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    442 repositories

    • 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
      •
      MIT License
      •12•12•30•1•Updated Aug 5, 2025Aug 5, 2025

    • Aind.Behavior.VrForaging

      Public
      Task implemention of VR Foraging experiment
      aind-behavior
      C#
      •
      MIT License
      •0•3•12•2•Updated Aug 5, 2025Aug 5, 2025

    • aind-vr-forgaging-processing-nwb-packaging

      Public
      Capsule that packages processed data for vr foraging behavior task
      Jupyter Notebook
      •
      MIT License
      •0•0•3•0•Updated Aug 5, 2025Aug 5, 2025

    • brainwasher

      Public
      0354: control software for automated tissue clearing system
      Python
      •
      MIT License
      •1•0•14•1•Updated Aug 5, 2025Aug 5, 2025

    • analysis-pipeline-utils

      Public
      Utilities to facilitate writing scientific analysis pipelines to run in Code Ocean, in conjunction with S3 and DocumentDB storage
      Python
      •
      MIT License
      •0•0•3•1•Updated Aug 4, 2025Aug 4, 2025

    • aind-nwb-utils

      Public
      Useful functions for reading and writing NWB files
      Python
      •
      MIT License
      •0•0•7•3•Updated Aug 4, 2025Aug 4, 2025

    • aind-file-standards

      Public
      MIT License
      •0•0•3•3•Updated Aug 4, 2025Aug 4, 2025

    • aind-data-access-api

      Public
      Library to interface with AIND databases
      aind-core-servicesaind-data-infrastructure
      Python
      •
      MIT License
      •0•2•8•1•Updated Aug 4, 2025Aug 4, 2025

    • aind-analysis-arch-result-access

      Public
      accessing results from aind analysis architecture
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • parallax

      Public
      Automatic detection of probe position from multiple camera views
      electrophysiologymachine-visionunder-developmentneuropixels
      Python
      •
      MIT License
      •1•5•7•3•Updated Aug 4, 2025Aug 4, 2025

    • aind-analysis-wrapper

      Public
      Capsule that serves a wrapper for running analysis functions on input data
      Jupyter Notebook
      •
      MIT License
      •1•0•3•2•Updated Aug 4, 2025Aug 4, 2025

    • aind-analysis-job-dispatch

      Public
      Capsule to create the input job model for analysis wrapper
      Python
      •
      MIT License
      •0•0•2•1•Updated Aug 4, 2025Aug 4, 2025

    • aind-exaspim-neuron-segmentation

      Public
      A Python package for performing neuron segmentation in ExaSPIM image datasets.
      segmentation
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • Bonsai.AllenNeuralDynamics

      Public
      A repository with Bonsai packages used in AIND
      bonsai-rxaind-behavior
      C#
      •
      Other
      •0•0•9•0•Updated Aug 4, 2025Aug 4, 2025

    • aind-analysis-pipeline-template

      Public
      Pipeline with job dispatch and analysis wrapper capsules that serves as template for analysis
      Nextflow
      •
      MIT License
      •0•0•1•1•Updated Aug 4, 2025Aug 4, 2025

    • aind-ephys-portal

      Public
      SpikeInterface GUI Portal
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • exaspim-control

      Public
      Python
      •
      MIT License
      •2•1•0•0•Updated Aug 4, 2025Aug 4, 2025

    • aind-mri-utils

      Public
      Allen Institute for Neural Dynamics MRI utilities
      Python
      •
      MIT License
      •0•2•1•3•Updated Aug 4, 2025Aug 4, 2025

    • aind-mri-targeting

      Public
      Scripts and useful functions to plan neuroscience experiments using structural MRIs
      Python
      •
      MIT License
      •0•0•0•1•Updated Aug 4, 2025Aug 4, 2025

    • Aind.Behavior.GitHubActions

      Public
      A repository with reusable github actions
      aind-behavior
      MIT License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • FIP_DAQ_Control

      Public
      C++
      •
      MIT License
      •0•0•4•1•Updated Aug 4, 2025Aug 4, 2025

    • Aind.Behavior.IsoForce

      Public
      A repository for a joystick task
      C#
      •
      MIT License
      •0•0•2•1•Updated Aug 3, 2025Aug 3, 2025

    • aind-single-plane-ophys-pipeline

      Public
      Nextflow
      •
      MIT License
      •0•1•1•1•Updated Aug 2, 2025Aug 2, 2025

    • thalmanac

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 2, 2025Aug 2, 2025

    • voxel

      Public
      General purpose microscope control repository
      Python
      •
      MIT License
      •4•4•13•0•Updated Aug 2, 2025Aug 2, 2025

    • device-spinner

      Public
      construct python objects from yaml files
      Python
      •
      MIT License
      •0•0•2•0•Updated Aug 1, 2025Aug 1, 2025

    • aind-z1-camera-alignment

      Public
      Code to align spectrally adjacent channels in Zeiss Lightsheet 7 (Z1) datasets
      Python
      •
      MIT License
      •0•0•5•3•Updated Aug 1, 2025Aug 1, 2025

    • AIND-CNC-BCI-Workshop

      Public
      Data and materials for the AIND - CNC Workshop held May 14, 2025 and the CoNectome Neurohackathon May 16-18
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Aug 1, 2025Aug 1, 2025

    • aind-spot-spectral-unmixing

      Public
      A capsule library for spectrally unmixing spots detected in multichannel lightsheet miscroscopy experiments.
      Python
      •
      MIT License
      •0•0•1•0•Updated Aug 1, 2025Aug 1, 2025

    • aind-smartspim-quantification

      Public
      Takes the output of segmentation and ccf registration to calculate cell counts per brain region
      Python
      •
      MIT License
      •2•1•4•0•Updated Aug 1, 2025Aug 1, 2025