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    318 repositories

    • easifish-spots-tools

      Public
      Various tools used by EASI-FISH pipeline for processing spots
      Python
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • easifish

      Public
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•1•0•Updated Apr 24, 2026Apr 24, 2026

    • napari-worm

      Public
      3D Cell Annotation Tool for C. elegans using Napari
      Python
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • BigStitcher-Spark

      Public
      Running compute-intense parts of BigStitcher distributed
      Java
      •
      BSD 2-Clause "Simplified" License
      •18•30•19•2•Updated Apr 24, 2026Apr 24, 2026

    • ephys-pipeline

      Public
      Pipeline to process electrophysiology data.
      Python
      •0•0•6•0•Updated Apr 24, 2026Apr 24, 2026

    • cryoet-ai

      Public
      Python
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • precompute-dashboard

      Public
      NeuronBridge precompute dashboard
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • pppm-website

      Public
      PatchPerPix Match website
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • DatasetGateway

      Public
      Unified authorization service for datasets (Connectomics)
      Python
      •0•0•0•0•Updated Apr 24, 2026Apr 24, 2026

    • fileglancer

      Public
      Browse, share, and publish OME-Zarr data
      microscopyimagingzarr
      microscopyimagingzarrngffome-zarrome-ngff
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •4•25•1•8•Updated Apr 23, 2026Apr 23, 2026

    • EM_recon_pipeline

      Public
      Pipeline scripts and tools for reconstructing Electron Microscopy volumes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•0•8•Updated Apr 23, 2026Apr 23, 2026

    • neuronbridge

      Public
      EM/LM neuron search
      awsneuroscienceneuroimaging
      awsneuroscienceneuroimagingneuronsdrosophilajanelia
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•17•Updated Apr 23, 2026Apr 23, 2026

    • containers

      Public
      Containers for workflow plugins
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Apr 23, 2026Apr 23, 2026

    • ReiserFlyDiscoSettings

      Public
      Settings folder for Reiser Lab
      Shell
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • janelia-unity-toolkit

      Public
      Packages for the Unity game engine, emphasizing animal studies in VR.
      C#
      •
      Other
      •13•19•7•3•Updated Apr 22, 2026Apr 22, 2026

    • BigStitcher

      Public
      ImgLib2/BDV implementation of Stitching for large datasets
      Java
      •
      GNU General Public License v2.0
      •17•80•91•2•Updated Apr 22, 2026Apr 22, 2026

    • dis-utilities

      Public
      Utilities for Data and Information Services
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•14•1•Updated Apr 22, 2026Apr 22, 2026

    • tensorswitch

      Public
      This package provides a unified entry point and organized task modules for managing N5/Zarr dataset conversions and downsampling. It centralizes your workflow i…
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•4•0•0•Updated Apr 22, 2026Apr 22, 2026

    • cellpose-tools

      Public
      Python code for the nf-cellpose pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • bigstream

      Public
      Tools for distributed alignment of massive images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •25•95•13•3•Updated Apr 22, 2026Apr 22, 2026

    • zarr-tools

      Public
      Zarr tools used by various nextflow modules
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 22, 2026Apr 22, 2026

    • multiview-reconstruction

      Public
      Software for the reconstruction of multi-view microscopic acquisitions like Selective Plane Illumination Microscopy (SPIM) Data
      Java
      •
      GNU General Public License v2.0
      •25•33•30•6•Updated Apr 21, 2026Apr 21, 2026

    • zarrcade

      Public
      Create web-based OME-Zarr galleries
      webappmicroscopy-imagesome-zarr
      webappmicroscopy-imagesome-zarr
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•23•1•0•Updated Apr 21, 2026Apr 21, 2026

    • neuronbridge-precompute

      Public
      Utilities for indexing and transferring of NeuronBridge-related files
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • neuronbridge-data

      Public
      Versioned NeuronBridge data files deployed to S3 buckets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 21, 2026Apr 21, 2026

    • UInt12Arrays.jl

      Public
      Julia package for supporting arrays of 12-bit integers
      Julia
      •
      Other
      •0•9•1•1•Updated Apr 20, 2026Apr 20, 2026

    • videoAnnotation

      Public
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Apr 20, 2026Apr 20, 2026

    • doi_common

      Public
      Library of common DOI-related functions for Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 20, 2026Apr 20, 2026

    • ShroffCelegansModels.jl

      Public
      Julia
      •
      MIT License
      •1•3•0•43•Updated Apr 18, 2026Apr 18, 2026

    • hortacloud-website

      Public
      Documentation website for HortaCloud
      neurosciencejaneliahortacloud
      neurosciencejaneliahortacloud
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•4•Updated Apr 15, 2026Apr 15, 2026
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