{ "cells": [ { "cell_type": "markdown", "id": "ce6594c1-702f-4724-b190-5370e7396d3e", "metadata": {}, "source": [ "# CytoTable mise en place\n", "\n", "This notebook includes a quick demonstration of CytoTable to help you understand the basics of using this project.\n", "\n", "The name of the notebook comes from the french _mise en place_:\n", "> \"Mise en place (French pronunciation: [mi zɑ̃ ˈplas]) is a French culinary phrase which means \"putting in place\"\n", "> or \"gather\". It refers to the setup required before cooking, and is often used in professional kitchens to\n", "> refer to organizing and arranging the ingredients ...\"\n", "> - [Wikipedia](https://en.wikipedia.org/wiki/Mise_en_place)" ] }, { "cell_type": "code", "execution_count": 1, "id": "c529e38f-8784-4a17-955b-06ea0b2375ce", "metadata": {}, "outputs": [], "source": [ "import pathlib\n", "from collections import Counter\n", "\n", "import pyarrow.parquet as pq\n", "\n", "import cytotable\n", "\n", "# setup variables for use throughout the notebook\n", "source_path = \"../../../tests/data/cellprofiler/examplehuman\"\n", "dest_path = \"./example.parquet\"" ] }, { "cell_type": "code", "execution_count": 2, "id": "c6e14f33-1c7a-437f-9a0f-9cda7e1620b2", "metadata": {}, "outputs": [], "source": [ "# remove the dest_path if it's present\n", "if pathlib.Path(dest_path).is_file():\n", " pathlib.Path(dest_path).unlink()" ] }, { "cell_type": "code", "execution_count": 3, "id": "d45b25f0-c115-4f95-8521-addc45bb8a90", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "[PosixPath('../../../tests/data/cellprofiler/examplehuman/Experiment.csv'),\n", " PosixPath('../../../tests/data/cellprofiler/examplehuman/PH3.csv'),\n", " PosixPath('../../../tests/data/cellprofiler/examplehuman/Cytoplasm.csv'),\n", " PosixPath('../../../tests/data/cellprofiler/examplehuman/Image.csv'),\n", " PosixPath('../../../tests/data/cellprofiler/examplehuman/Nuclei.csv'),\n", " PosixPath('../../../tests/data/cellprofiler/examplehuman/Cells.csv')]" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# show the files we will use as source data with CytoTable\n", "list(pathlib.Path(source_path).glob(\"*.csv\"))" ] }, { "cell_type": "code", "execution_count": 4, "id": "78f1f734-16f5-4957-9aeb-ad421d3d1bae", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "CPU times: user 327 ms, sys: 201 ms, total: 528 ms\n", "Wall time: 22.4 s\n" ] }, { "data": { "text/plain": [ "'example.parquet'" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "%%time\n", "\n", "# run cytotable convert\n", "result = cytotable.convert(\n", " source_path=source_path,\n", " dest_path=dest_path,\n", " # specify a destination data format type\n", " dest_datatype=\"parquet\",\n", " # specify a preset which enables quick use of common input file