Repositories list

• jacs-dashboard

  Public
  Dashboard interface for the JACSv2 services ecosystem.

  JavaScript

  •

  MIT License

  •0•0•4•8•Updated Nov 27, 2025Nov 27, 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 Nov 27, 2025Nov 27, 2025

• zarr-tools

  Public
  Zarr tools used by various nextflow modules

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 26, 2025Nov 26, 2025

• neuronbridge

  Public
  EM/LM neuron search

  awsneuroscienceneuroimaging+ 3neuronsdrosophilajanelia

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •1•5•0•13•Updated Nov 26, 2025Nov 26, 2025

• viv-experimental

  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•1•Updated Nov 26, 2025Nov 26, 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•4•Updated Nov 26, 2025Nov 26, 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 Nov 26, 2025Nov 26, 2025

• 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•29•29•6•Updated Nov 26, 2025Nov 26, 2025

• ShroffCelegansModels.jl

  Public
  Julia

  •

  MIT License

  •1•3•0•42•Updated Nov 25, 2025Nov 25, 2025

• fileglancer-docs

  Public
  Fileglancer user documentation site

  MDX

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•2•Updated Nov 25, 2025Nov 25, 2025

• dis-utilities

  Public
  Utilities for Data and Information Services

  JavaScript

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•14•1•Updated Nov 25, 2025Nov 25, 2025

• fileglancer-hub

  Public
  Production deployment scripts for Fileglancer

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 25, 2025Nov 25, 2025

• fileglancer

  Public
  Browse, share, and publish OME-Zarr data

  microscopyimagingzarr+ 3ngffome-zarrome-ngff

  TypeScript

  •

  BSD 3-Clause "New" or "Revised" License

  •2•15•0•1•Updated Nov 25, 2025Nov 25, 2025

• BigStitcher-Spark

  Public
  Running compute-intense parts of BigStitcher distributed

  Java

  •

  BSD 2-Clause "Simplified" License

  •15•28•18•2•Updated Nov 25, 2025Nov 25, 2025

• UInt12Arrays.jl

  Public
  Julia package for supporting arrays of 12-bit integers

  Julia

  •

  Other

  •0•9•1•0•Updated Nov 24, 2025Nov 24, 2025

• n5-zstandard

  Public
  Zstandard Compression for N5

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•0•Updated Nov 24, 2025Nov 24, 2025

• triton-sam2

  Public
  SAM2 deployed with Triton Inference Server

  Python

  •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

• colormipsearch

  Public
  Distributed Color Depth MIP Search

  neurosciencesearch-algorithmneuron

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•2•0•2•Updated Nov 20, 2025Nov 20, 2025

• cellpose-tools

  Public
  Python code for the nf-cellpose pipeline

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 19, 2025Nov 19, 2025

• Ax2

  Public
  acoustic segmenter

  Julia

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•0•Updated Nov 17, 2025Nov 17, 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 Nov 14, 2025Nov 14, 2025

• flycore-utilities

  Public
  Utility programs for synchronization with the Fly Facility's FLYF2 database

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Nov 14, 2025Nov 14, 2025

• easifish

  Public
  Nextflow

  •

  BSD 3-Clause "New" or "Revised" License

  •0•1•0•0•Updated Nov 14, 2025Nov 14, 2025

• containers

  Public
  Containers for workflow plugins

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •0•0•0•1•Updated Nov 13, 2025Nov 13, 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 Nov 12, 2025Nov 12, 2025

• tmt

  Public
  A toolbox of Matlab functions useful for data analysis, especially of electrophysiology data.

  MATLAB

  •1•2•0•0•Updated Nov 11, 2025Nov 11, 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 Nov 11, 2025Nov 11, 2025

• SOFIMA-scripts

  Public
  wrapper to batch jobs to cluster

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Nov 11, 2025Nov 11, 2025

• VVDViewer

  Public
  3D/4D volumetric rendering of microscopy data

  renderingneurosciencemicroscopy+ 1vvd-viewer

  C++

  •

  BSD 3-Clause "New" or "Revised" License

  •6•26•3•1•Updated Nov 10, 2025Nov 10, 2025

• G4_Display_Tools

  Public
  Collection of tools for the G4 LED arena displays.

  MATLAB

  •

  Creative Commons Attribution 4.0 International

  •5•2•12•0•Updated Nov 7, 2025Nov 7, 2025