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    254 repositories

    • lamf_analysis_lims

      Public
      Dev site for testing analysis pipelines and qc for learning mFISH project. Anything related to 2p data (plus behavior and spatial transcriptomics)
      Jupyter Notebook
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • aind-slims-api

      Public
      AIND-specific access to data stored in SLIMS
      Python
      •
      MIT License
      •1•0•3•2•Updated Oct 2, 2024Oct 2, 2024

    • aind-metadata-upgrader

      Public
      Upgrade JSON metadata from old versions of aind-data-schema
      Python
      •
      MIT License
      •0•1•4•2•Updated Oct 2, 2024Oct 2, 2024

    • harp.device.treadmill-driver

      Public
      a Harp-compatible device for controlling an instrumented mouse treadmill
      harp
      Jupyter Notebook
      •0•1•11•1•Updated Oct 2, 2024Oct 2, 2024

    • aind-data-schema

      Public
      A library that defines AIND data schema and validates JSON.
      aind-core-services
      Python
      •
      MIT License
      •15•19•35•6•Updated Oct 1, 2024Oct 1, 2024

    • parallax

      Public
      GUI control software for the Modular Insertion System (MIS)
      processingacquisitionunder-development
      Python
      •
      MIT License
      •1•5•0•2•Updated Oct 1, 2024Oct 1, 2024

    • aind-metadata-mapper

      Public
      Repository to help gather and map metadata from different sources
      aind-core-services
      Python
      •
      MIT License
      •2•0•15•3•Updated Oct 1, 2024Oct 1, 2024

    • nmcp-deploy

      Public
      Shell
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • Aind.Behavior.Services

      Public
      C#
      •
      MIT License
      •0•0•21•2•Updated Oct 1, 2024Oct 1, 2024

    • harp.core.rp2040

      Public
      A Harp core implementation on the RP2040
      harp
      C++
      •
      MIT License
      •0•3•17•0•Updated Oct 1, 2024Oct 1, 2024

    • aind-ophys-motion-correction

      Public
      Python
      •
      MIT License
      •0•1•5•1•Updated Oct 1, 2024Oct 1, 2024

    • aind-ophys-extraction-suite2p

      Public
      Combines cellpose and suite2p to extract sources, i.e. ROIs and their traces.
      Python
      •
      MIT License
      •0•0•3•0•Updated Oct 1, 2024Oct 1, 2024

    • dynamic-foraging-task

      Public
      Bonsai/Harp workflow for Dynamic Foraging with Python GUI for visualization and control
      Python
      •
      MIT License
      •4•5•70•1•Updated Oct 1, 2024Oct 1, 2024

    • lightsheet-denoising-tests

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • voxel

      Public
      General purpose microscope control repository
      Python
      •
      MIT License
      •2•3•13•3•Updated Oct 1, 2024Oct 1, 2024

    • exaspim-control

      Public
      Python
      •
      MIT License
      •0•1•3•1•Updated Oct 1, 2024Oct 1, 2024

    • thalamus-merfish-analysis

      Public
      Code Ocean capsule for sharing analysis of thalamus MERFISH data
      Jupyter Notebook
      •
      MIT License
      •1•2•2•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-smartspim-flatfield-estimation

      Public
      Performs large-scale flatfield correction using zarr format
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-single-plane-ophys-pipeline

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-ophys-oasis-event-detection

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-ophys-dff

      Public
      Python
      •
      MIT License
      •0•0•1•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-smartspim-pipeline

      Public
      Repository that hosts the SmartSPIM pipeline code
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Sep 30, 2024Sep 30, 2024

    • 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
      Jupyter Notebook
      •
      MIT License
      •0•1•20•4•Updated Sep 30, 2024Sep 30, 2024

    • NWB-Ecephys-DANDI-Upload

      Public
      Capsule for uploading Ecephys NWBs to DANDI
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • harp.device.lickety-split

      Public
      an ephys-compliant capacitive lick detector
      harp
      C++
      •
      MIT License
      •0•0•16•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-data-transfer-models

      Public
      Repository for data models used in aind-data-transfer-service
      Python
      •
      MIT License
      •0•0•3•1•Updated Sep 30, 2024Sep 30, 2024

    • Bonsai.AllenNeuralDynamics

      Public
      A Bonsai package for version control and manipulation of Git repositories
      C#
      •
      Other
      •0•0•16•5•Updated Sep 30, 2024Sep 30, 2024

    • metadata-chatbot

      Public
      LLM (Anthropic Claude) based chatbot that can query, ingest and summarize metadata in a conversational form
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • NWB_Packaging_Ecephys_Capsule

      Public
      Code Ocean capsule to create an NWB file for Neuropixels data
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • aind-watchdog-service

      Public
      Data staging service that prepares acquistion data for cloud upload to Amazon S3 and Code Ocean processing.
      Python
      •
      MIT License
      •0•2•16•3•Updated Sep 30, 2024Sep 30, 2024