formats\n", " preset=\"cellprofiler_csv\",\n", ")\n", "result.name" ] }, { "cell_type": "code", "execution_count": 5, "id": "1601b045-2631-46d7-a001-39ae6cfb27fb", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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Metadata_ImageNumberMetadata_Cells_Parent_NucleiMetadata_Cytoplasm_Parent_CellsMetadata_Cytoplasm_Parent_NucleiMetadata_ObjectNumberImage_FileName_DNAImage_FileName_OrigOverlayImage_FileName_PH3Image_FileName_cellbodyCytoplasm_AreaShape_Area...Nuclei_Location_Center_XNuclei_Location_Center_YNuclei_Location_Center_ZNuclei_Location_MaxIntensity_X_DNANuclei_Location_MaxIntensity_X_PH3Nuclei_Location_MaxIntensity_Y_DNANuclei_Location_MaxIntensity_Y_PH3Nuclei_Location_MaxIntensity_Z_DNANuclei_Location_MaxIntensity_Z_PH3Nuclei_Number_Object_Number
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" ], "text/plain": [ " Metadata_ImageNumber Metadata_Cells_Parent_Nuclei \\\n", "0 1 1 \n", "1 1 2 \n", "2 1 3 \n", "3 1 4 \n", "4 1 5 \n", "\n", " Metadata_Cytoplasm_Parent_Cells Metadata_Cytoplasm_Parent_Nuclei \\\n", "0 1 1 \n", "1 2 2 \n", "2 3 3 \n", "3 4 4 \n", "4 5 5 \n", "\n", " Metadata_ObjectNumber Image_FileName_DNA \\\n", "0 1 AS_09125_050116030001_D03f00d0.tif \n", "1 2 AS_09125_050116030001_D03f00d0.tif \n", "2 3 AS_09125_050116030001_D03f00d0.tif \n", "3 4 AS_09125_050116030001_D03f00d0.tif \n", "4 5 AS_09125_050116030001_D03f00d0.tif \n", "\n", " Image_FileName_OrigOverlay \\\n", "0 AS_09125_050116030001_D03f00d0_Overlay.png \n", "1 AS_09125_050116030001_D03f00d0_Overlay.png \n", "2 AS_09125_050116030001_D03f00d0_Overlay.png \n", "3 AS_09125_050116030001_D03f00d0_Overlay.png \n", "4 AS_09125_050116030001_D03f00d0_Overlay.png \n", "\n", " Image_FileName_PH3 Image_FileName_cellbody \\\n", "0 AS_09125_050116030001_D03f00d1.tif AS_09125_050116030001_D03f00d2.tif \n", "1 AS_09125_050116030001_D03f00d1.tif AS_09125_050116030001_D03f00d2.tif \n", "2 AS_09125_050116030001_D03f00d1.tif AS_09125_050116030001_D03f00d2.tif \n", "3 AS_09125_050116030001_D03f00d1.tif AS_09125_050116030001_D03f00d2.tif \n", "4 AS_09125_050116030001_D03f00d1.tif AS_09125_050116030001_D03f00d2.tif \n", "\n", " Cytoplasm_AreaShape_Area ... Nuclei_Location_Center_X \\\n", "0 288 ... 477.099237 \n", "1 256 ... 495.750000 \n", "2 52 ... 438.959184 \n", "3 466 ... 80.459184 \n", "4 296 ... 58.423077 \n", "\n", " Nuclei_Location_Center_Y Nuclei_Location_Center_Z \\\n", "0 7.580153 0 \n", "1 11.098684 0 \n", "2 11.374150 0 \n", "3 11.163265 0 \n", "4 15.509615 0 \n", "\n", " Nuclei_Location_MaxIntensity_X_DNA Nuclei_Location_MaxIntensity_X_PH3 \\\n", "0 477.0 478.0 \n", "1 495.0 502.0 \n", "2 440.0 439.0 \n", "3 80.0 81.0 \n", "4 62.0 52.0 \n", "\n", " Nuclei_Location_MaxIntensity_Y_DNA Nuclei_Location_MaxIntensity_Y_PH3 \\\n", "0 8.0 13.0 \n", "1 9.0 14.0 \n", "2 11.0 