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@AllenNeuralDynamics

Allen Institute for Neural Dynamics

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  1. aind-data-schema aind-data-schema Public

    A library that defines AIND data schema and validates JSON.

    Python 26 18

  2. aind-ephys-pipeline aind-ephys-pipeline Public

    AIND pipeline for processing extracellular electrophysiology data

    Nextflow 23 8

  3. openscope-community-predictive-processing openscope-community-predictive-processing Public

    This repository serves as a hub for community-driven contributions, documentation, and project tracking of the OpenScope Predictive Processing Community project.

    Python 15 13

  4. aind-ephys-spikesort-kilosort25-full aind-ephys-spikesort-kilosort25-full Public

    CodeOcean capsule for full electrophysiology analysis pipeline using Kilosort2.5 via SpikeInterface.

    Python 13 3

  5. ibl-ephys-alignment-gui ibl-ephys-alignment-gui Public

    Forked from int-brain-lab/iblapps

    Tool for aligning electrophysiological features to anatomical landmarks

    Python 10 4

  6. segmentation-skeleton-metrics segmentation-skeleton-metrics Public

    A Python package for evaluating the topological accuracy of a neuron segmentation by computing skeleton-based metrics.

    Python 8

Repositories

Showing 10 of 551 repositories
  • AllenNeuralDynamics.HamamatsuCamera Public

    A bonsai package to interface with Hamamatsu cameras

    AllenNeuralDynamics/AllenNeuralDynamics.HamamatsuCamera’s past year of commit activity
    C# 1 MIT 0 7 0 Updated Jan 14, 2026
  • analysis-pipeline-utils Public

    Utilities to facilitate writing scientific analysis pipelines to run in Code Ocean, in conjunction with S3 and DocumentDB storage

    AllenNeuralDynamics/analysis-pipeline-utils’s past year of commit activity
    Python 0 MIT 0 6 1 Updated Jan 14, 2026
  • aind-dft-ephys-analysis Public

    shared library for dynamic foraging task (DFT) - neuropixels analysis

    AllenNeuralDynamics/aind-dft-ephys-analysis’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 14, 2026
  • aind-data-transfer-lite Public

    A lightweight version of AIND Data Transfer Service.

    AllenNeuralDynamics/aind-data-transfer-lite’s past year of commit activity
    Python 0 MIT 1 6 2 Updated Jan 14, 2026
  • AutoTomeQC Public

    Automates sectioning quality control for the Prototome/Pylasso. Analyzes block face images to grade cuts (Go/No-Go/Unsure) based on knife marks, splits, thickness, etc.

    AllenNeuralDynamics/AutoTomeQC’s past year of commit activity
    Python 0 MIT 0 4 1 Updated Jan 14, 2026
  • aind-metadata-queries Public

    Libarary to host useful queries to AIND's metadata document database.

    AllenNeuralDynamics/aind-metadata-queries’s past year of commit activity
    Python 0 MIT 0 3 1 Updated Jan 14, 2026
  • aind-exaspim-data-transformation Public

    A library to convert imaris (ims) files to zarr v3 in the compression step of the aind-data-transfer-service upload process from AIND network to S3 bucket.

    AllenNeuralDynamics/aind-exaspim-data-transformation’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jan 14, 2026
  • aind-metadata-service Public

    REST API to compile metadata from various databases

    AllenNeuralDynamics/aind-metadata-service’s past year of commit activity
    Python 3 MIT 1 6 0 Updated Jan 14, 2026
  • aind-qc-portal Public

    Quality control portal

    AllenNeuralDynamics/aind-qc-portal’s past year of commit activity
    Python 2 MIT 0 21 0 Updated Jan 14, 2026
  • dynamic-foraging-task Public

    Bonsai/Harp workflow for Dynamic Foraging with Python GUI for visualization and control

    AllenNeuralDynamics/dynamic-foraging-task’s past year of commit activity
    Python 5 MIT 5 29 (1 issue needs help) 3 Updated Jan 14, 2026