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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 29 19

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

    AIND pipeline for processing extracellular electrophysiology data

    Nextflow 26 9

  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 16 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. supervoxel-loss supervoxel-loss Public

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

    Python 12 3

  6. 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

Repositories

Showing 10 of 560 repositories
  • 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 Feb 10, 2026
  • aind-qc-portal Public

    Quality control portal

    AllenNeuralDynamics/aind-qc-portal’s past year of commit activity
    Python 2 MIT 0 17 1 Updated Feb 10, 2026
  • aind-vr-foraging-primary-data-nwb-packaging Public

    Capsule that packages primary data for VR Foraging task using data contract

    AllenNeuralDynamics/aind-vr-foraging-primary-data-nwb-packaging’s past year of commit activity
    Python 0 MIT 0 1 1 Updated Feb 10, 2026
  • aind-dynamic-foraging-qc Public

    Capsule for the QC of the dynamic foraging task

    AllenNeuralDynamics/aind-dynamic-foraging-qc’s past year of commit activity
    Python 0 MIT 0 5 2 Updated Feb 10, 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 Feb 10, 2026
  • brainslosher-web-ui Public
    AllenNeuralDynamics/brainslosher-web-ui’s past year of commit activity
    TypeScript 0 0 1 0 Updated Feb 10, 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 7 1 Updated Feb 10, 2026
  • aind-smartspim-pipeline Public

    Repository that hosts the SmartSPIM pipeline code

    AllenNeuralDynamics/aind-smartspim-pipeline’s past year of commit activity
    Nextflow 4 MIT 3 1 0 Updated Feb 10, 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 0 Updated Feb 10, 2026
  • aind-smartspim-quantification Public

    Takes the output of segmentation and ccf registration to calculate cell counts per brain region

    AllenNeuralDynamics/aind-smartspim-quantification’s past year of commit activity
    Python 1 MIT 2 4 0 Updated Feb 10, 2026
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