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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 25 17

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

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

    Python 11 3

  3. aind-ephys-pipeline aind-ephys-pipeline Public

    AIND pipeline for processing extracellular electrophysiology data

    Nextflow 9 4

  4. 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 6

  5. parallax parallax Public

    GUI control software for the Modular Insertion System (MIS)

    Python 5 1

  6. TigerASI TigerASI Public

    a lightweight python interface for ASI brand Tiger Controllers

    Python 5 2

Repositories

Showing 10 of 357 repositories
  • aind-data-schema Public

    A library that defines AIND data schema and validates JSON.

    AllenNeuralDynamics/aind-data-schema’s past year of commit activity
    Python 25 MIT 17 48 4 Updated Mar 13, 2025
  • aind-data-schema-models Public

    Data models used in aind-data-schema

    AllenNeuralDynamics/aind-data-schema-models’s past year of commit activity
    Python 0 MIT 3 6 0 Updated Mar 13, 2025
  • aind-analyisis-wrapper Public

    Capsule that serves a wrapper for running analysis functions on input data

    AllenNeuralDynamics/aind-analyisis-wrapper’s past year of commit activity
    Dockerfile 0 MIT 0 0 0 Updated Mar 13, 2025
  • 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 0 21 1 Updated Mar 13, 2025
  • aind-smartspim-data-transformation Public

    Data transformations applied to the SmartSPIM data before uploading to the cloud storage service.

    AllenNeuralDynamics/aind-smartspim-data-transformation’s past year of commit activity
    Python 0 MIT 0 2 0 Updated Mar 12, 2025
  • metadata-chatbot Public

    LLM (Anthropic Claude) based chatbot that can query, ingest and summarize metadata in a conversational form

    AllenNeuralDynamics/metadata-chatbot’s past year of commit activity
    Python 2 MIT 0 10 0 Updated Mar 12, 2025
  • 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 Mar 12, 2025
  • aind-metadata-mapper Public

    Repository to help gather and map metadata from different sources

    AllenNeuralDynamics/aind-metadata-mapper’s past year of commit activity
    Python 0 MIT 2 31 5 Updated Mar 12, 2025
  • 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 4 100 (1 issue needs help) 12 Updated Mar 12, 2025
  • aind-data-transfer-service Public

    FastAPI service to run data compression and transfer jobs on the hpc

    AllenNeuralDynamics/aind-data-transfer-service’s past year of commit activity
    Python 3 MIT 0 14 (1 issue needs help) 1 Updated Mar 12, 2025
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