hoa-tools 1.0__py3-none-any.whl

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_complete-upper-lobe_26.38um_bm05.json

@@ -0,0 +1,208 @@
+{
+  "name": "FO-20-129_lung_left_upper_lobe_complete-upper-lobe_26.38um_bm05",
+  "dataset_type": "overview",
+  "voi": "complete-upper-lobe",
+  "data": {
+    "shape": [3629, 2724, 5413],
+    "voxel_size_um": 26.38,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/FO-20-129/lung-left_upper_lobe/26.38um_complete-upper-lobe_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "left_upper_lobe",
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": null,
+    "stabilisation_medium": null,
+    "degassing_method": null,
+    "scan_solvent": null,
+    "scan_solvent_concentration": null,
+    "scan_temperature": "room temperature"
+  },
+  "donor": {
+    "id": "FO-20-129",
+    "age": 54,
+    "sex": "M",
+    "weight": null,
+    "height": null,
+    "cause_of_death": "Covid",
+    "date_of_death": null,
+    "medical_history": "21 days after hospitalisation, mechanical ventilation, pulmonary failure, renal failure,bacterial pneumonia with Klebsiella aerogenes, general brain edema, subarachnoidal and intracranial bleeding",
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-06-02",
+    "beamline": "BM05",
+    "energy": 74.0,
+    "current_start": 200.0,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 0,
+    "n_dark": 400,
+    "latency_time": null,
+    "exposure_time": 0.15,
+    "subframe_time": null,
+    "n_subframes": 5,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 68,
+    "acquisition": "half",
+    "z_step": -2.25,
+    "scan_time": 540.0,
+    "filters": [
+      "Al 3.5mm",
+      "Glassy carbon 135mm rods 27x5mm",
+      "Glassy carbon 48mm rods 12x4mm"
+    ],
+    "scintillator": "LuAG:Ce 2000um",
+    "optic": "DZoom",
+    "optic_magnification": 0.24,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3675.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": 172,
+    "sensor_roi_y_size": 172,
+    "sensor_binning": null,
+    "pixel_size": 26.38,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1252",
+    "title": "Multiscale Quantification of Covid-19's impact on lung vasculature from whole lobe to alveolar/microvascular scales",
+    "proposers": [
+      "Peter Lee",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Maximilian Ackermann",
+      "Mark P. Kuhnel",
+      "Elodie Boller",
+      "Willi Wagner"
+    ]
+  },
+  "registration": null,
+  "citation": {
+    "title": "Overview at 26.38um of the lung of donor FO-20-129, scanned at ESRF on beamline BM05.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "first_name": "Claire",
+        "last_name": "Walsh",
+        "orcid": "0000-0003-3769-3392",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "first_name": "Danny",
+        "last_name": "Jonigk",
+        "orcid": "0000-0002-5251-2281",
+        "roles": ["Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "David",
+        "last_name": "Stansby",
+        "orcid": "0000-0002-1365-1908",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Elodie",
+        "last_name": "Boller",
+        "orcid": null,
+        "roles": ["Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Guillaume",
+        "last_name": "Gaisne",
+        "orcid": "0000-0002-3401-7930",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Hector",
+        "last_name": "Dejea I Velardo",
+        "orcid": "0000-0003-2584-9812",
+        "roles": ["Data curation", "Investigation"]
+      },
+      {
+        "first_name": "Joanna",
+        "last_name": "Purzycka",
+        "orcid": "0000-0001-8742-5279",
+        "roles": ["Data curation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Mark",
+        "last_name": "P. Kuhnel",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Paul",
+        "last_name": "Tafforeau",
+        "orcid": "0000-0002-5962-1683",
+        "roles": [
+          "Conceptualization",
+          "Data curation",
+          "Funding acquisition",
+          "Investigation"
+        ]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Willi",
+        "last_name": "Wagner",
+        "orcid": null,
+        "roles": ["Funding acquisition", "Investigation"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-571998188",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Mark P. Kuhnel",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "0.9"
+}

hoa_tools/data/metadata/metadata/FO-20-129_lung_right_upper_lobe_core-biopsy_2.25um_bm05.json

