Skip to content

@AllenNeuralDynamics Allen Institute for Neural Dynamics

Change the repository type filter

All

    Repositories list

    511 repositories

    • ibl-ephys-alignment-gui

      Public
      Tool for aligning electrophysiological features to anatomical landmarks
      Python
      •
      MIT License
      •17•8•0•2•Updated Nov 1, 2025Nov 1, 2025

    • Aind.Behavior.VrForaging.Curricula

      Public
      A repository with curricula for the VrForaging platform
      Python
      •
      MIT License
      •0•0•3•2•Updated Nov 1, 2025Nov 1, 2025

    • aind-proteomics-stitch

      Public
      Stitching for the proteomics pipeline
      Python
      •
      MIT License
      •0•0•3•0•Updated Nov 1, 2025Nov 1, 2025

    • Aind.Experiment.VrForaging-Fip

      Public
      A repository to run VrForaging + Fip experiments
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 1, 2025Nov 1, 2025

    • aind-data-transfer-service

      Public
      FastAPI service to run data compression and transfer jobs on the hpc
      aind-data-infrastructure
      Python
      •
      MIT License
      •0•3•8•0•Updated Oct 31, 2025Oct 31, 2025

    • Aind.Physiology.Fip

      Public
      C#
      •
      MIT License
      •0•0•7•2•Updated Oct 31, 2025Oct 31, 2025

    • aind-neuroglancer-game

      Public
      TypeScript
      •
      Apache License 2.0
      •1•0•14•1•Updated Oct 31, 2025Oct 31, 2025

    • neurogabber

      Public
      Tall to embedded neuroglancer views with an LLM.
      Python
      •
      MIT License
      •0•0•0•2•Updated Oct 31, 2025Oct 31, 2025

    • image-compression-challenge

      Public
      A python package for scoring submissions to an image compression challenge on Kaggle.
      kaggle-competitionimage-compressionlight-microscopy
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-metadata-extractor

      Public
      Metadata extractors for AIND
      Python
      •
      MIT License
      •0•0•1•7•Updated Oct 31, 2025Oct 31, 2025

    • foraging-behavior-browser

      Public
      Foraging behavior browser (streamlit)
      Python
      •
      MIT License
      •2•2•13•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-metadata-mapper

      Public
      Repository to help gather and map metadata from different sources
      aind-data-infrastructure
      Python
      •
      MIT License
      •2•0•35•4•Updated Oct 31, 2025Oct 31, 2025

    • aind-dynamic-foraging-behavior-video-analysis

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-fiber-photometry-standalone-pipeline

      Public
      Nextflow
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • ephys-sorting-manual-curation

      Public
      Repository for collecting manual curation data for spike-sorting
      aind-data-infrastructure
      Python
      •0•1•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-fip-dff

      Public
      This capsule takes an input raw NWB file of fiber data and creates processed DFF traces
      Python
      •
      MIT License
      •0•0•4•1•Updated Oct 31, 2025Oct 31, 2025

    • clabe

      Public
      Command-line-interface Launcher for AIND Behavior Experiments
      aind-behavior
      Python
      •
      MIT License
      •0•0•12•4•Updated Oct 31, 2025Oct 31, 2025

    • aind-fip-qc-raw

      Public
      a capsule to generate QC based on fip raw data asest
      Python
      •
      MIT License
      •0•0•1•1•Updated Oct 31, 2025Oct 31, 2025

    • dynamic-foraging-task

      Public
      Bonsai/Harp workflow for Dynamic Foraging with Python GUI for visualization and control
      Python
      •
      MIT License
      •5•5•24•4•Updated Oct 31, 2025Oct 31, 2025

    • aind-analysis-pipeline-template

      Public
      Pipeline with job dispatch and analysis wrapper capsules that serves as template for analysis
      Nextflow
      •
      MIT License
      •0•1•2•0•Updated Oct 31, 2025Oct 31, 2025

    • zombie-squirrel

      Public
      Caching tools for storing expensive DocDB queries and S3 data tables in Redshift
      Python
      •
      MIT License
      •0•0•3•0•Updated Oct 31, 2025Oct 31, 2025

    • analysis-pipeline-utils

      Public
      Utilities to facilitate writing scientific analysis pipelines to run in Code Ocean, in conjunction with S3 and DocumentDB storage
      Python
      •
      MIT License
      •0•0•6•1•Updated Oct 31, 2025Oct 31, 2025

    • allen-powerplatform-client

      Public
      Service to read and write from Dataverse.
      Python
      •
      MIT License
      •0•0•1•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-pophys-pipeline

      Public
      2P planar optical physiology processing pipeline
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-beh-ephys-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-ephys-portal

      Public
      SpikeInterface GUI Portal
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-fip-nwb-base-capsule-standalone

      Public
      Capsule to package fiber photometry data
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-ephys-cleanup

      Public
      Tools for finding compressed raw ephys data uploaded to S3 corresponding to the original, uncompressed raw data files stored locally or on network drives, for checking the integrity of the uploaded data, and for identifying original files that can be safely deleted.
      Python
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • aind-dft-ephys-analysis

      Public
      shared library for dynamic foraging task (DFT) - neuropixels analysis
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 30, 2025Oct 30, 2025

    • dynamicrouting-decoding-tests

      Public
      Python
      •
      MIT License
      •2•0•0•0•Updated Oct 30, 2025Oct 30, 2025