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Add image data to CytoTable processing #35

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Oct 25, 2024
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Add image data to CytoTable processing #35

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19 changes: 19 additions & 0 deletions 0.download_data/1.process_JUMP_plates_with_CytoTable.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,25 @@
executors=[ThreadPoolExecutor(label="tpe_for_jump_processing")]
),
sort_output=False,
# add a custom join statement to include all image data
# for use during analysis.
joins="""
SELECT
image.*,
cytoplasm.* EXCLUDE (Metadata_ImageNumber),
cells.* EXCLUDE (Metadata_ImageNumber),
nuclei.* EXCLUDE (Metadata_ImageNumber)
FROM
read_parquet('cytoplasm.parquet') AS cytoplasm
LEFT JOIN read_parquet('cells.parquet') AS cells ON
cells.Metadata_ImageNumber = cytoplasm.Metadata_ImageNumber
AND cells.Metadata_ObjectNumber = cytoplasm.Cytoplasm_Parent_Cells
LEFT JOIN read_parquet('nuclei.parquet') AS nuclei ON
nuclei.Metadata_ImageNumber = cytoplasm.Metadata_ImageNumber
AND nuclei.Metadata_ObjectNumber = cytoplasm.Cytoplasm_Parent_Nuclei
LEFT JOIN read_parquet('image.parquet') AS image ON
image.Metadata_ImageNumber = cytoplasm.Metadata_ImageNumber
""",
)

# read only the metadata from parquet file
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