16.0 \n", "3 13.0 10.0 \n", "4 14.0 15.0 \n", "\n", " Nuclei_Location_MaxIntensity_Z_DNA Nuclei_Location_MaxIntensity_Z_PH3 \\\n", "0 0.0 0.0 \n", "1 0.0 0.0 \n", "2 0.0 0.0 \n", "3 0.0 0.0 \n", "4 0.0 0.0 \n", "\n", " Nuclei_Number_Object_Number \n", "0 1 \n", "1 2 \n", "2 3 \n", "3 4 \n", "4 5 \n", "\n", "[5 rows x 312 columns]" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# show the table head using pandas\n", "pq.read_table(source=result).to_pandas().head()" ] }, { "cell_type": "code", "execution_count": 6, "id": "5b11b6ac-e8e9-4640-b2ae-53234c83ee8c", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "\n", " created_by: parquet-cpp-arrow version 20.0.0\n", " num_columns: 312\n", " num_rows: 289\n", " num_row_groups: 1\n", " format_version: 2.6\n", " serialized_size: 87762" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# show metadata for the result file\n", "pq.read_metadata(result)" ] }, { "cell_type": "code", "execution_count": 7, "id": "b7956459-a258-4a25-90b1-b47b5f0b6778", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{b'data-producer': b'https://github.com/cytomining/CytoTable',\n", " b'data-producer-version': b'0.0.15.post15.dev0+c2a924c'}" ] }, "execution_count": 7, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# show schema metadata which includes CytoTable information\n", "# note: this information will travel with the file.\n", "pq.read_schema(result).metadata" ] }, { "cell_type": "code", "execution_count": 8, "id": "23eb97cf-eff4-4a00-94f3-24526b5f76d6", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Column name prefix counts:\n" ] }, { "data": { "text/plain": [ "{'Metadata': 5, 'Image': 4, 'Cytoplasm': 99, 'Cells': 101, 'Nuclei': 103}" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# show schema column name summaries\n", "print(\"Column name prefix counts:\")\n", "dict(Counter(w.split(\"_\", 1)[0] for w in pq.read_schema(result).names))" ] }, { "cell_type": "code", "execution_count": 9, "id": "1a2812ed-877d-40e0-a4bf-ea4d8f4f129e", "metadata": {}, "outputs": [ { "data": { "text/plain": [ "Metadata_ImageNumber: int64\n", "Metadata_Cells_Parent_Nuclei: int64\n", "Metadata_Cytoplasm_Parent_Cells: int64\n", "Metadata_Cytoplasm_Parent_Nuclei: int64\n", "Metadata_ObjectNumber: int64\n", "Image_FileName_DNA: string\n", "Image_FileName_OrigOverlay: string\n", "Image_FileName_PH3: string\n", "Image_FileName_cellbody: string\n", "Cytoplasm_AreaShape_Area: int64\n", "Cytoplasm_AreaShape_BoundingBoxArea: int64\n", "Cytoplasm_AreaShape_BoundingBoxMaximum_X: int64\n", "Cytoplasm_AreaShape_BoundingBoxMaximum_Y: int64\n", "Cytoplasm_AreaShape_BoundingBoxMinimum_X: int64\n", "Cytoplasm_AreaShape_BoundingBoxMinimum_Y: int64\n", "Cytoplasm_AreaShape_Center_X: double\n", "Cytoplasm_AreaShape_Center_Y: double\n", "Cytoplasm_AreaShape_Compactness: