HCS exploration¶

Explore a plate and aggregate tables across it.

Open an OME-Zarr plate with ngio, see what it contains, aggregate a table across every image in it, and write the result back to the plate. The last section creates a new empty plate from scratch.

Step 1: show what's in the plate¶

from pathlib import Path

from ngio import open_ome_zarr_plate
from ngio.utils import download_ome_zarr_dataset

# Download the dataset
download_dir = Path("./data").absolute()

hcs_path = download_ome_zarr_dataset("CardiomyocyteTinyMip", download_dir=download_dir)
hcs_zarr = open_ome_zarr_plate(hcs_path)
print(hcs_zarr)
print(f"Rows: {hcs_zarr.rows}, Columns: {hcs_zarr.columns}")

# Get all the images in the plate
print(hcs_zarr.get_images())

Plate([rows x columns] (1 x 1)) Rows: ['B'], Columns: ['03'] {'B/03/0': OmeZarrContainer(levels=5, labels=['nuclei'], #tables=4)}

Step 2: aggregate tables across all images¶

# Aggregate all table across all images
table = hcs_zarr.concatenate_image_tables(name="nuclei")
print(table_html(table.dataframe.head()))

label	area	bbox_area	equivalent_diameter	max_intensity	mean_intensity	min_intensity	standard_deviation_intensity	row	column
1	1360.00	1664.00	13.75	268.00	184.58	125.00	24.50	B	03
2	2464.00	2992.00	16.76	461.00	273.25	132.00	51.79	B	03
3	1968.00	2688.00	15.55	429.00	277.29	143.00	41.82	B	03
4	5120.00	6400.00	21.38	413.00	279.04	118.00	44.38	B	03
5	288.00	352.00	8.19	341.00	243.32	147.00	41.86	B	03

Step 3: save the table in the plate¶

# Save the table in the HCS plate
hcs_zarr.add_table(name="nuclei", table=table, overwrite=True)

# Read the table back for sanity check
print(table_html(hcs_zarr.get_table("nuclei").dataframe.head()))

label	area	bbox_area	equivalent_diameter	max_intensity	mean_intensity	min_intensity	standard_deviation_intensity	row	column
1	1360.00	1664.00	13.75	268.00	184.58	125.00	24.50	B	03
2	2464.00	2992.00	16.76	461.00	273.25	132.00	51.79	B	03
3	1968.00	2688.00	15.55	429.00	277.29	143.00	41.82	B	03
4	5120.00	6400.00	21.38	413.00	279.04	118.00	44.38	B	03
5	288.00	352.00	8.19	341.00	243.32	147.00	41.86	B	03

Step 4: create a new empty plate¶

from ngio import ImageInWellPath, create_empty_plate

test_plate = create_empty_plate(
    store="./data/empty_plate.zarr",
    name="Test Plate",
    images=[
        ImageInWellPath(row="A", column="01", path="0"),
        ImageInWellPath(row="A", column="02", path="0"),
        ImageInWellPath(row="A", column="02", path="1", acquisition_id=1),
    ],
    overwrite=True,
)

print(test_plate)
print(f"Rows: {test_plate.rows}, Columns: {test_plate.columns}")

Plate([rows x columns] (1 x 2)) Rows: ['A'], Columns: ['01', '02']

Next steps¶

HCS plates — the plate API in depth.
HCS API reference — OmeZarrPlate and OmeZarrWell.