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:
ome_zarr info 6001240.zarr/
view
Use the ome_zarr command to view Zarr data in the https://ome.github.io/ome-ngff-validator:
ome_zarr view 6001240.zarr/
download
To download all the resolutions and metadata for an image use ome_zarr download. This creates 6001240.zarr locally:
ome_zarr download https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/6001240.zarr/
Specify a different 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 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 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