double\n", "Cytoplasm_AreaShape_Eccentricity: double\n", "Cytoplasm_AreaShape_EquivalentDiameter: double\n", "Cytoplasm_AreaShape_EulerNumber: int64\n", "Cytoplasm_AreaShape_Extent: double\n", "Cytoplasm_AreaShape_FormFactor: double\n", "Cytoplasm_AreaShape_MajorAxisLength: double\n", "Cytoplasm_AreaShape_MaxFeretDiameter: double\n", "Cytoplasm_AreaShape_MaximumRadius: double\n", "Cytoplasm_AreaShape_MeanRadius: double\n", "Cytoplasm_AreaShape_MedianRadius: double\n", "Cytoplasm_AreaShape_MinFeretDiameter: double\n", "Cytoplasm_AreaShape_MinorAxisLength: double\n", "Cytoplasm_AreaShape_Orientation: double\n", "Cytoplasm_AreaShape_Perimeter: double\n", "Cytoplasm_AreaShape_Solidity: double\n", "Cytoplasm_AreaShape_Zernike_0_0: double\n", "Cytoplasm_AreaShape_Zernike_1_1: double\n", "Cytoplasm_AreaShape_Zernike_2_0: double\n", "Cytoplasm_AreaShape_Zernike_2_2: double\n", "Cytoplasm_AreaShape_Zernike_3_1: double\n", "Cytoplasm_AreaShape_Zernike_3_3: double\n", "Cytoplasm_AreaShape_Zernike_4_0: double\n", "Cytoplasm_AreaShape_Zernike_4_2: double\n", "Cytoplasm_AreaShape_Zernike_4_4: double\n", "Cytoplasm_AreaShape_Zernike_5_1: double\n", "Cytoplasm_AreaShape_Zernike_5_3: double\n", "Cytoplasm_AreaShape_Zernike_5_5: double\n", "Cytoplasm_AreaShape_Zernike_6_0: double\n", "Cytoplasm_AreaShape_Zernike_6_2: double\n", "Cytoplasm_AreaShape_Zernike_6_4: double\n", "Cytoplasm_AreaShape_Zernike_6_6: double\n", "Cytoplasm_AreaShape_Zernike_7_1: double\n", "Cytoplasm_AreaShape_Zernike_7_3: double\n", "Cytoplasm_AreaShape_Zernike_7_5: double\n", "Cytoplasm_AreaShape_Zernike_7_7: double\n", "Cytoplasm_AreaShape_Zernike_8_0: double\n", "Cytoplasm_AreaShape_Zernike_8_2: double\n", "Cytoplasm_AreaShape_Zernike_8_4: double\n", "Cytoplasm_AreaShape_Zernike_8_6: double\n", "Cytoplasm_AreaShape_Zernike_8_8: double\n", "Cytoplasm_AreaShape_Zernike_9_1: double\n", "Cytoplasm_AreaShape_Zernike_9_3: double\n", "Cytoplasm_AreaShape_Zernike_9_5: double\n", "Cytoplasm_AreaShape_Zernike_9_7: double\n", "Cytoplasm_AreaShape_Zernike_9_9: double\n", "Cytoplasm_Intensity_IntegratedIntensityEdge_DNA: double\n", "Cytoplasm_Intensity_IntegratedIntensityEdge_PH3: double\n", "Cytoplasm_Intensity_IntegratedIntensity_DNA: double\n", "Cytoplasm_Intensity_IntegratedIntensity_PH3: double\n", "Cytoplasm_Intensity_LowerQuartileIntensity_DNA: double\n", "Cytoplasm_Intensity_LowerQuartileIntensity_PH3: double\n", "Cytoplasm_Intensity_MADIntensity_DNA: double\n", "Cytoplasm_Intensity_MADIntensity_PH3: double\n", "Cytoplasm_Intensity_MassDisplacement_DNA: double\n", "Cytoplasm_Intensity_MassDisplacement_PH3: double\n", "Cytoplasm_Intensity_MaxIntensityEdge_DNA: double\n", "Cytoplasm_Intensity_MaxIntensityEdge_PH3: double\n", "Cytoplasm_Intensity_MaxIntensity_DNA: double\n", "Cytoplasm_Intensity_MaxIntensity_PH3: