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

hoa_tools/data/metadata/metadata/LADAF-2021-17_heart_ROI-02_6.5um_bm05.json

@@ -1,265 +0,0 @@
-{
-  "name": "LADAF-2021-17_heart_ROI-02_6.5um_bm05",
-  "dataset_type": "zoom",
-  "voi": "ROI-02",
-  "data": {
-    "shape": [3844, 3844, 11600],
-    "voxel_size_um": 6.5,
-    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2021-17/heart/6.5um_ROI-02_bm05/"
-  },
-  "sample": {
-    "organ": "heart",
-    "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-2021-17",
-    "age": 63,
-    "sex": "M",
-    "weight": 60.0,
-    "height": 178.0,
-    "cause_of_death": "Pancreatic cancer",
-    "date_of_death": "2020-03-27",
-    "medical_history": "stomach hypertrophy noticed during autopsy, stomach liquid into the lungs",
-    "diabetes": null,
-    "hypertension": null,
-    "smoker": null
-  },
-  "scan": {
-    "date": "2021-10-09",
-    "beamline": "BM05",
-    "energy": 83.0,
-    "current_start": 194.183,
-    "filling_mode": null,
-    "n_frames": 6000,
-    "n_ref": 1,
-    "n_dark": 0,
-    "latency_time": 0.0015,
-    "exposure_time": 0.01,
-    "subframe_time": null,
-    "n_subframes": 4,
-    "scan_type": "zseries",
-    "scan_range": 360.0,
-    "n_scans": null,
-    "acquisition": "half",
-    "z_step": null,
-    "scan_time": 312.0,
-    "filters": ["Mo 0.24mm", "SiO2 16mm rods 4x4mm"],
-    "scintillator": "LuAG:Ce 1000um",
-    "optic": "DZoom",
-    "optic_magnification": 1.0,
-    "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": "md1290",
-    "title": "Bridging the gap between cellular and whole body imaging using Hierarchical Phase-Contrast Tomography: HiP-CT",
-    "proposers": [
-      "Peter Lee",
-      "Claire Walsh",
-      "Brian Bay",
-      "Elodie Boller",
-      "Maximilian Ackermann",
-      "Alexandre Bellier",
-      "Olivier Palombi",
-      "Paul Tafforeau",
-      "Simon Walker-Samuel",
-      "Philippe Chaffanjon",
-      "Danny Jonigk",
-      "Willi Wagner",
-      "Rebecca Shipley"
-    ]
-  },
-  "registration": {
-    "source_dataset": "LADAF-2021-17_heart_ROI-02_6.5um_bm05",
-    "target_dataset": "LADAF-2021-17_heart_complete-organ_25.08um_bm05",
-    "translation": [2172.985766207824, 2472.6079970770766, 3372.3504794445334],
-    "rotation": 0.9996969981004458,
-    "scale": 0.25917184128180976
-  },
-  "citation": {
-    "title": "Zoom (ROI-02) at 6.5um of the heart of donor LADAF-2021-17, scanned at ESRF on beamline BM05.",
-    "contributors": [
-      {
-        "first_name": "The",
-        "last_name": "Human Organ Atlas Collaboration",
-        "orcid": null,
-        "roles": []
-      },
-      {
-        "first_name": "Alexandre",
-        "last_name": "Bellier",
-        "orcid": "0000-0003-0907-0315",
-        "roles": ["Funding acquisition", "Investigation"]
-      },
-      {
-        "first_name": "Brian",
-        "last_name": "Bay",
-        "orcid": "0000-0002-6870-259X",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Claire",
-        "last_name": "Walsh",
-        "orcid": "0000-0003-3769-3392",
-        "roles": ["Conceptualization", "Funding acquisition", "Investigation"]
-      },
-      {
-        "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": "Maximilian",
-        "last_name": "Ackermann",
-        "orcid": "0000-0001-9996-2477",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Olivier",
-        "last_name": "Palombi",
-        "orcid": null,
-        "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": "Philippe",
-        "last_name": "Chaffanjon",
-        "orcid": null,
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Rebecca",
-        "last_name": "Shipley",
-        "orcid": "0000-0002-2818-6228",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Rui",
-        "last_name": "Xian",
-        "orcid": null,
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Shahrokh",
-        "last_name": "Rahmani",
-        "orcid": "0000-0002-5773-7076",
-        "roles": ["Investigation"]
-      },
-      {
-        "first_name": "Simon",
-        "last_name": "Walker-Samuel",
-        "orcid": "0000-0003-3530-9166",
-        "roles": ["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-1773966233",
-    "author_list": [
-      "The Human Organ Atlas Collaboration",
-      "Alexandre Bellier",
-      "Brian Bay",
-      "Claire Walsh",
-      "Danny Jonigk",
-      "David Stansby",
-      "Elodie Boller",
-      "Guillaume Gaisne",
-      "Hector Dejea I Velardo",
-      "Joanna Purzycka",
-      "Joseph Brunet",
-      "Maximilian Ackermann",
-      "Olivier Palombi",
-      "Paul Tafforeau",
-      "Peter Lee",
-      "Philippe Chaffanjon",
-      "Rebecca Shipley",
-      "Rui Xian",
-      "Shahrokh Rahmani",
-      "Simon Walker-Samuel",
-      "Theresa Urban",
-      "Willi Wagner"
-    ]
-  },
-  "metadata_version": "0.9"
-}

