---
tags: NGFF
---

# OMEZarrReader & OMERO import

Background: see also recent Tuesday presentation from Kevin for an alternate workflow (ZarrPixelBuffer)

## Specification & sample data

- [Specification](ngff.openmicroscopy.org/0.4/)
- Sample data
- https://www.openmicroscopy.org/2021/12/16/ome-ngff.html
- https://www.openmicroscopy.org/2020/12/01/zarr-hcs.html
- https://www.openmicroscopy.org/2020/11/04/zarr-data.html
- https://github.com/ome/ome-ngff-prototypes#data-availability
- Data access in testing systems
- Mirrored under /uod/idr/repos/curated/unsupported/ome-ngff on UoD GPFS (except idr0044) idr2-slot3
- organized by version, then provenance (idr vs embl)
- Todos
- rationalization of sample layout/scheme
- DOIs?

## OMEZarrReader & OMERO integration

- Bio-Formats reader [OMEZarrReader](https://github.com/ome/ZarrReader/):
- Maintained externally of the main Bio-Formats repository i.e. tagged independently
- Declared in main Bio-Formats readers.txt
- BSD-2 licensed,
- Usable in Command-line tools, ImageJ plugin, OMERO...
- Features
- Support for OME-NGFF specification up to 0.4
- includes 2D-5D, HCS
- labels ignored
- OMERO.server lib/client, lib/server include OMEZarrReader
- (/home/omero/workspace/OMERO-server/OMERO.server/lib/server)

## Import workflow

- Using UoD merge-c Idr2-slot3 (merge-ci)
- Import options
- In-place: --transfer=ln_s --skip=checksum
- --parallel-upload
- --depth
- --skip=minmax

## Working examples

- 0.3 spec: idr0095A
- 0.4 spec: embl samples

## Limitations

- Zarr
- Depth
- Name
- [HCS validation errors](https://github.com/ome/ZarrReader/issues/22)
- [Incorrect handling of images with labels](https://github.com/ome/ZarrReader/issues/18)