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    21 repositories

    • volara

      Public
      Block-wise operations for large nD volumes
      Python
      •
      MIT License
      •2•45•11•0•Updated Feb 4, 2026Feb 4, 2026

    • nf-BigStitcher-Spark

      Public
      Run BigStitcher-Spark using Nextflow
      Nextflow
      •
      BSD 3-Clause "New" or "Revised" License
      •2•0•0•0•Updated Jan 21, 2026Jan 21, 2026

    • volara-torch

      Public
      Plugin for volara for torch functionality
      Python
      •0•0•0•0•Updated Dec 18, 2025Dec 18, 2025

    • prism_training

      Public
      Training scripts and models for Prism paper
      Python
      •1•6•0•0•Updated Nov 26, 2025Nov 26, 2025

    • SBReadFile22-Python

      Public
      SBReadFile 2022 .sldy (Python)
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •6•0•0•0•Updated Oct 24, 2025Oct 24, 2025

    • Preprint-Barcode-Analysis

      Public
      Intern barcode analysis team doing barcode distribution analysis.
      Jupyter Notebook
      •0•1•4•0•Updated Sep 30, 2025Sep 30, 2025

    • open-data-registry

      Public
      A registry of publicly available datasets on AWS
      Python
      •
      Apache License 2.0
      •1.1k•0•0•0•Updated Sep 22, 2025Sep 22, 2025

    • e11-open-data

      Public
      Jupyter Notebook
      •1•5•0•0•Updated Sep 20, 2025Sep 20, 2025

    • fiji-friends

      Public
      fiji macro scripts and other helpers, as needed
      Jupyter Notebook
      •0•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • combinatorics_dash

      Public
      n choose k options and trends, for calculating ideal math x biological x imaging constraints
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

    • voxelflow

      Public
      Workflow for stitching and registration
      Nextflow
      •0•0•11•1•Updated May 9, 2025May 9, 2025

    • funlib.show.neuroglancer

      Public
      Scripts and helpers for the neuroglancer WebGL viewer.
      Python
      •12•1•0•1•Updated Jan 27, 2025Jan 27, 2025

    • ClusterWrap

      Public
      Wrappers around dask-jobqueue functions for specific clusters
      Python
      •
      MIT License
      •6•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • funlib.persistence

      Public
      Interfaces for data (arrays and graphs) and storage formats (databases and file formats)
      Python
      •
      MIT License
      •12•0•0•0•Updated May 17, 2024May 17, 2024

    • streamline

      Public
      E11 for of BigStream - Tools for distributed alignment of massive images
      Python
      •
      MIT License
      •22•0•0•0•Updated May 13, 2024May 13, 2024

    • scale_pyramid

      Public
      Script to generate a scale pyramid for zarr/N5 datasets.
      Python
      •
      MIT License
      •3•1•0•0•Updated Mar 19, 2024Mar 19, 2024

    • dacapo

      Public
      Python
      •6•0•0•0•Updated Feb 14, 2024Feb 14, 2024

    • pybdv

      Public
      python tools for BigDataViewer
      Python
      •
      MIT License
      •7•0•0•0•Updated Apr 2, 2023Apr 2, 2023

    • lsd

      Public
      🌈
      Python
      •
      MIT License
      •41•0•0•0•Updated Dec 16, 2022Dec 16, 2022

    • well-plate-assay

      Public
      Code for processing well plate assays
      Jupyter Notebook
      •0•0•0•0•Updated Sep 27, 2022Sep 27, 2022

    • funlib.run

      Public
      Python wrapper for submitting jobs via bsub with the option to do so in a container environment.
      Python
      •4•0•0•0•Updated Oct 27, 2021Oct 27, 2021