---
# System prepended metadata

title: OMEZarrReader & OMERO import
tags: [NGFF]

---

---
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)