hoa-tools 1.0__py3-none-any.whl → 1.0.1b1__py3-none-any.whl

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-06-lower-lobe-basal_6.05um_bm05.json

@@ -1,210 +0,0 @@
-{
-  "name": "LADAF-2020-27_lung_left_VOI-06-lower-lobe-basal_6.05um_bm05",
-  "dataset_type": "zoom",
-  "voi": "VOI-06-lower-lobe-basal",
-  "data": {
-    "shape": [3815, 3815, 8111],
-    "voxel_size_um": 6.05,
-    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/lung-left/6.05um_VOI-06-lower-lobe-basal_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": 89.0,
-    "current_start": 200.0,
-    "filling_mode": null,
-    "n_frames": 6000,
-    "n_ref": 0,
-    "n_dark": 400,
-    "latency_time": 0.015,
-    "exposure_time": 0.06,
-    "subframe_time": null,
-    "n_subframes": 4,
-    "scan_type": "zseries",
-    "scan_range": 360.0,
-    "n_scans": 14,
-    "acquisition": "half",
-    "z_step": 3.5,
-    "scan_time": 420.0,
-    "filters": ["Al 3mm", "SiO2 60mm rods 12x5mm"],
-    "scintillator": "LuAG:Ce 2000um",
-    "optic": "DZoom",
-    "optic_magnification": 1.0,
-    "distance_source_sample": null,
-    "distance_sample_detector": 3475.0,
-    "sensor_name": "PCO edge 4.2 CLHS",
-    "sensor_mode": "rolling shutter",
-    "sensor_roi_x_size": 688,
-    "sensor_roi_y_size": 688,
-    "sensor_binning": null,
-    "pixel_size": 6.05,
-    "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-06-lower-lobe-basal_6.05um_bm05",
-    "target_dataset": "LADAF-2020-27_lung_left_complete-organ_25.08um_bm05",
-    "translation": [1767.3777384511768, 2304.0100366281936, 5756.583391119505],
-    "rotation": -1.6004248928431077,
-    "scale": 0.24122739120392628
-  },
-  "citation": {
-    "title": "Zoom (VOI-06-lower-lobe-basal) at 6.05um 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-572232527",
-    "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/LADAF-2020-27_lung_left_complete-organ_25.08um_bm05.json

@@ -1,204 +0,0 @@
-{
-  "name": "LADAF-2020-27_lung_left_complete-organ_25.08um_bm05",
-  "dataset_type": "overview",
-  "voi": "complete-organ",
-  "data": {
-    "shape": [5984, 5984, 8712],
-    "voxel_size_um": 25.08,
-    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/lung-left/25.08um_complete-organ_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": "2020-07-11",
-    "beamline": "BM05",
-    "energy": 93.0,
-    "current_start": 200.0,
-    "filling_mode": null,
-    "n_frames": 9990,
-    "n_ref": 0,
-    "n_dark": 400,
-    "latency_time": 0.006,
-    "exposure_time": 0.036,
-    "subframe_time": null,
-    "n_subframes": 6,
-    "scan_type": "zseries",
-    "scan_range": 360.0,
-    "n_scans": 196,
-    "acquisition": "quarter",
-    "z_step": 2.2,
-    "scan_time": 420.0,
-    "filters": ["Mo 0.1mm", "Al 2mm", "SiO2 60mm rods 12x5mm"],
-    "scintillator": "LuAG:Ce 2000um",
-    "optic": "DZoom",
-    "optic_magnification": 0.24,
-    "distance_source_sample": null,
-    "distance_sample_detector": 3475.0,
-    "sensor_name": "PCO edge 4.2 CLHS",
-    "sensor_mode": "rolling shutter",
-    "sensor_roi_x_size": 176,
-    "sensor_roi_y_size": 176,
-    "sensor_binning": null,
-    "pixel_size": 25.08,
-    "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 25.08um 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-572196058",
-    "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/LADAF-2020-27_spleen_central-column_1.29um_bm05.json

@@ -1,210 +0,0 @@
-{
-  "name": "LADAF-2020-27_spleen_central-column_1.29um_bm05",
-  "dataset_type": "zoom",
-  "voi": "central-column",
-  "data": {
-    "shape": [3823, 3823, 10982],
-    "voxel_size_um": 1.29,
-    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/spleen/1.29um_central-column_bm05/"
-  },
-  "sample": {
-    "organ": "spleen",
-    "organ_context": null,
-    "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": "2020-07-20",
-    "beamline": "BM05",
-    "energy": 74.0,
-    "current_start": 200.0,
-    "filling_mode": null,
-    "n_frames": 6000,
-    "n_ref": 0,
-    "n_dark": 400,
-    "latency_time": 0.12,
-    "exposure_time": 0.12,
-    "subframe_time": null,
-    "n_subframes": 1,
-    "scan_type": "zseries",
-    "scan_range": 360.0,
-    "n_scans": 10,
-    "acquisition": "half",
-    "z_step": 2.3,
-    "scan_time": 720.0,
-    "filters": ["Mo 0.1mm", "Al 2mm", "SiO2 60mm rods 12x5mm"],
-    "scintillator": "LuAG:Ce 250um",
-    "optic": "Zoom",
-    "optic_magnification": 5.0,
-    "distance_source_sample": null,
-    "distance_sample_detector": 500.0,
-    "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": 1.29,
-    "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_spleen_central-column_1.29um_bm05",
-    "target_dataset": "LADAF-2020-27_spleen_complete-organ_25.08um_bm05",
-    "translation": [933.3984395585187, 1267.3488342319704, 405.53657079063635],
-    "rotation": -0.30002735514589357,
-    "scale": 0.05143542165286007
-  },
-  "citation": {
-    "title": "Zoom (central-column) at 1.29um of the spleen 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-572242562",
-    "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"
-}