double\n", "Cytoplasm_Intensity_MeanIntensityEdge_DNA: double\n", "Cytoplasm_Intensity_MeanIntensityEdge_PH3: double\n", "Cytoplasm_Intensity_MeanIntensity_DNA: double\n", "Cytoplasm_Intensity_MeanIntensity_PH3: double\n", "Cytoplasm_Intensity_MedianIntensity_DNA: double\n", "Cytoplasm_Intensity_MedianIntensity_PH3: double\n", "Cytoplasm_Intensity_MinIntensityEdge_DNA: double\n", "Cytoplasm_Intensity_MinIntensityEdge_PH3: double\n", "Cytoplasm_Intensity_MinIntensity_DNA: double\n", "Cytoplasm_Intensity_MinIntensity_PH3: double\n", "Cytoplasm_Intensity_StdIntensityEdge_DNA: double\n", "Cytoplasm_Intensity_StdIntensityEdge_PH3: double\n", "Cytoplasm_Intensity_StdIntensity_DNA: double\n", "Cytoplasm_Intensity_StdIntensity_PH3: double\n", "Cytoplasm_Intensity_UpperQuartileIntensity_DNA: double\n", "Cytoplasm_Intensity_UpperQuartileIntensity_PH3: double\n", "Cytoplasm_Location_CenterMassIntensity_X_DNA: double\n", "Cytoplasm_Location_CenterMassIntensity_X_PH3: double\n", "Cytoplasm_Location_CenterMassIntensity_Y_DNA: double\n", "Cytoplasm_Location_CenterMassIntensity_Y_PH3: double\n", "Cytoplasm_Location_CenterMassIntensity_Z_DNA: double\n", "Cytoplasm_Location_CenterMassIntensity_Z_PH3: double\n", "Cytoplasm_Location_Center_X: double\n", "Cytoplasm_Location_Center_Y: double\n", "Cytoplasm_Location_MaxIntensity_X_DNA: double\n", "Cytoplasm_Location_MaxIntensity_X_PH3: double\n", "Cytoplasm_Location_MaxIntensity_Y_DNA: double\n", "Cytoplasm_Location_MaxIntensity_Y_PH3: double\n", "Cytoplasm_Location_MaxIntensity_Z_DNA: double\n", "Cytoplasm_Location_MaxIntensity_Z_PH3: double\n", "Cytoplasm_Number_Object_Number: int64\n", "Cells_AreaShape_Area: int64\n", "Cells_AreaShape_BoundingBoxArea: int64\n", "Cells_AreaShape_BoundingBoxMaximum_X: int64\n", "Cells_AreaShape_BoundingBoxMaximum_Y: int64\n", "Cells_AreaShape_BoundingBoxMinimum_X: int64\n", "Cells_AreaShape_BoundingBoxMinimum_Y: int64\n", "Cells_AreaShape_Center_X: double\n", "Cells_AreaShape_Center_Y: double\n", "Cells_AreaShape_Compactness: double\n", "Cells_AreaShape_Eccentricity: double\n", "Cells_AreaShape_EquivalentDiameter: double\n", "Cells_AreaShape_EulerNumber: int64\n", "Cells_AreaShape_Extent: double\n", "Cells_AreaShape_FormFactor: double\n", "Cells_AreaShape_MajorAxisLength: double\n", "Cells_AreaShape_MaxFeretDiameter: double\n", "Cells_AreaShape_MaximumRadius: double\n", "Cells_AreaShape_MeanRadius: double\n", "Cells_AreaShape_MedianRadius: double\n", "Cells_AreaShape_MinFeretDiameter: double\n", "Cells_AreaShape_MinorAxisLength: double\n", "Cells_AreaShape_Orientation: double\n", "Cells_AreaShape_Perimeter: double\n", "Cells_AreaShape_Solidity: double\n", "Cells_AreaShape_Zernike_0_0: double\n", "Cells_AreaShape_Zernike_1_1: double\n", "Cells_AreaShape_Zernike_2_0: double\n", "Cells_AreaShape_Zernike_2_2: