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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 31 19

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

    AIND pipeline for processing extracellular electrophysiology data

    Nextflow 29 10

  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 17 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 14 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 581 repositories
  • aind-fip-dff Public

    This capsule takes an input raw NWB file of fiber data and creates processed DFF traces

    AllenNeuralDynamics/aind-fip-dff’s past year of commit activity
    Python 0 MIT 0 8 2 Updated Mar 11, 2026
  • AllenNeuralDynamics/dr-llm-modelling-tests’s past year of commit activity
    Python 0 1 0 0 Updated Mar 11, 2026
  • package-brain-atlas-assets Public

    Reorganize various brain atlas data assets into a standard organization and metadata convention.

    AllenNeuralDynamics/package-brain-atlas-assets’s past year of commit activity
    Python 0 MIT 0 4 2 Updated Mar 11, 2026
  • brainwasher Public

    0354: control software for automated tissue clearing system

    AllenNeuralDynamics/brainwasher’s past year of commit activity
    Python 0 MIT 1 18 1 Updated Mar 11, 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 8 2 Updated Mar 11, 2026
  • hcr-unmix-to-cells Public

    A capsule to be run on HCR data after it has been processed by main the pipeline. Can run alternate unmixing strategies and generate cell x gene tables annotated with cell labels (e.g. de novo clustering or taxonomy mapping).

    AllenNeuralDynamics/hcr-unmix-to-cells’s past year of commit activity
    Jupyter Notebook 0 MIT 0 0 0 Updated Mar 11, 2026
  • .github Public
    AllenNeuralDynamics/.github’s past year of commit activity
    0 0 1 1 Updated Mar 11, 2026
  • Aind.Behavior.Pirouette Public

    A repository with source code for long-term, freely moving, electrophisiology recordings in mice

    AllenNeuralDynamics/Aind.Behavior.Pirouette’s past year of commit activity
    C# 0 MIT 0 7 1 Updated Mar 11, 2026
  • lamf-analysis Public

    Place for scientists & engineers on ophys-mFish projects (Learning mFISH, omFISH) to put ophys data processing development code, especially as a place to ease transition from LIMS to Codeocean

    AllenNeuralDynamics/lamf-analysis’s past year of commit activity
    Jupyter Notebook 1 MIT 1 21 1 Updated Mar 11, 2026
  • aind-hcr-data-loader Public

    Data loading for AIND HCR datasets (v1.0)

    AllenNeuralDynamics/aind-hcr-data-loader’s past year of commit activity
    Jupyter Notebook 0 MIT 0 2 1 Updated Mar 11, 2026