Command-line tool

Open Zarr filesets containing images with associated OME metadata. The examples below use the image at

All examples can be made more or less verbose by passing -v or -q one or more times:

ome_zarr -vvv ...


Use the ome_zarr command to interrogate Zarr datasets.

Remote data:

ome_zarr info

Local data:

ome_zarr info 6001240.zarr/


Use the ome_zarr command to view Zarr data in the

ome_zarr view 6001240.zarr/


To download all the resolutions and metadata for an image use ome_zarr download. This creates 6001240.zarr locally:

ome_zarr download

Specify a different output directory:

ome_zarr download --output image_dir


To create sample OME-Zarr image from the skimage data.

Create an OME-Zarr image in coinsdata/ dir:

ome_zarr create coinsdata

Create an rgb image from skimage astronaut in testimage dir:

ome_zarr create testimage --method=astronaut

csv to labels

The csv_to_labels command uses a CSV file to add key:value properties to labels under an OME-Zarr Image or Plate.

The OME-Zarr labels metadata must already contain a properties list of {key:value} objects, each with a unique key:ID. This key is omero:shapeId in the example below.

This ID can be used to identify a single row of the CSV table by specifying the name of a column with unique values, e.g. shape_id below. This row is used to add additional column_name:value data to the label properties.

You also need to specify which columns from the CSV to use, e.g. “area,X,Y,Width,Height”. You can also specify the column types (as in to specify the data-type for each column (string by default).

  • d: DoubleColumn, for floating point numbers

  • l: LongColumn, for integer numbers

  • s: StringColumn, for text

  • b: BoolColumn, for true/false

Use e.g. #d as a suffix in the column name to denote a float column, no spaces etc.:


For example, to take values from columns named area, label_text, Width and Height within a CSV file named labels_data.csv with an ID column named shape_id and add these values to label properties with an ID key of omero:shapeId in an Image or Plate named 123.zarr:

ome_zarr csv_to_labels labels_data.csv shape_id "area#d,label_text#s,Width#l,Height#l" 123.zarr omero:shapeId