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    662 repositories

    • aind-disrnn-dispatcher

      Public
      Job dispatcher for AIND-disRNN project
      Python
      •
      MIT License
      •0•0•18•0•Updated Jul 12, 2026Jul 12, 2026

    • zombie

      Public
      JavaScript
      •
      MIT License
      •1•0•10•0•Updated Jul 12, 2026Jul 12, 2026

    • aind-disrnn-wrapper

      Public
      Job wrapper for AIND-disRNN project
      Python
      •
      MIT License
      •1•0•7•0•Updated Jul 12, 2026Jul 12, 2026

    • aind-beh-ephys-analysis

      Public
      Jupyter Notebook
      •
      MIT License
      •1•1•12•1•Updated Jul 12, 2026Jul 12, 2026

    • exaspim-flatfield-correction

      Public
      Illumination correction library for large 3D images
      Jupyter Notebook
      •1•3•4•0•Updated Jul 11, 2026Jul 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 t…
      Jupyter Notebook
      •
      MIT License
      •1•1•21•1•Updated Jul 11, 2026Jul 11, 2026

    • voxel

      Public
      General purpose microscope control repository.
      Python
      •
      MIT License
      •0•2•0•0•Updated Jul 11, 2026Jul 11, 2026

    • data-curation-aind-analysis-wrapper

      Public
      Rachel's capsule for data-curation. This serves a wrapper for running analysis functions on input data
      Jupyter Notebook
      •
      MIT License
      •4•0•0•0•Updated Jul 11, 2026Jul 11, 2026

    • aind-dynamic-foraging-basic-analysis

      Public
      compute behavioral metrics and generate basic plottings for the dynamic foraging task
      Python
      •
      MIT License
      •0•1•21•1•Updated Jul 11, 2026Jul 11, 2026

    • posetail

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Jul 11, 2026Jul 11, 2026

    • LC-NE_retrograde_viral_labelling_analyses

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Jul 11, 2026Jul 11, 2026

    • dynamic-foraging-processing

      Public
      A library for opening and processing
      Python
      •
      MIT License
      •0•0•8•2•Updated Jul 11, 2026Jul 11, 2026

    • camstim-behavior-processing

      Public
      Python
      •
      MIT License
      •0•0•2•2•Updated Jul 10, 2026Jul 10, 2026

    • aind-pophys-pipeline

      Public
      2P planar optical physiology processing pipeline
      Nextflow
      •
      MIT License
      •0•0•4•1•Updated Jul 10, 2026Jul 10, 2026

    • aind-fiber-photometry-pipeline

      Public
      Nextflow
      •
      MIT License
      •0•0•13•1•Updated Jul 10, 2026Jul 10, 2026

    • aind-metadata-manager

      Public
      Metadata manager for pipeline to ensure metadata are in derived assets
      Python
      •
      MIT License
      •0•0•5•4•Updated Jul 10, 2026Jul 10, 2026

    • ibl-ephys-alignment-gui

      Public
      Tool for aligning electrophysiological features to anatomical landmarks
      Python
      •
      MIT License
      •19•12•4•2•Updated Jul 10, 2026Jul 10, 2026

    • dynamic-foraging-processing-pipeline

      Public
      Pipeline to process dynamic foraging behavior only data acquired on new standard
      Nextflow
      •0•0•0•0•Updated Jul 10, 2026Jul 10, 2026

    • ophys-mfish-dataset-catalog

      Public
      A version-controlled dataset catalog for ophys-mFISH datasets, with one JSON record per dataset for portable access across workstations. Mainly HCR right now.
      Python
      •0•0•0•0•Updated Jul 10, 2026Jul 10, 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 annotate…
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 10, 2026Jul 10, 2026

    • LCNE_transcriptomics

      Public
      all the transcriptomics analysis for LC-NE paper
      Jupyter Notebook
      •0•0•1•0•Updated Jul 10, 2026Jul 10, 2026

    • aind-ophys-decrosstalk-roi-images

      Public
      Python
      •
      MIT License
      •0•0•10•0•Updated Jul 10, 2026Jul 10, 2026

    • one-liner

      Public
      adapter pattern implemented as zmq client/server
      Python
      •
      MIT License
      •0•2•26•3•Updated Jul 10, 2026Jul 10, 2026

    • aind-dynamic-foraging-data-utils

      Public
      Tools for the analysis of behavior and neural data from the dynamic foraging task
      Python
      •
      MIT License
      •1•2•23•2•Updated Jul 10, 2026Jul 10, 2026

    • LC_H2B_points_to_mesh

      Public
      Python
      •
      MIT License
      •2•0•1•0•Updated Jul 10, 2026Jul 10, 2026

    • Aind.Behavior.DynamicForaging

      Public
      A repository for the Dynamic Foraging task.
      C#
      •
      MIT License
      •0•0•21•3•Updated Jul 10, 2026Jul 10, 2026

    • Aind.Behavior.VrForaging.Packaging

      Public
      A repository to package primary data from Aind.Behavior.VrForaging
      Python
      •
      MIT License
      •0•0•4•0•Updated Jul 10, 2026Jul 10, 2026

    • aind-data-schema

      Public
      A library that defines AIND data schema and validates JSON.
      aind-core-services
      aind-core-services
      Python
      •
      MIT License
      •21•34•56•2•Updated Jul 10, 2026Jul 10, 2026

    • prototome-web-ui

      Public
      TypeScript
      •0•0•10•2•Updated Jul 10, 2026Jul 10, 2026

    • aind-torch-utils

      Public
      Generic, queue-based, multi-GPU PyTorch inference pipeline for large volumetric (3D or 5D T,C,Z,Y,X) data.
      machine-learningcomputer-visionimage-processing
      machine-learningcomputer-visionimage-processingartificial-intelligencescientific-computing
      Python
      •
      MIT License
      •0•3•4•3•Updated Jul 10, 2026Jul 10, 2026
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