In preparation for the International OME-NGFF Workshop in November and as the exclusive commercial partner of the Open Microscopy Environment (OME), Glencoe is publishing its roadmap for NGFF contributions in the upcoming 6 months.

Join us in Zurich this November and at the OME meeting next April to discuss more and hear our updates.

NGFF specification

The NGFF specification continues to evolve. Glencoe plans to make the following contributions by end of Q1 2026:

  • Propose our contribution as an official reviewer of RFC-8 (collections).
  • Define the Long Term Support (LTS) version(s) of the NGFF specification expected to be supported in the Glencoe tools (bioformats2raw, raw2ometiff, OMERO Plus, etc.). Roadmaps for these tools are also outlined below. NGFF specification version 0.4 is currently supported by the latest versions of these tools.
  • Continue to evaluate the impact of proposed RFCs on Glencoe-maintained tools and supported workflows and provide public feedback accordingly.

Bioformats2raw and raw2ometiff

Glencoe Software developed and maintains the reference implementation for OME-Zarr writing and reading, bioformats2raw and raw2ometiff. These are wrapped in the GUI application NGFF-Converter for wider usability. Our customers and the wider OME community rely on these tools for conversion from Bio-Formats-supported file formats into the open standards OME-Zarr and OME-TIFF.

As a part of our commitment to these open source standards, Glencoe Software will:

  • Add support for Zarr v3 in bioformats2raw and raw2ometiff using zarr-java (Q4 2025)
  • Evaluate the switch to zarr-java for reading and writing Zarr v2 and v3 in bioformats2raw and raw2ometiff (Q1 2026)
  • Release bioformats2raw, raw2ometiff, and NGFF-Converter with support for OME-Zarr datasets adhering to the LTS version of the NGFF specification defined above (TBD).

OMERO and OMERO Plus

Glencoe Software delivers scalable data management solutions to some of the world’s largest pharmaceutical, biotechnology, and academic institutions. These solutions are built using OMERO Plus, which maintains the same core as open source OMERO.

OMERO Plus has built-in support for OME-Zarr data in object storage (AWS S3) and more traditional file storage. This includes support for importing and viewing images and labels.

Below are our next steps to extend support for OME-Zarr data following NGFF specification 0.4 in OMERO Plus (planned release in Q4 2025):

  • Images/labels with fewer than 5 dimensions (T, C, Z, Y, and X)
  • Images/labels hosted on public object storage buckets
  • Images/labels hosted on S3-compatible object stores
  • Images/labels with missing chunks

In 2024, Glencoe optimized its implementation of OME-Zarr reading in OMERO Plus and made public its strategy and source code. One proposed topic for the upcoming OME Meeting is to evaluate the inclusion of this implementation into OME’s open source OMERO.server

Other Glencoe tooling surrounding OME-Zarr may also be open sourced in 2026:

  • OME-Zarr Java importer (omero-importer-ngff)
  • Python library, JSON API, and CLI plugin to register, read, and update the location of OME-Zarr labels and images

Get in touch

The Glencoe team is dedicated to maintaining its contributions to the OME ecosystem and participating in the conversations with community members to learn how those contributions could be most impactful. Join us at these upcoming events or reach out to our team with the form below to learn more.