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MicheleBortolMicheleBortol
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Made Polylux output coordinates integers.
1 parent 79bacfa commit c640569

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Lines changed: 7 additions & 4 deletions

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‎xenium_ROI_extractor.py‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -96,7 +96,7 @@ def get_arguments():
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# Read image
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print(f"Reading Maximum Projection Image File: {mip_tiff_file_path}")
99-
image = tiffile.imread(mip_tiff_file_path)
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image = tifffile.imread(mip_tiff_file_path)
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os.makedirs(ouptut_folder, exist_ok = True)
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@@ -137,6 +137,9 @@ def get_arguments():
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# Make transcript table for reding with the Polylux viewer (Resolve Biosciences)
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polylux_tx = sub_transcripts[["x_location_px_ROI", "y_location_px_ROI", "z_location_px", "feature_name", "qv"]]
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polylux_tx["x_location_px_ROI"] = polylux_tx["x_location_px_ROI"].astype(np.int32)
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polylux_tx["y_location_px_ROI"] = polylux_tx["y_location_px_ROI"].astype(np.int32)
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polylux_tx["z_location_px"] = polylux_tx["z_location_px"].astype(np.int32)
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# Output
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print(f"Writing {roi_string}")
@@ -161,15 +164,15 @@ def get_arguments():
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f_to_write.create_dataset("name", data=feature_h5["features"]["name"])
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# Write other output
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tiffile.imwrite(os.path.join(subfolder, roi_string + "-morphology_mip.ome.tif"), data = sub_image, ome = True, compression = "lzw")
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tifffile.imwrite(os.path.join(subfolder, roi_string + "-morphology_mip.ome.tif"), data = sub_image, ome = True, compression = "lzw")
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sub_transcripts.to_parquet(os.path.join(subfolder, roi_string + "-transcritps.parquet"))
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sub_transcripts.to_csv(os.path.join(subfolder, roi_string + "-transcritps.csv"))
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polylux_tx.to_csv(os.path.join(subfolder, roi_string + "-Polylux_transcritps.tsv"), header = None, index = False, sep = "\t")
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polylux_tx.to_csv(os.path.join(subfolder, roi_string + "-Polylux_transcritps.txt"), header = None, index = False, sep = "\t")
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sub_cells.to_parquet(os.path.join(subfolder, roi_string + "-cells.parquet"))
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sub_cells.to_csv(os.path.join(subfolder, roi_string + "-cells.csv"))
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sub_cell_boundaries.to_parquet(os.path.join(subfolder, roi_string + "-cell_boundaries.parquet"))
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sub_cell_boundaries.to_csv(os.path.join(subfolder, roi_string + "-cell_boundaries.csv"))
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sub_features.to_csv(os.path.join(subfolder, roi_string + "-feature_matrix.csv"))
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tiffile.imwrite(os.path.join(subfolder, roi_string + "-xenium_cell_mask.ome.tif"), data = cell_mask, ome = True, compression = "lzw")
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tifffile.imwrite(os.path.join(subfolder, roi_string + "-xenium_cell_mask.ome.tif"), data = cell_mask, ome = True, compression = "lzw")
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