hoa-tools 1.0.10__py3-none-any.whl

hoa_tools/data/metadata/metadata/S-20-29_lung_left_VOI-05_6.5um_bm05.json

@@ -0,0 +1,210 @@
+{
+  "name": "S-20-29_lung_left_VOI-05_6.5um_bm05",
+  "dataset_type": "zoom",
+  "voi": "VOI-05",
+  "data": {
+    "shape": [3833, 3833, 20077],
+    "voxel_size_um": 6.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/lung-left/6.5um_VOI-05_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": "S-20-29",
+    "age": 80,
+    "sex": "M",
+    "weight": 170.0,
+    "height": 90.0,
+    "cause_of_death": "Acute right heart failure with extensive Pulmonary artery thrombembolism, diffuse alveolar damage, shock kidneys bilateral with acute kidney failure, and acute liver failure COVID-19 disease",
+    "date_of_death": null,
+    "medical_history": "Kidney failure, arterial hypertension, Z.n. Spondylodesis LWK 2 and sacral vertebra 2, SARS-CoV2 infection, symptoms of memory loss and predementia, Dandy-Walker syndrome variant, post-mortem diagnostic.",
+    "diabetes": "Type 2",
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-11-07",
+    "beamline": "BM05",
+    "energy": 95.0,
+    "current_start": 192.033,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.0015,
+    "exposure_time": 0.06,
+    "subframe_time": 0.015,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 59,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": 420.0,
+    "filters": ["Mo 0.1mm", "SiO2 50mm rods 10x5mm"],
+    "scintillator": "LuAG:Ce 1000um",
+    "optic": "Zoom",
+    "optic_magnification": 0.941,
+    "distance_source_sample": null,
+    "distance_sample_detector": 500.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": 2043,
+    "sensor_roi_y_size": 20077,
+    "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": {
+    "source_dataset": "S-20-29_lung_left_VOI-05_6.5um_bm05",
+    "target_dataset": "S-20-29_lung_left_complete-organ_25.31um_bm05",
+    "translation": [1257.7257673685622, 1005.485226013251, 789.8548884643609],
+    "rotation": -5.299835000447964,
+    "scale": 0.2568154947103331
+  },
+  "citation": {
+    "title": "Zoom (VOI-05) at 6.5um of the lung of donor S-20-29, 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",
+          "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"]
+      }
+    ],
+    "doi": "10.15151/ESRF-DC-1773964041",
+    "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": "1.1"
+}

hoa_tools/data/metadata/metadata/S-20-29_lung_left_complete-organ_25.31um_bm05.json

@@ -0,0 +1,199 @@
+{
+  "name": "S-20-29_lung_left_complete-organ_25.31um_bm05",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [3814, 5350, 6391],
+    "voxel_size_um": 25.31,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/lung-left/25.31um_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": "S-20-29",
+    "age": 80,
+    "sex": "M",
+    "weight": 170.0,
+    "height": 90.0,
+    "cause_of_death": "Acute right heart failure with extensive Pulmonary artery thrombembolism, diffuse alveolar damage, shock kidneys bilateral with acute kidney failure, and acute liver failure COVID-19 disease",
+    "date_of_death": null,
+    "medical_history": "Kidney failure, arterial hypertension, Z.n. Spondylodesis LWK 2 and sacral vertebra 2, SARS-CoV2 infection, symptoms of memory loss and predementia, Dandy-Walker syndrome variant, post-mortem diagnostic.",
+    "diabetes": "Type 2",
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-10-27",
+    "beamline": "BM05",
+    "energy": 96.0,
+    "current_start": 190.786,
+    "filling_mode": null,
+    "n_frames": 9990,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.0007,
+    "exposure_time": 0.028,
+    "subframe_time": 0.007,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "quarter",
+    "z_step": null,
+    "scan_time": 330.0,
+    "filters": ["Mo 0.1mm", "SiO2 50mm rods 10x5mm"],
+    "scintillator": "LuAG:Ce 1000um",
+    "optic": "Zoom",
+    "optic_magnification": 2.154,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3650.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": null,
+    "sensor_roi_y_size": null,
+    "sensor_binning": null,
+    "pixel_size": 25.31,
+    "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 25.31um of the lung of donor S-20-29, 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-1773966447",
+    "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": "1.1"
+}

hoa_tools/data/metadata/metadata/S-21-33_brain_complete-organ_19.57um_bm18.json

@@ -0,0 +1,240 @@
+{
+  "name": "S-21-33_brain_complete-organ_19.57um_bm18",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [7629, 7629, 9080],
+    "voxel_size_um": 19.57,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-21-33/brain/19.57um_complete-organ_bm18/"
+  },
+  "sample": {
+    "organ": "brain",
+    "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": "S-21-33",
+    "age": 72,
+    "sex": "M",
+    "weight": 170.0,
+    "height": 63.0,
+    "cause_of_death": "Septic-ischaemic cardiovascular failure",
+    "date_of_death": null,
+    "medical_history": "transfemoral amputations presentation with right residual limb insufficiency. Antibiotics and stump revision for sepsis.Stabilisation in the ICU and transfer to the normal ward. Renewed septic collapse, died in septic shock with multiple organ failure. Generalised atherosclerosis Nicotine abuse Arterial hypertension, right thigh as infectious focus a septic event with bronchopneumonia, consumption coagulopathy with the development of leg vein thrombosis and consecutive sub-acute recurrent pulmonary artery embolisms. with infarction pneumonia and pronounced pleural effusions (each approx 1000ml). In addition, development of pseudomembranous and ischaemic colitis of the entire colitis of the entire colon and rectum.",
+    "diabetes": null,
+    "hypertension": "Yes",
+    "smoker": null
+  },
+  "scan": {
+    "date": "2022-07-22",
+    "beamline": "BM18",
+    "energy": 72.0,
+    "current_start": null,
+    "filling_mode": "16 bunch",
+    "n_frames": 9900,
+    "n_ref": 3,
+    "n_dark": 100,
+    "latency_time": 0.002,
+    "exposure_time": 0.08,
+    "subframe_time": 0.02,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": null,
+    "z_step": 7.0,
+    "scan_time": null,
+    "filters": ["Sapphire 5mm", "SiO2 15mm block"],
+    "scintillator": null,
+    "optic": null,
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 15000.0,
+    "sensor_name": null,
+    "sensor_mode": null,
+    "sensor_roi_x_size": 3944,
+    "sensor_roi_y_size": 9080,
+    "sensor_binning": null,
+    "pixel_size": 19.57,
+    "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": null,
+  "citation": {
+    "title": "Overview at 19.57um of the brain of donor S-21-33, 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": "0000-0002-7954-2798",
+        "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": null,
+    "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": "1.1"
+}