Supported Formats

OME-Zarr and beyond. Here is what the viewer opens today, and how.

OME-Zarr

OME-Zarr is the viewer's home format. It opens in place: nothing is converted and nothing is uploaded. New to the format? Why OME-Zarr Is Taking Over Microscopy covers what it is good for.

• OME-NGFF versions 0.3, 0.4, 0.5 and 0.6.
• Zarr v2, uncompressed or compressed with blosc, zlib or gzip.
• Zarr v3, sharded or not, compressed with blosc, zstd, gzip or zlib.
• Single images, and datasets with several series from bioformats2raw.
• HCS plates, with plate, well and field views. See HCS Plates.
• Labels in the image's labels/ group. They load with the image. On a plate, press Discover. See Labels.

How it opens

• A web address. Paste an https:// address. The server must allow CORS. See Remote URLs.
• An s3:// address. Paste s3://bucket/path and the viewer reads the bucket's public https address. A bucket name with a dot works this way in us-east-1. In other regions, paste its regional https address.
• A folder on your disk, in Chrome and Edge. See Local Files.
• A .ozx or .zip archive, in any browser. See A Dataset in a Single File.
• Private data, with a Bearer token or AWS SigV4. See Authenticated Sources.

Local or remote? Your OME-ZARR Storage Setup Is Slowing You Down helps you pick.

Opera Phenix plates

Plates exported by Harmony from an Opera Phenix open straight from their index. The Opera Phenix plates of the Cell Painting Gallery open this way, such as the JUMP Cell Painting pilot plate CPJUMP1.

• What opens: a Harmony index next to its TIFFs: Index.idx.xml (Harmony V5) or Index.xml (Harmony V6).
• From where: an https:// or s3:// address, a folder on your disk, or a saved plate manifest.
• What to point at: the measurement folder, its Images/ folder, or the index itself.
• Field view only. Harmony stores each field at one resolution, so Plate and Well view are off.

See Opera Phenix Plates, and Opera Phenix Plates in the Browser on our blog for a real JUMP plate.

Yokogawa CellVoyager plates

Plates from a Yokogawa CellVoyager CV8000 or CV7000 open straight from their measurement folder. More than 1,000 JUMP Cell Painting plates in the Cell Painting Gallery come from a CellVoyager CV8000 or CV7000 and open this way.

• What opens: MeasurementDetail.mrf, the .mes file it names and MeasurementData.mlf, next to their TIFFs.
• From where: an https:// or s3:// address, or a folder on your disk.
• What to point at: the measurement folder, MeasurementDetail.mrf or MeasurementData.mlf.
• Field view only, and plane 1 of every channel.
• Not yet: folders without MeasurementDetail.mrf, and the Yokogawa CQ1.

See Yokogawa CellVoyager Plates.

Companion data

• Label masks that live outside the image: a Zarr label array from a URL, or from a folder in Chrome and Edge. See Labels.
• Measurements and analysis bundles: a CSV or Parquet table with one row per object, up to a run manifest that lists several masks and tables, all from one URL. A table also opens from your disk in Chrome and Edge. See Analytics Data Format, and HCS Analytics in the Browser for a real screen.
• Plate manifests: a small JSON file that describes an Opera Phenix or Yokogawa CellVoyager plate. Save one from the viewer and open it by URL. The format is a published JSON Schema: plate-manifest/v1.json.

Which browser opens what

What you open	Chrome, Edge	Firefox, Safari
A web address: image, plate, label, table or bundle	Yes	Yes
An s3:// address of an image or plate	Yes	Yes
A dataset zipped into one .ozx or .zip file	Yes	Yes
A folder: OME-Zarr, Opera Phenix plate, Yokogawa CellVoyager plate or label	Yes	No
A measurement table from your disk	Yes	No

Not supported yet

Other vendor formats open after conversion to OME-Zarr. How to Convert Any Microscopy File to OME-Zarr shows how.

Which format should we add next? Tell us at info@find-nuclei.com.