@@ -0,0 +1,204 @@
+{
+  "name": "FO-20-129_lung_right_upper_lobe_core-biopsy_2.25um_bm05",
+  "dataset_type": "zoom",
+  "voi": "core-biopsy",
+  "data": {
+    "shape": [3621, 3621, 6291],
+    "voxel_size_um": 2.25,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/FO-20-129/lung-right_upper_lobe/2.25um_core-biopsy_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "right_upper_lobe",
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": null,
+    "stabilisation_medium": null,
+    "degassing_method": null,
+    "scan_solvent": null,
+    "scan_solvent_concentration": null,
+    "scan_temperature": "room temperature"
+  },
+  "donor": {
+    "id": "FO-20-129",
+    "age": 54,
+    "sex": "M",
+    "weight": null,
+    "height": null,
+    "cause_of_death": "Covid",
+    "date_of_death": null,
+    "medical_history": "21 days after hospitalisation, mechanical ventilation, pulmonary failure, renal failure,bacterial pneumonia with Klebsiella aerogenes, general brain edema, subarachnoidal and intracranial bleeding",
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-05-20",
+    "beamline": "BM05",
+    "energy": 44.0,
+    "current_start": 200.0,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 0,
+    "n_dark": 400,
+    "latency_time": 0.002,
+    "exposure_time": 0.025,
+    "subframe_time": null,
+    "n_subframes": 3,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 11,
+    "acquisition": "half",
+    "z_step": 2.2,
+    "scan_time": 552.0,
+    "filters": ["Al 1mm", "SiO2 12mm rods 3x4mm"],
+    "scintillator": "LuAG:Ce 100um, lead glass meniscus",
+    "optic": "Hasselblad tandem optic 100mm/300mm",
+    "optic_magnification": 3.0,
+    "distance_source_sample": null,
+    "distance_sample_detector": 605.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": 2048,
+    "sensor_roi_y_size": 2048,
+    "sensor_binning": null,
+    "pixel_size": 2.25,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1252",
+    "title": "Multiscale Quantification of Covid-19's impact on lung vasculature from whole lobe to alveolar/microvascular scales",
+    "proposers": [
+      "Peter Lee",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Maximilian Ackermann",
+      "Mark P. Kuhnel",
+      "Elodie Boller",
+      "Willi Wagner"
+    ]
+  },
+  "registration": null,
+  "citation": {
+    "title": "Zoom (core-biopsy) at 2.25um of the lung of donor FO-20-129, scanned at ESRF on beamline BM05.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "first_name": "Claire",
+        "last_name": "Walsh",
+        "orcid": "0000-0003-3769-3392",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "first_name": "Danny",
+        "last_name": "Jonigk",
+        "orcid": "0000-0002-5251-2281",
+        "roles": ["Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "David",
+        "last_name": "Stansby",
+        "orcid": "0000-0002-1365-1908",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Elodie",
+        "last_name": "Boller",
+        "orcid": null,
+        "roles": ["Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Guillaume",
+        "last_name": "Gaisne",
+        "orcid": "0000-0002-3401-7930",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Hector",
+        "last_name": "Dejea I Velardo",
+        "orcid": "0000-0003-2584-9812",
+        "roles": ["Data curation", "Investigation"]
+      },
+      {
+        "first_name": "Joanna",
+        "last_name": "Purzycka",
+        "orcid": "0000-0001-8742-5279",
+        "roles": ["Data curation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Mark",
+        "last_name": "P. Kuhnel",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Paul",
+        "last_name": "Tafforeau",
+        "orcid": "0000-0002-5962-1683",
+        "roles": [
+          "Conceptualization",
+          "Data curation",
+          "Funding acquisition",
+          "Investigation"
+        ]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Willi",
+        "last_name": "Wagner",
+        "orcid": null,
+        "roles": ["Funding acquisition", "Investigation"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-578823778",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Mark P. Kuhnel",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "0.9"
+}

hoa_tools/data/metadata/metadata/GLR-163_lung_right_lower_lobe_core-biopsy_2.45um_bm05.json

