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    474 repositories

    • mtrain_regimens

      Public
      Repository to track training stages and regimens for visual behavior
      Python
      •
      Other
      •4•3•14•0•Updated Apr 19, 2026Apr 19, 2026

    • 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 Apr 18, 2026Apr 18, 2026

    • SPOCTT

      Public
      Tools, tutorials, and resources associated with the SPOCTT initiative (Scientific and Public Outreach of Cell Type Taxonomies)
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•0•0•Updated Apr 18, 2026Apr 18, 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 18, 2026Apr 18, 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 17, 2026Apr 17, 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•0•Updated Apr 17, 2026Apr 17, 2026

    • biorealistic-v1-model

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•9•4•0•Updated Apr 17, 2026Apr 17, 2026

    • aibs-informatics-core

      Public
      Core library to be used as foundation across multiple projects
      aibs-informatics
      aibs-informatics
      Python
      •
      Other
      •0•2•0•0•Updated Apr 17, 2026Apr 17, 2026

    • MultiTaskMPN

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Apr 17, 2026Apr 17, 2026

    • ACE

      Public
      R Shiny app for comparison of annotations (e.g., cell type assignments)
      R
      •
      Other
      •1•4•8•0•Updated Apr 17, 2026Apr 17, 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
      •5•17•108•6•Updated Apr 16, 2026Apr 16, 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 Apr 16, 2026Apr 16, 2026

    • CCF-MAP

      Public
      Primer and examples for using templates and atlases in HMBA/BICAN
      HTML
      •0•0•0•0•Updated Apr 16, 2026Apr 16, 2026

    • acq4

      Public
      Data acquisition for patch clamp ephys / optogenetics / imaging experiments
      Python
      •
      MIT License
      •53•1•0•3•Updated Apr 16, 2026Apr 16, 2026

    • neuron_morphology

      Public
      Tools for working with single-neuron morphological reconstructions
      Python
      •
      Other
      •9•22•35•4•Updated Apr 16, 2026Apr 16, 2026

    • xenium_analysis_tools

      Public
      Jupyter Notebook
      •
      MIT License
      •0•2•1•3•Updated Apr 16, 2026Apr 16, 2026

    • npc_ephys

      Public
      Tools for accessing and processing raw ephys data, compatible with data in the cloud.
      Python
      •
      MIT License
      •2•0•0•0•Updated Apr 15, 2026Apr 15, 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 Apr 14, 2026Apr 14, 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 14, 2026Apr 14, 2026

    • npc_sync

      Public
      Repackaging of AllenSDK.SyncDataset with extra functionality, compatible with data in the cloud.
      Python
      •
      MIT License
      •0•0•0•1•Updated Apr 14, 2026Apr 14, 2026

    • npc_stim

      Public
      Tools for accessing and processing stim data, compatible with data in the cloud.
      Python
      •
      MIT License
      •0•0•0•0•Updated Apr 14, 2026Apr 14, 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•5•Updated Apr 13, 2026Apr 13, 2026

    • sweep_qc_tool

      Public
      manual quality control for intracellular electrophysiology experiments
      Python
      •
      GNU General Public License v3.0
      •2•1•27•2•Updated Apr 13, 2026Apr 13, 2026

    • MIES

      Public
      Multichannel Igor Electrophysiology Suite
      electrophysiologyigor-prosupported
      electrophysiologyigor-prosupported
      IGOR Pro
      •
      Other
      •9•29•278•11•Updated Apr 12, 2026Apr 12, 2026

    • openscope_psycode

      Public
      This repository contains the stimulus behind the PsyCode project
      Jupyter Notebook
      •
      Apache License 2.0
      •8•1•0•0•Updated Apr 10, 2026Apr 10, 2026

    • aibs-informatics-cdk-lib

      Public
      Library for AWS CDK Constructs related to AIBS Informatics Services
      aibs-informatics
      aibs-informatics
      Python
      •
      Other
      •0•1•0•1•Updated Apr 9, 2026Apr 9, 2026

    • transcriptomic_clustering

      Public
      improved clustering pipeline for transcriptomic data
      Python
      •
      Other
      •4•6•17•7•Updated Apr 8, 2026Apr 8, 2026

    • PeakRankR

      Public
      Package to rank enhancer peaks for cloning
      R
      •
      Other
      •0•2•3•0•Updated Apr 8, 2026Apr 8, 2026

    • dynamic_routing_analysis

      Public
      Tools for accessing, processing and presenting data from Dynamic Routing experiments.
      Jupyter Notebook
      •0•2•0•0•Updated Apr 8, 2026Apr 8, 2026

    • scrattch

      Public
      Single cell RNA-seq analysis for transcriptomic type characterization
      rumbrellatranscriptomics
      rumbrellatranscriptomicsscrattch
      HTML
      •
      Other
      •5•40•2•0•Updated Apr 7, 2026Apr 7, 2026
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