hoa_tools/data/metadata/metadata/LADAF-2021-17_heart_ROI-03_6.36um_bm18.json

@@ -1,246 +0,0 @@
-{
-  "name": "LADAF-2021-17_heart_ROI-03_6.36um_bm18",
-  "dataset_type": "zoom",
-  "voi": "ROI-03",
-  "data": {
-    "shape": [3821, 3821, 8279],
-    "voxel_size_um": 6.36,
-    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2021-17/heart/6.36um_ROI-03_bm18/"
-  },
-  "sample": {
-    "organ": "heart",
-    "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-2021-17",
-    "age": 63,
-    "sex": "M",
-    "weight": 60.0,
-    "height": 178.0,
-    "cause_of_death": "Pancreatic cancer",
-    "date_of_death": "2020-03-27",
-    "medical_history": "stomach hypertrophy noticed during autopsy, stomach liquid into the lungs",
-    "diabetes": null,
-    "hypertension": null,
-    "smoker": null
-  },
-  "scan": {
-    "date": "2022-05-06",
-    "beamline": "BM18",
-    "energy": 103.0,
-    "current_start": 64.386,
-    "filling_mode": null,
-    "n_frames": 6000,
-    "n_ref": 3,
-    "n_dark": 100,
-    "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
-    "n_subframes": 4,
-    "scan_type": "zseries",
-    "scan_range": 360.0,
-    "n_scans": null,
-    "acquisition": "half",
-    "z_step": null,
-    "scan_time": null,
-    "filters": ["Mo 0.21mm"],
-    "scintillator": "LuAG:Ce 2000um",
-    "optic": "DZoom",
-    "optic_magnification": null,
-    "distance_source_sample": null,
-    "distance_sample_detector": 10000.0,
-    "sensor_name": "PCO edge 4.2 CLHS",
-    "sensor_mode": null,
-    "sensor_roi_x_size": 2048,
-    "sensor_roi_y_size": 1696,
-    "sensor_binning": null,
-    "pixel_size": 6.36,
-    "xray_magnification": null,
-    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
-    "experiment_type": "Tomography"
-  },
-  "proposal": {
-    "proposal_number": "md1290",
-    "title": "Bridging the gap between cellular and whole body imaging using Hierarchical Phase-Contrast Tomography: HiP-CT",
-    "proposers": [
-      "Peter Lee",
-      "Claire Walsh",
-      "Brian Bay",
-      "Elodie Boller",
-      "Maximilian Ackermann",
-      "Alexandre Bellier",
-      "Olivier Palombi",
-      "Paul Tafforeau",
-      "Simon Walker-Samuel",
-      "Philippe Chaffanjon",
-      "Danny Jonigk",
-      "Willi Wagner",
-      "Rebecca Shipley"
-    ]
-  },
-  "registration": {
-    "source_dataset": "LADAF-2021-17_heart_ROI-03_6.36um_bm18",
-    "target_dataset": "LADAF-2021-17_heart_complete-organ_25.08um_bm05",
-    "translation": [3249.291442795554, 2246.6437743125866, 1865.206317566279],
-    "rotation": 50.000003859181405,
-    "scale": 0.25358901448745863
-  },
-  "citation": {
-    "title": "Zoom (ROI-03) at 6.36um of the heart of donor LADAF-2021-17, scanned at ESRF on beamline BM18.",
-    "contributors": [
-      {
-        "first_name": "The",
-        "last_name": "Human Organ Atlas Collaboration",
-        "orcid": null,
-        "roles": []
-      },
-      {
-        "first_name": "Alexandre",
-        "last_name": "Bellier",
-        "orcid": "0000-0003-0907-0315",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Brian",
-        "last_name": "Bay",
-        "orcid": "0000-0002-6870-259X",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "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": "Maximilian",
-        "last_name": "Ackermann",
-        "orcid": "0000-0001-9996-2477",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Olivier",
-        "last_name": "Palombi",
-        "orcid": null,
-        "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": "Philippe",
-        "last_name": "Chaffanjon",
-        "orcid": null,
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Rebecca",
-        "last_name": "Shipley",
-        "orcid": "0000-0002-2818-6228",
-        "roles": ["Funding acquisition"]
-      },
-      {
-        "first_name": "Simon",
-        "last_name": "Walker-Samuel",
-        "orcid": "0000-0003-3530-9166",
-        "roles": ["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-1659302234",
-    "author_list": [
-      "The Human Organ Atlas Collaboration",
-      "Alexandre Bellier",
-      "Brian Bay",
-      "Claire Walsh",
-      "Danny Jonigk",
-      "David Stansby",
-      "Elodie Boller",
-      "Guillaume Gaisne",
-      "Hector Dejea I Velardo",
-      "Joanna Purzycka",
-      "Joseph Brunet",
-      "Maximilian Ackermann",
-      "Olivier Palombi",
-      "Paul Tafforeau",
-      "Peter Lee",
-      "Philippe Chaffanjon",
-      "Rebecca Shipley",
-      "Simon Walker-Samuel",
-      "Theresa Urban",
-      "Willi Wagner"
-    ]
-  },
-  "metadata_version": "0.9"
-}