double\n", "Cells_AreaShape_Zernike_3_1: double\n", "Cells_AreaShape_Zernike_3_3: double\n", "Cells_AreaShape_Zernike_4_0: double\n", "Cells_AreaShape_Zernike_4_2: double\n", "Cells_AreaShape_Zernike_4_4: double\n", "Cells_AreaShape_Zernike_5_1: double\n", "Cells_AreaShape_Zernike_5_3: double\n", "Cells_AreaShape_Zernike_5_5: double\n", "Cells_AreaShape_Zernike_6_0: double\n", "Cells_AreaShape_Zernike_6_2: double\n", "Cells_AreaShape_Zernike_6_4: double\n", "Cells_AreaShape_Zernike_6_6: double\n", "Cells_AreaShape_Zernike_7_1: double\n", "Cells_AreaShape_Zernike_7_3: double\n", "Cells_AreaShape_Zernike_7_5: double\n", "Cells_AreaShape_Zernike_7_7: double\n", "Cells_AreaShape_Zernike_8_0: double\n", "Cells_AreaShape_Zernike_8_2: double\n", "Cells_AreaShape_Zernike_8_4: double\n", "Cells_AreaShape_Zernike_8_6: double\n", "Cells_AreaShape_Zernike_8_8: double\n", "Cells_AreaShape_Zernike_9_1: double\n", "Cells_AreaShape_Zernike_9_3: double\n", "Cells_AreaShape_Zernike_9_5: double\n", "Cells_AreaShape_Zernike_9_7: double\n", "Cells_AreaShape_Zernike_9_9: double\n", "Cells_Children_Cytoplasm_Count: int64\n", "Cells_Intensity_IntegratedIntensityEdge_DNA: double\n", "Cells_Intensity_IntegratedIntensityEdge_PH3: double\n", "Cells_Intensity_IntegratedIntensity_DNA: double\n", "Cells_Intensity_IntegratedIntensity_PH3: double\n", "Cells_Intensity_LowerQuartileIntensity_DNA: double\n", "Cells_Intensity_LowerQuartileIntensity_PH3: double\n", "Cells_Intensity_MADIntensity_DNA: double\n", "Cells_Intensity_MADIntensity_PH3: double\n", "Cells_Intensity_MassDisplacement_DNA: double\n", "Cells_Intensity_MassDisplacement_PH3: double\n", "Cells_Intensity_MaxIntensityEdge_DNA: double\n", "Cells_Intensity_MaxIntensityEdge_PH3: double\n", "Cells_Intensity_MaxIntensity_DNA: double\n", "Cells_Intensity_MaxIntensity_PH3: double\n", "Cells_Intensity_MeanIntensityEdge_DNA: double\n", "Cells_Intensity_MeanIntensityEdge_PH3: double\n", "Cells_Intensity_MeanIntensity_DNA: double\n", "Cells_Intensity_MeanIntensity_PH3: double\n", "Cells_Intensity_MedianIntensity_DNA: double\n", "Cells_Intensity_MedianIntensity_PH3: double\n", "Cells_Intensity_MinIntensityEdge_DNA: double\n", "Cells_Intensity_MinIntensityEdge_PH3: double\n", "Cells_Intensity_MinIntensity_DNA: double\n", "Cells_Intensity_MinIntensity_PH3: double\n", "Cells_Intensity_StdIntensityEdge_DNA: double\n", "Cells_Intensity_StdIntensityEdge_PH3: double\n", "Cells_Intensity_StdIntensity_DNA: double\n", "Cells_Intensity_StdIntensity_PH3: double\n", "Cells_Intensity_UpperQuartileIntensity_DNA: double\n", "Cells_Intensity_UpperQuartileIntensity_PH3: double\n", "Cells_Location_CenterMassIntensity_X_DNA: double\n", "Cells_Location_CenterMassIntensity_X_PH3: double\n", "Cells_Location_CenterMassIntensity_Y_DNA: double\n", "Cells_Location_CenterMassIntensity_Y_PH3: