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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 561 repositories
  • aind-qc-portal Public

    Quality control portal

    AllenNeuralDynamics/aind-qc-portal’s past year of commit activity
    Python 2 MIT 0 15 0 Updated Feb 12, 2026
  • Rhapso Public

    An open-source Python toolkit for large-scale fluorescence microscopy data alignment and fusion.

    AllenNeuralDynamics/Rhapso’s past year of commit activity
    Jupyter Notebook 6 MIT 0 7 5 Updated Feb 12, 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 9 Updated Feb 12, 2026
  • brainwasher Public

    0354: control software for automated tissue clearing system

    AllenNeuralDynamics/brainwasher’s past year of commit activity
    Python 0 MIT 1 18 2 Updated Feb 12, 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 Feb 12, 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 0 Updated Feb 12, 2026
  • posetail Public
    AllenNeuralDynamics/posetail’s past year of commit activity
    Python 1 BSD-3-Clause 0 0 0 Updated Feb 12, 2026
  • aind-disrnn-wrapper Public

    Job wrapper for AIND-disRNN project

    AllenNeuralDynamics/aind-disrnn-wrapper’s past year of commit activity
    Python 0 MIT 0 9 3 Updated Feb 12, 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 3 Updated Feb 12, 2026
  • AllenNeuralDynamics/openscope-params’s past year of commit activity
    Python 0 0 0 0 Updated Feb 12, 2026

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