OME-Arrow and CytoDataFrame#

This notebook demonstrates how OME-Arrow works in context with CytoDataFrame.

import pyarrow as pa
import pyarrow.parquet as pq
from ome_arrow import OMEArrow

from cytodataframe import CytoDataFrame

# load a tiff using OME Arrow
oa_img = OMEArrow(
    "../../../tests/data/cytotable/JUMP_plate_BR00117006/images/orig/r01c01f01p01-ch2sk1fk1fl1.tiff"
)
oa_img

2D image, single-channel - shape (T=1, C=1, Z=1, Y=1080, X=1080)

../_images/a0d868842f3cff00c872d0f8737d871cac384e0275e8f8d9a84aff71ba47cea5.png

# make a "slice" (crop) from the overall image
oa_img_slice = oa_img.slice(x_min=240, x_max=310, y_min=360, y_max=430)
oa_img_slice

2D image, single-channel - shape (T=1, C=1, Z=1, Y=70, X=70)

../_images/1953b33fe2a1d716303b775b4485bc048789c03113e6c5b4d015b9a53caf2ae0.png

# show the OME Arrow struct
oa_img_slice.data

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# create a pyarrow table for writing the data
table = pa.table(
    {
        # two columns, two values each, both int64 type
        "metadata_1": pa.array([0, 2], type=pa.int64()),
        "feature_1": pa.array([1, 2], type=pa.int64()),
        # add an image column with repeated entries based on the image slice
        "image": pa.repeat(oa_img_slice.data, 2),
    }
)

# write a parquet table
pq.write_table(table, "example.ome.parquet")

# read the parquet table with cytodataframe
# (showing the OME-Arrow image that was written)
CytoDataFrame("example.ome.parquet")

Static snapshot (for non-interactive view)

	metadata_1	feature_1	image
0	0	1
1	2	2

OME-Arrow and CytoDataFrame#

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