OME-Zarr Creation¶

This is a minimal example of how to create an OME-Zarr image using ngio.

This example is just a simple demonstration but for more complex conversion tasks please refer to the converter tooling library ome-zarr-converters-tools.

Let's start by converting a sample image from skimage to OME-Zarr format.

In [1]:

import skimage
from matplotlib import pyplot as plt

plt.imshow(skimage.data.human_mitosis(), cmap="gray")
plt.axis("off")
plt.show()

import skimage from matplotlib import pyplot as plt plt.imshow(skimage.data.human_mitosis(), cmap="gray") plt.axis("off") plt.show()

Downloading file 'data/mitosis.tif' from 'https://gitlab.com/scikit-image/data/-/raw/2cdc5ce89b334d28f06a58c9f0ca21aa6992a5ba/AS_09125_050116030001_D03f00d0.tif' to '/home/runner/.cache/scikit-image/0.25.2'.

In [2]:

from ngio import create_ome_zarr_from_array

ome_zarr = create_ome_zarr_from_array(
    store="./data/human_mitosis.zarr",
    array=skimage.data.human_mitosis(),
    xy_pixelsize=0.1,  # Just a guess
)
ome_zarr

from ngio import create_ome_zarr_from_array ome_zarr = create_ome_zarr_from_array( store="./data/human_mitosis.zarr", array=skimage.data.human_mitosis(), xy_pixelsize=0.1, # Just a guess ) ome_zarr

Out[2]:

OmeZarrContainer(levels=5)

Adding Rois to OME-Zarr¶

Often, is useful to add ROIs to OME-Zarr images to be able to retrieve them later.
This can be done using the ngio library as follows.

In [3]:

# create a roi for the whole image
roi_table = ome_zarr.build_image_roi_table(name="image_roi")
ome_zarr.add_table("image_roi_table", roi_table)

# create a roi for the whole image roi_table = ome_zarr.build_image_roi_table(name="image_roi") ome_zarr.add_table("image_roi_table", roi_table)