double\n", "Cells_Location_CenterMassIntensity_Z_DNA: double\n", "Cells_Location_CenterMassIntensity_Z_PH3: double\n", "Cells_Location_Center_X: double\n", "Cells_Location_Center_Y: double\n", "Cells_Location_Center_Z: int64\n", "Cells_Location_MaxIntensity_X_DNA: double\n", "Cells_Location_MaxIntensity_X_PH3: double\n", "Cells_Location_MaxIntensity_Y_DNA: double\n", "Cells_Location_MaxIntensity_Y_PH3: double\n", "Cells_Location_MaxIntensity_Z_DNA: double\n", "Cells_Location_MaxIntensity_Z_PH3: double\n", "Cells_Number_Object_Number: int64\n", "Nuclei_AreaShape_Area: int64\n", "Nuclei_AreaShape_BoundingBoxArea: int64\n", "Nuclei_AreaShape_BoundingBoxMaximum_X: int64\n", "Nuclei_AreaShape_BoundingBoxMaximum_Y: int64\n", "Nuclei_AreaShape_BoundingBoxMinimum_X: int64\n", "Nuclei_AreaShape_BoundingBoxMinimum_Y: int64\n", "Nuclei_AreaShape_Center_X: double\n", "Nuclei_AreaShape_Center_Y: double\n", "Nuclei_AreaShape_Compactness: double\n", "Nuclei_AreaShape_Eccentricity: double\n", "Nuclei_AreaShape_EquivalentDiameter: double\n", "Nuclei_AreaShape_EulerNumber: int64\n", "Nuclei_AreaShape_Extent: double\n", "Nuclei_AreaShape_FormFactor: double\n", "Nuclei_AreaShape_MajorAxisLength: double\n", "Nuclei_AreaShape_MaxFeretDiameter: double\n", "Nuclei_AreaShape_MaximumRadius: double\n", "Nuclei_AreaShape_MeanRadius: double\n", "Nuclei_AreaShape_MedianRadius: double\n", "Nuclei_AreaShape_MinFeretDiameter: double\n", "Nuclei_AreaShape_MinorAxisLength: double\n", "Nuclei_AreaShape_Orientation: double\n", "Nuclei_AreaShape_Perimeter: double\n", "Nuclei_AreaShape_Solidity: double\n", "Nuclei_AreaShape_Zernike_0_0: double\n", "Nuclei_AreaShape_Zernike_1_1: double\n", "Nuclei_AreaShape_Zernike_2_0: double\n", "Nuclei_AreaShape_Zernike_2_2: double\n", "Nuclei_AreaShape_Zernike_3_1: double\n", "Nuclei_AreaShape_Zernike_3_3: double\n", "Nuclei_AreaShape_Zernike_4_0: double\n", "Nuclei_AreaShape_Zernike_4_2: double\n", "Nuclei_AreaShape_Zernike_4_4: double\n", "Nuclei_AreaShape_Zernike_5_1: double\n", "Nuclei_AreaShape_Zernike_5_3: double\n", "Nuclei_AreaShape_Zernike_5_5: double\n", "Nuclei_AreaShape_Zernike_6_0: double\n", "Nuclei_AreaShape_Zernike_6_2: double\n", "Nuclei_AreaShape_Zernike_6_4: double\n", "Nuclei_AreaShape_Zernike_6_6: double\n", "Nuclei_AreaShape_Zernike_7_1: double\n", "Nuclei_AreaShape_Zernike_7_3: double\n", "Nuclei_AreaShape_Zernike_7_5: double\n", "Nuclei_AreaShape_Zernike_7_7: double\n", "Nuclei_AreaShape_Zernike_8_0: double\n", "Nuclei_AreaShape_Zernike_8_2: double\n", "Nuclei_AreaShape_Zernike_8_4: double\n", "Nuclei_AreaShape_Zernike_8_6: double\n", "Nuclei_AreaShape_Zernike_8_8: double\n", "Nuclei_AreaShape_Zernike_9_1: double\n", "Nuclei_AreaShape_Zernike_9_3: double\n", "Nuclei_AreaShape_Zernike_9_5: double\n", "Nuclei_AreaShape_Zernike_9_7: