Repositories list

• upptime

  Public
  Site monitoring

  uptime-monitorstatus-pageupptime

  uptime-monitorstatus-pageupptime

  Markdown

  •

  MIT License

  •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

• gide-search

  Public
  Search system across multiple biological imaging databases

  Python

  •0•1•1•0•Updated Mar 5, 2026Mar 5, 2026

• bia-integrator

  Public
  Python

  •

  Apache License 2.0

  •4•3•33•9•Updated Mar 5, 2026Mar 5, 2026

• BIA-astro

  Public
  Astro

  •1•1•0•6•Updated Mar 4, 2026Mar 4, 2026

• gide-ro-crate

  Public
  0•0•0•0•Updated Feb 27, 2026Feb 27, 2026

• bia-training

  Public
  BIA training materials

  Jupyter Notebook

  •

  Other

  •2•2•0•0•Updated Feb 9, 2026Feb 9, 2026

• bia-binder

  Public
  Continuous deployment for binderhub at the BioImageArchive

  HTML

  •

  MIT License

  •1•5•14•0•Updated Feb 6, 2026Feb 6, 2026

• bia-ingest-pipeline

  Public
  Pipeline for ingestion of studies into BIA MongoDB and conversion of images to OME-Zarr

  Shell

  •

  Apache License 2.0

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

• bia-zarr

  Public
  Minimal BIA OME-Zarr tools

  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 23, 2026Jan 23, 2026

• bia-agent

  Public
  BioImage Archive local submission assistant

  Python

  •

  Apache License 2.0

  •1•3•1•0•Updated Jan 21, 2026Jan 21, 2026

• bia-ro-crate-examples

  Public
  Examples of BIA ro-crates

  Apache License 2.0

  •0•0•0•0•Updated Jan 13, 2026Jan 13, 2026

• logging-and-monitoring

  Public
  BIA/EMPIAR Logging and Monitoring

  Shell

  •0•0•0•0•Updated Dec 12, 2025Dec 12, 2025

• bia-study-tracker

  Public
  BIA study tracker tracks studies ingested, images converted and sends the report via slack

  Python

  •0•0•0•0•Updated Nov 10, 2025Nov 10, 2025

• empiar-cets

  Public
  For interoperability between EMPIAR and cryoET standards (CETS)

  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Sep 16, 2025Sep 16, 2025

• fastheader

  Public
  Python

  •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

• BIA-ro-crate

  Public
  A CLI tool to convert between BioImage Archive API objects and RO-crate (specifically include those used in the ome-zarr v4 stastandard).

  Python

  •0•1•0•0•Updated Apr 29, 2025Apr 29, 2025

• bia-bmz-integration

  Public
  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•1•Updated Apr 23, 2025Apr 23, 2025

• emfir

  Public
  EMPIAR fast image reader

  Rust

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• bia-treebrowse

  Public
  Tree browser widget for file display

  TypeScript

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• bia-study-stats

  Public
  Python

  •0•0•0•0•Updated Feb 21, 2025Feb 21, 2025

• empiar-study-stats

  Public
  0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• imc-ome-zarr

  Public
  Simple tools for working with IMC data with OME-Zarr

  Python

  •0•0•0•0•Updated Feb 9, 2025Feb 9, 2025

• bia-converter

  Public
  Python

  •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• DToL-processing

  Public
  Code to process DToL-like data using BioSamples

  Jupyter Notebook

  •0•0•0•0•Updated Jan 28, 2025Jan 28, 2025

• ebi-ngff-challenge-samples

  Public
  EBI imaging samples for 2024 OME NGFF challenge

  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• ome2024-ngff-challenge

  Public
  Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data

  Python

  •20•0•0•0•Updated Aug 8, 2024Aug 8, 2024

• bia-converter-deprecated

  Public
  BioImage Archive conversion pipelining software

  Python

  •

  Apache License 2.0

  •0•1•0•0•Updated Jul 4, 2024Jul 4, 2024

• ebi_summer_school

  Public
  0•0•0•0•Updated Jun 17, 2024Jun 17, 2024

• bia-explorer

  Public
  Python package for exploring BIA data

  Jupyter Notebook

  •

  Apache License 2.0

  •2•3•3•1•Updated Jun 13, 2024Jun 13, 2024

• pytorch_tutorial

  Public
  pyTorch demo(s)

  Jupyter Notebook

  •1•6•0•0•Updated Jun 11, 2024Jun 11, 2024