Command-line Tool

Open Zarr filesets containing images with associated OME metadata. The examples below use the image at http://idr.openmicroscopy.org/webclient/?show=image-6001240.

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

# ome_zarr -vvv ...

info

Use the ome_zarr command to interrogate Zarr datasets:

# Remote data
$ ome_zarr info https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/

# Local data (after downloading as below)
$ ome_zarr info 6001240.zarr/

view

Use the ome_zarr command to view Zarr data in the https://ome.github.io/ome-ngff-validator:

# Local data (after downloading as below)
$ ome_zarr view 6001240.zarr/

download

To download all the resolutions and metadata for an image:

# creates local 6001240.zarr/
$ ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/

# Specify output directory
$ ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/ --output image_dir

create

To create sample OME-Zarr image from the skimage coins image:

# 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 https://github.com/ome/omero-metadata/) 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.: ` "area#d,label_text#s,Width#l,Height#l" `

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```