double\n", "Nuclei_AreaShape_Zernike_9_9: double\n", "Nuclei_Children_Cells_Count: int64\n", "Nuclei_Children_Cytoplasm_Count: int64\n", "Nuclei_Children_PH3_Count: int64\n", "Nuclei_Intensity_IntegratedIntensityEdge_DNA: double\n", "Nuclei_Intensity_IntegratedIntensityEdge_PH3: double\n", "Nuclei_Intensity_IntegratedIntensity_DNA: double\n", "Nuclei_Intensity_IntegratedIntensity_PH3: double\n", "Nuclei_Intensity_LowerQuartileIntensity_DNA: double\n", "Nuclei_Intensity_LowerQuartileIntensity_PH3: double\n", "Nuclei_Intensity_MADIntensity_DNA: double\n", "Nuclei_Intensity_MADIntensity_PH3: double\n", "Nuclei_Intensity_MassDisplacement_DNA: double\n", "Nuclei_Intensity_MassDisplacement_PH3: double\n", "Nuclei_Intensity_MaxIntensityEdge_DNA: double\n", "Nuclei_Intensity_MaxIntensityEdge_PH3: double\n", "Nuclei_Intensity_MaxIntensity_DNA: double\n", "Nuclei_Intensity_MaxIntensity_PH3: double\n", "Nuclei_Intensity_MeanIntensityEdge_DNA: double\n", "Nuclei_Intensity_MeanIntensityEdge_PH3: double\n", "Nuclei_Intensity_MeanIntensity_DNA: double\n", "Nuclei_Intensity_MeanIntensity_PH3: double\n", "Nuclei_Intensity_MedianIntensity_DNA: double\n", "Nuclei_Intensity_MedianIntensity_PH3: double\n", "Nuclei_Intensity_MinIntensityEdge_DNA: double\n", "Nuclei_Intensity_MinIntensityEdge_PH3: double\n", "Nuclei_Intensity_MinIntensity_DNA: double\n", "Nuclei_Intensity_MinIntensity_PH3: double\n", "Nuclei_Intensity_StdIntensityEdge_DNA: double\n", "Nuclei_Intensity_StdIntensityEdge_PH3: double\n", "Nuclei_Intensity_StdIntensity_DNA: double\n", "Nuclei_Intensity_StdIntensity_PH3: double\n", "Nuclei_Intensity_UpperQuartileIntensity_DNA: double\n", "Nuclei_Intensity_UpperQuartileIntensity_PH3: double\n", "Nuclei_Location_CenterMassIntensity_X_DNA: double\n", "Nuclei_Location_CenterMassIntensity_X_PH3: double\n", "Nuclei_Location_CenterMassIntensity_Y_DNA: double\n", "Nuclei_Location_CenterMassIntensity_Y_PH3: double\n", "Nuclei_Location_CenterMassIntensity_Z_DNA: double\n", "Nuclei_Location_CenterMassIntensity_Z_PH3: double\n", "Nuclei_Location_Center_X: double\n", "Nuclei_Location_Center_Y: double\n", "Nuclei_Location_Center_Z: int64\n", "Nuclei_Location_MaxIntensity_X_DNA: double\n", "Nuclei_Location_MaxIntensity_X_PH3: double\n", "Nuclei_Location_MaxIntensity_Y_DNA: double\n", "Nuclei_Location_MaxIntensity_Y_PH3: double\n", "Nuclei_Location_MaxIntensity_Z_DNA: double\n", "Nuclei_Location_MaxIntensity_Z_PH3: double\n", "Nuclei_Number_Object_Number: int64\n", "-- schema metadata --\n", "data-producer: 'https://github.com/cytomining/CytoTable'\n", "data-producer-version: '0.0.15.post15.dev0+c2a924c'" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# show full schema details\n", "pq.read_schema(result)" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.16" } }, "nbformat": 4, "nbformat_minor": 5 }