@@ -0,0 +1,204 @@
+{
+  "name": "GLR-163_lung_right_lower_lobe_core-biopsy_2.45um_bm05",
+  "dataset_type": "zoom",
+  "voi": "core-biopsy",
+  "data": {
+    "shape": [3893, 3893, 4141],
+    "voxel_size_um": 2.45,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/GLR-163/lung-right_lower_lobe/2.45um_core-biopsy_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "right_lower_lobe",
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": null,
+    "stabilisation_medium": null,
+    "degassing_method": null,
+    "scan_solvent": null,
+    "scan_solvent_concentration": null,
+    "scan_temperature": "room temperature"
+  },
+  "donor": {
+    "id": "GLR-163",
+    "age": 77,
+    "sex": "M",
+    "weight": null,
+    "height": null,
+    "cause_of_death": null,
+    "date_of_death": null,
+    "medical_history": "resection of the lower lobe segment 6 due to small pulmonary adenocarcinoma (1.4 cm), coronary heart disease, chronic rheumatic disease (polymyalgia rheumatica)",
+    "diabetes": null,
+    "hypertension": "Yes",
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-07-25",
+    "beamline": "BM05",
+    "energy": 83.0,
+    "current_start": 192.01,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 41,
+    "n_dark": 40,
+    "latency_time": 0.0005,
+    "exposure_time": 0.08,
+    "subframe_time": null,
+    "n_subframes": null,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": null,
+    "filters": null,
+    "scintillator": null,
+    "optic": null,
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 1500.0,
+    "sensor_name": null,
+    "sensor_mode": "FFM",
+    "sensor_roi_x_size": 2048,
+    "sensor_roi_y_size": 2048,
+    "sensor_binning": null,
+    "pixel_size": 2.45,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1252",
+    "title": "Multiscale Quantification of Covid-19's impact on lung vasculature from whole lobe to alveolar/microvascular scales",
+    "proposers": [
+      "Peter Lee",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Maximilian Ackermann",
+      "Mark P. Kuhnel",
+      "Elodie Boller",
+      "Willi Wagner"
+    ]
+  },
+  "registration": null,
+  "citation": {
+    "title": "Zoom (core-biopsy) at 2.45um of the lung of donor GLR-163, scanned at ESRF on beamline BM05.",
+    "contributors": [
+      {
+        "first_name": "The",
+        "last_name": "Human Organ Atlas Collaboration",
+        "orcid": null,
+        "roles": []
+      },
+      {
+        "first_name": "Claire",
+        "last_name": "Walsh",
+        "orcid": "0000-0003-3769-3392",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "first_name": "Danny",
+        "last_name": "Jonigk",
+        "orcid": "0000-0002-5251-2281",
+        "roles": ["Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "David",
+        "last_name": "Stansby",
+        "orcid": "0000-0002-1365-1908",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Elodie",
+        "last_name": "Boller",
+        "orcid": null,
+        "roles": ["Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Guillaume",
+        "last_name": "Gaisne",
+        "orcid": "0000-0002-3401-7930",
+        "roles": ["Data curation", "Software"]
+      },
+      {
+        "first_name": "Hector",
+        "last_name": "Dejea I Velardo",
+        "orcid": "0000-0003-2584-9812",
+        "roles": ["Data curation", "Investigation"]
+      },
+      {
+        "first_name": "Joanna",
+        "last_name": "Purzycka",
+        "orcid": "0000-0001-8742-5279",
+        "roles": ["Data curation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Mark",
+        "last_name": "P. Kuhnel",
+        "orcid": null,
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Maximilian",
+        "last_name": "Ackermann",
+        "orcid": "0000-0001-9996-2477",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Paul",
+        "last_name": "Tafforeau",
+        "orcid": "0000-0002-5962-1683",
+        "roles": [
+          "Conceptualization",
+          "Data curation",
+          "Funding acquisition",
+          "Investigation"
+        ]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Willi",
+        "last_name": "Wagner",
+        "orcid": null,
+        "roles": ["Funding acquisition", "Investigation"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-574369994",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Mark P. Kuhnel",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "0.9"
+}