hoa-tools 1.0.1b1__py3-none-any.whl → 1.0.2__py3-none-any.whl

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-B_25.25um_bm05.json

@@ -0,0 +1,205 @@
+{
+  "name": "LADAF-2020-27_lung_left_FSC-B_25.25um_bm05",
+  "dataset_type": "zoom",
+  "voi": "FSC-B",
+  "data": {
+    "shape": [2564, 2005, 247],
+    "voxel_size_um": 25.25,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/lung-left/25.25um_FSC-B_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "left",
+    "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": "LADAF-2020-27",
+    "age": 94,
+    "sex": "F",
+    "weight": 45.0,
+    "height": 140.0,
+    "cause_of_death": null,
+    "date_of_death": "2020-06-11",
+    "medical_history": "right sylvian and right cerebellar stroke, Cognitive disorders of vascular origin, Depressive syndrome, Rhythmic and hypertensive heart disease (AF), Micro-crystalline arthritis (gout), Right lung pneumopathy (3 years before death), Left cataract, Left temporal squamous cell carcinoma.",
+    "diabetes": null,
+    "hypertension": "Yes",
+    "smoker": null
+  },
+  "scan": {
+    "date": "2021-06-04",
+    "beamline": "BM05",
+    "energy": 86.0,
+    "current_start": null,
+    "filling_mode": null,
+    "n_frames": 9990,
+    "n_ref": null,
+    "n_dark": null,
+    "latency_time": 0.005,
+    "exposure_time": 0.005,
+    "subframe_time": null,
+    "n_subframes": 5,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": null,
+    "z_step": null,
+    "scan_time": null,
+    "filters": ["Mo 0.23mm", "Al 2.3mm", "SiO2 120mm rods 24x5mm"],
+    "scintillator": null,
+    "optic": null,
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3475.0,
+    "sensor_name": null,
+    "sensor_mode": null,
+    "sensor_roi_x_size": null,
+    "sensor_roi_y_size": null,
+    "sensor_binning": null,
+    "pixel_size": 25.25,
+    "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": {
+    "source_dataset": "LADAF-2020-27_lung_left_FSC-B_25.25um_bm05",
+    "target_dataset": "LADAF-2020-27_lung_left_complete-organ_25.08um_bm05",
+    "translation": [3102.9459944737982, 4570.164580669598, 7281.21648381264],
+    "rotation": 154.00079118285254,
+    "scale": 1.0067785103184779
+  },
+  "citation": {
+    "title": "Zoom (FSC-B) at 25.25um of the lung of donor LADAF-2020-27, 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"]
+      },
+      {
+        "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"]
+      },
+      {
+        "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"]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "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"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-572221247",
+    "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": "1.0"
+}

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-B_6.5um_bm05.json

@@ -0,0 +1,199 @@
+{
+  "name": "LADAF-2020-27_lung_left_FSC-B_6.5um_bm05",
+  "dataset_type": "zoom",
+  "voi": "FSC-B",
+  "data": {
+    "shape": [2676, 2658, 989],
+    "voxel_size_um": 6.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/lung-left/6.5um_FSC-B_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "left",
+    "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": "LADAF-2020-27",
+    "age": 94,
+    "sex": "F",
+    "weight": 45.0,
+    "height": 140.0,
+    "cause_of_death": null,
+    "date_of_death": "2020-06-11",
+    "medical_history": "right sylvian and right cerebellar stroke, Cognitive disorders of vascular origin, Depressive syndrome, Rhythmic and hypertensive heart disease (AF), Micro-crystalline arthritis (gout), Right lung pneumopathy (3 years before death), Left cataract, Left temporal squamous cell carcinoma.",
+    "diabetes": null,
+    "hypertension": "Yes",
+    "smoker": null
+  },
+  "scan": {
+    "date": "2021-06-04",
+    "beamline": "BM05",
+    "energy": 83.0,
+    "current_start": 199.626,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.0008,
+    "exposure_time": 0.007,
+    "subframe_time": null,
+    "n_subframes": 5,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": 270.0,
+    "filters": ["Al 2.3mm", "Mo 0.23mm", "SiO2 24mm block"],
+    "scintillator": "LuAG:Ce 1000um",
+    "optic": "DZoom",
+    "optic_magnification": 0.941,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3500.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": null,
+    "sensor_roi_x_size": null,
+    "sensor_roi_y_size": null,
+    "sensor_binning": null,
+    "pixel_size": 6.5,
+    "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 (FSC-B) at 6.5um of the lung of donor LADAF-2020-27, 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"]
+      },
+      {
+        "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"]
+      },
+      {
+        "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"]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "Funding acquisition"]
+      },
+      {
+        "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"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-572235527",
+    "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": "1.0"
+}

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_2.45um_bm05.json

@@ -0,0 +1,210 @@
+{
+  "name": "LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_2.45um_bm05",
+  "dataset_type": "zoom",
+  "voi": "VOI-01-upper-lobe-apical",
+  "data": {
+    "shape": [3815, 3815, 3479],
+    "voxel_size_um": 2.45,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/lung-left/2.45um_VOI-01-upper-lobe-apical_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "left",
+    "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": "LADAF-2020-27",
+    "age": 94,
+    "sex": "F",
+    "weight": 45.0,
+    "height": 140.0,
+    "cause_of_death": null,
+    "date_of_death": "2020-06-11",
+    "medical_history": "right sylvian and right cerebellar stroke, Cognitive disorders of vascular origin, Depressive syndrome, Rhythmic and hypertensive heart disease (AF), Micro-crystalline arthritis (gout), Right lung pneumopathy (3 years before death), Left cataract, Left temporal squamous cell carcinoma.",
+    "diabetes": null,
+    "hypertension": "Yes",
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-07-26",
+    "beamline": "BM05",
+    "energy": 79.0,
+    "current_start": 200.0,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 0,
+    "n_dark": 400,
+    "latency_time": 0.05,
+    "exposure_time": 0.15,
+    "subframe_time": null,
+    "n_subframes": 3,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 2,
+    "acquisition": "half",
+    "z_step": 3.5,
+    "scan_time": 978.0,
+    "filters": ["Mo 0.1mm", "SiO2 32mm rods 8x4mm"],
+    "scintillator": "LuAG:Ce 250um",
+    "optic": "Zoom",
+    "optic_magnification": 2.61,
+    "distance_source_sample": null,
+    "distance_sample_detector": 1500.0,
+    "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": 2.45,
+    "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": {
+    "source_dataset": "LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_2.45um_bm05",
+    "target_dataset": "LADAF-2020-27_lung_left_complete-organ_25.08um_bm05",
+    "translation": [2318.4394144810663, 1849.001817582029, 1493.227518704038],
+    "rotation": -3.499779265959912,
+    "scale": 0.0976873880912458
+  },
+  "citation": {
+    "title": "Zoom (VOI-01-upper-lobe-apical) at 2.45um of the lung of donor LADAF-2020-27, 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-572191396",
+    "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": "1.0"
+}