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    301 repositories

    • 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
      •24•31•29•6•Updated Dec 28, 2025Dec 28, 2025

    • dis-utilities

      Public
      Utilities for Data and Information Services
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•14•1•Updated Dec 23, 2025Dec 23, 2025

    • ShroffCelegansModels.jl

      Public
      Julia
      •
      MIT License
      •1•3•0•42•Updated Dec 23, 2025Dec 23, 2025

    • fileglancer

      Public
      Browse, share, and publish OME-Zarr data
      microscopyimagingzarrngffome-zarrome-ngff
      TypeScript
      •
      BSD 3-Clause "New" or "Revised" License
      •2•16•0•5•Updated Dec 23, 2025Dec 23, 2025

    • triton-sam2

      Public
      SAM2 deployed with Triton Inference Server
      Python
      •0•1•0•0•Updated Dec 23, 2025Dec 23, 2025

    • doi_common

      Public
      Library of common DOI-related functions for Python
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 22, 2025Dec 22, 2025

    • ReiserFlyDiscoSettings

      Public
      Settings folder for Reiser Lab
      Shell
      •0•0•0•0•Updated Dec 21, 2025Dec 21, 2025

    • EM_recon_pipeline

      Public
      Pipeline scripts and tools for reconstructing Electron Microscopy volumes.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•3•0•5•Updated Dec 21, 2025Dec 21, 2025

    • bigstream

      Public
      Tools for distributed alignment of massive images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •22•90•13•3•Updated Dec 19, 2025Dec 19, 2025

    • easifish

      Public
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Dec 19, 2025Dec 19, 2025

    • nextflow-modules

      Public
      Nextflow modules for use with nf-core tooling
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Dec 19, 2025Dec 19, 2025

    • nf-cellpose

      Public
      Nextflow pipeline for cellpose segmentation
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • fileglancer-hub

      Public
      Production deployment scripts for Fileglancer
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • Ax2

      Public
      acoustic segmenter
      Julia
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • transfero

      Public
      Python scripts for transferring data from rig computers
      Python
      •0•0•3•0•Updated Dec 19, 2025Dec 19, 2025

    • neuronbridge

      Public
      EM/LM neuron search
      awsneuroscienceneuroimagingneuronsdrosophilajanelia
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•15•Updated Dec 18, 2025Dec 18, 2025

    • neuronbridge-data

      Public
      Versioned NeuronBridge data files deployed to S3 buckets
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • 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 Dec 17, 2025Dec 17, 2025

    • viv

      Public
      Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
      JavaScript
      •
      MIT License
      •57•0•0•0•Updated Dec 17, 2025Dec 17, 2025

    • containers

      Public
      Containers for workflow plugins
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•1•Updated Dec 17, 2025Dec 17, 2025

    • easifish-spots-tools

      Public
      Various tools used by EASI-FISH pipeline for processing spots
      Python
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • cellpose-tools

      Public
      Python code for the nf-cellpose pipeline
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • zarr-tools

      Public
      Zarr tools used by various nextflow modules
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • phase-change

      Public
      archive data to cold storage
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • micropattern_cell_analysis

      Public
      Micropattern Cell Analysis for the Gladkova and Vale Labs
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 15, 2025Dec 15, 2025

    • BigStitcher-Spark

      Public
      Running compute-intense parts of BigStitcher distributed
      Java
      •
      BSD 2-Clause "Simplified" License
      •15•28•18•2•Updated Dec 12, 2025Dec 12, 2025

    • x2s3

      Public
      S3 Proxy Service
      s3s3-buckets3-storage
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•12•0•0•Updated Dec 11, 2025Dec 11, 2025

    • videoAnnotation

      Public
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Dec 11, 2025Dec 11, 2025

    • nf-omezarr

      Public
      Nextflow pipeline for converting images to OME-Zarr using bioformats2raw
      ome-zarr-converter
      Groovy
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Dec 8, 2025Dec 8, 2025

    • janelia-unity-toolkit

      Public
      Packages for the Unity game engine, emphasizing animal studies in VR.
      C#
      •
      Other
      •11•18•6•2•Updated Dec 6, 2025Dec 6, 2025