Repositories list

• nps

  Public
  Simple CLI for point cloud sampling from segmentation volumes

  Python

  •0•2•0•0•Updated Mar 24, 2026Mar 24, 2026

• volara

  Public
  Block-wise operations for large nD volumes

  Python

  •

  MIT License

  •4•45•10•2•Updated Mar 23, 2026Mar 23, 2026

• volara-ml

  Public
  Plugin for volara for torch functionality

  Python

  •1•0•0•0•Updated Mar 23, 2026Mar 23, 2026

• scale_pyramid

  Public
  Script to generate a scale pyramid for zarr/N5 datasets.

  Python

  •

  MIT License

  •3•1•0•0•Updated Feb 19, 2026Feb 19, 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

• prism_training

  Public
  Training scripts and models for Prism paper

  Python

  •3•7•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

• pool-analysis

  Public
  Code for processing and analyzing the Nanopore data of viral pools.

  Jupyter Notebook

  •0•0•4•0•Updated Aug 25, 2025Aug 25, 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

  •24•0•0•0•Updated May 13, 2024May 13, 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

  •42•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