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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 19

  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. supervoxel-loss supervoxel-loss Public

    Efficient connectivity-preserving loss function for training neural networks to perform instance segmentation.

    Python 10 3

Repositories

Showing 10 of 554 repositories
  • Aind.Physiology.Hsfp Public

    A repository for the Hyper-Spectral Fiber Photometry (HSFP) system

    AllenNeuralDynamics/Aind.Physiology.Hsfp’s past year of commit activity
    C# 0 MIT 0 1 0 Updated Jan 25, 2026
  • aind-smartspim-classification Public

    Code for classifying the cell candidate outputs from aind-smartspim-segmentation within smartspim pipeline

    AllenNeuralDynamics/aind-smartspim-classification’s past year of commit activity
    Python 0 MIT 0 0 1 Updated Jan 25, 2026
  • dynamic-routing-bonsai Public

    Repo for conversion of Dynamic Routing python scripts to Bonsai/Harp.

    AllenNeuralDynamics/dynamic-routing-bonsai’s past year of commit activity
    0 MIT 0 1 0 Updated Jan 24, 2026
  • segmentation-skeleton-metrics Public

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

    AllenNeuralDynamics/segmentation-skeleton-metrics’s past year of commit activity
    Python 8 MIT 0 0 0 Updated Jan 24, 2026
  • harp.device.quad-dac Public

    0364: This repository contains the hardware, firmware, and software related to the Harp quad DAC

    AllenNeuralDynamics/harp.device.quad-dac’s past year of commit activity
    C++ 0 MIT 0 26 1 Updated Jan 24, 2026
  • aind-ophys-nwb Public

    Write NWB files for data generated with two-photon ophys pipelines (currently multiplane only)

    AllenNeuralDynamics/aind-ophys-nwb’s past year of commit activity
    Jupyter Notebook 1 MIT 0 9 3 Updated Jan 24, 2026
  • rp2040.pio-ltc264x Public

    RP2040 driver for controlling a 16-bit DAC chip using the PIO

    AllenNeuralDynamics/rp2040.pio-ltc264x’s past year of commit activity
    C++ 0 MIT 0 0 1 Updated Jan 24, 2026
  • aind-nwb-utils Public

    Useful functions for reading and writing NWB files

    AllenNeuralDynamics/aind-nwb-utils’s past year of commit activity
    Python 1 MIT 0 12 2 Updated Jan 24, 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 0 Updated Jan 24, 2026
  • Aind.Experiment.MotorObservatory-Fip Public

    An experiment that combines multi-camera behavior recordings with fiber photometry

    AllenNeuralDynamics/Aind.Experiment.MotorObservatory-Fip’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Jan 24, 2026

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