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    335 repositories

    • exaspim-control

      Public
      Python
      •
      MIT License
      •2•1•0•0•Updated Feb 7, 2025Feb 7, 2025

    • dynamic-routing-unit-drift-qc-dashboard

      Public
      Python
      •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • coherent-lasers

      Public
      Python drivers for coherent lasers
      Python
      •
      MIT License
      •2•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • aind-qc-portal

      Public
      Quality control portal
      Python
      •
      MIT License
      •0•1•14•2•Updated Feb 7, 2025Feb 7, 2025

    • dynamicrouting-encoding-fit

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 7, 2025Feb 7, 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
      Jupyter Notebook
      •
      MIT License
      •0•1•21•0•Updated Feb 7, 2025Feb 7, 2025

    • foraging-behavior-browser

      Public
      Foraging behavior browser (streamlit)
      Python
      •
      MIT License
      •2•2•12•0•Updated Feb 7, 2025Feb 7, 2025

    • Aind.Behavior.Services

      Public
      A repository containing code for data acquisition and processing for AIND behavior rigs.
      aind-behavior
      Python
      •
      MIT License
      •0•0•6•1•Updated Feb 7, 2025Feb 7, 2025

    • thalamus-merfish-analysis

      Public
      Code Ocean capsule for sharing analysis of thalamus MERFISH data
      Jupyter Notebook
      •
      MIT License
      •1•2•2•0•Updated Feb 6, 2025Feb 6, 2025

    • harp.device.sniff-detector

      Public
      Signal conditioning board for an implanted thermistor
      harp
      C#
      •
      MIT License
      •0•0•2•0•Updated Feb 6, 2025Feb 6, 2025

    • harp.device.white-rabbit

      Public
      0361: A 16-output Harp clock synchronizer
      harp
      C#
      •0•1•1•0•Updated Feb 6, 2025Feb 6, 2025

    • harp.core.pico

      Public
      A Harp core implementation on the RP2040
      harp
      C++
      •
      MIT License
      •0•4•18•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-multiplane-ophys-pipeline

      Public
      Nextflow
      •
      MIT License
      •0•0•3•1•Updated Feb 6, 2025Feb 6, 2025

    • aind-multiplane-ophys-pipeline-without-splitting

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-exaspim-soma-detection

      Public
      A Python package for detecting somas in ExaSPIM image datasets. Includes tools for image preprocessing and deep learning-based classification and training.
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Feb 6, 2025Feb 6, 2025

    • aind_data_schema_embeddings

      Public
      Embeddings of aind-data-schema codebase for GAMER RAG database
      metadata-chatbot
      Python
      •
      MIT License
      •0•1•0•0•Updated Feb 6, 2025Feb 6, 2025

    • dynamicrouting-encoding-io

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • dynamic-foraging-task

      Public
      Bonsai/Harp workflow for Dynamic Foraging with Python GUI for visualization and control
      Python
      •
      MIT License
      •4•5•103•9•Updated Feb 6, 2025Feb 6, 2025

    • Aind.Behavior.VrForaging

      Public
      Task implemention of VR Foraging experiment
      aind-behavior
      C#
      •
      MIT License
      •0•2•12•0•Updated Feb 6, 2025Feb 6, 2025

    • lc_analysis_demonstration

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-dynamic-foraging-qc

      Public
      Capsule for the QC of the dynamic foraging task
      Python
      •
      MIT License
      •0•0•2•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-fip-qc-raw

      Public
      a capsule to generate QC based on fip raw data asest
      Python
      •
      MIT License
      •0•0•3•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-smartspim-microscope-to-zarr

      Public
      Converts tiff/png stacks of tiles to zarr format.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-units-nwb

      Public
      Code Ocean capsule to export ephys units data to NWB
      Python
      •
      MIT License
      •0•0•2•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-metadata-validator

      Public
      Package to support validation checks for aind-data-schema for export to other services
      Python
      •
      MIT License
      •0•0•5•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-smartspim-pipeline

      Public
      Repository that hosts the SmartSPIM pipeline code
      Nextflow
      •
      MIT License
      •1•2•1•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-smartspim-classification

      Public
      Code for classifying the cell candidate outputs from aind-smartspim-segmentation within smartspim pipeline
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 6, 2025Feb 6, 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 Feb 6, 2025Feb 6, 2025

    • aind-SmartSPIM-segmentation

      Public
      segmentation module for SmartSPIM cloud pipeline
      Python
      •
      MIT License
      •1•2•1•0•Updated Feb 6, 2025Feb 6, 2025

    • aind-ccf-registration

      Public
      Registration of lightsheet whole brain images to the Allen CCF V3 Atlas
      Python
      •
      MIT License
      •4•3•4•0•Updated Feb 6, 2025Feb 6, 2025