated Apr 21, 2026Apr 21, 2026

    • pfeiffer-turbo

      Public
      Python interface for Pfeiffer turbo drive units
      Python
      •
      MIT License
      •1•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • npc_sessions_cache

      Public
      Scripts, notebooks and plots that operate on NWB or NWB-like objects from `npc_sessions` in the cloud.
      Jupyter Notebook
      •0•0•0•1•Updated Apr 20, 2026Apr 20, 2026

    • CHARGE_taxonomy

      Public
      GitHub repo for the script used to generate CHARGE Rmd files starting from AIT files. This needs to be separated from the CHARGE app repo to avoid requiring a …
      R
      •
      Other
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026
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