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

hoa_tools/data/metadata/metadata/LADAF-2020-27_heart_L-vent-muscle_2.22um_bm05.json

@@ -0,0 +1,210 @@
+{
+  "name": "LADAF-2020-27_heart_L-vent-muscle_2.22um_bm05",
+  "dataset_type": "zoom",
+  "voi": "L-vent-muscle",
+  "data": {
+    "shape": [3775, 3775, 12890],
+    "voxel_size_um": 2.22,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/heart/2.22um_L-vent-muscle_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-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": "2020-07-08",
+    "beamline": "BM05",
+    "energy": 84.0,
+    "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": 8,
+    "acquisition": "half",
+    "z_step": -4.0,
+    "scan_time": 720.0,
+    "filters": ["Mo 0.25mm", "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": 970.0,
+    "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": 2.22,
+    "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_heart_L-vent-muscle_2.22um_bm05",
+    "target_dataset": "LADAF-2020-27_heart_complete-organ_25.08um_bm05",
+    "translation": [2625.230560497797, 2018.327139631631, 3543.9270523661153],
+    "rotation": -10.100117314518169,
+    "scale": 0.08851658498342181
+  },
+  "citation": {
+    "title": "Zoom (L-vent-muscle) at 2.22um of the heart 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-572185639",
+    "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_heart_LR-vent-muscles-ramus-interventricularis-anterior_6.05um_bm05.json

@@ -0,0 +1,210 @@
+{
+  "name": "LADAF-2020-27_heart_LR-vent-muscles-ramus-interventricularis-anterior_6.05um_bm05",
+  "dataset_type": "zoom",
+  "voi": "LR-vent-muscles-ramus-interventricularis-anterior",
+  "data": {
+    "shape": [3827, 3827, 10022],
+    "voxel_size_um": 6.05,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/heart/6.05um_LR-vent-muscles-ramus-interventricularis-anterior_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-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": "2020-07-07",
+    "beamline": "BM05",
+    "energy": 95.0,
+    "current_start": 200.0,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 0,
+    "n_dark": 400,
+    "latency_time": 0.03,
+    "exposure_time": 0.09,
+    "subframe_time": null,
+    "n_subframes": 3,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 15,
+    "acquisition": "half",
+    "z_step": -4.0,
+    "scan_time": 487.80000000000007,
+    "filters": ["Al 2mm", "SiO2 80mm rods 16x5mm"],
+    "scintillator": "LuAG:Ce 2000um",
+    "optic": "DZoom",
+    "optic_magnification": 3.0,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3475.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": 768,
+    "sensor_roi_y_size": 768,
+    "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_heart_LR-vent-muscles-ramus-interventricularis-anterior_6.05um_bm05",
+    "target_dataset": "LADAF-2020-27_heart_complete-organ_25.08um_bm05",
+    "translation": [3158.307749194994, 1534.7162012185129, 3207.91920800401],
+    "rotation": -10.699962832400786,
+    "scale": 0.2412283910535249
+  },
+  "citation": {
+    "title": "Zoom (LR-vent-muscles-ramus-interventricularis-anterior) at 6.05um of the heart 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-572190117",
+    "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_heart_ROI-01_6.5um_bm18.json

@@ -0,0 +1,272 @@
+{
+  "name": "LADAF-2020-27_heart_ROI-01_6.5um_bm18",
+  "dataset_type": "zoom",
+  "voi": "ROI-01",
+  "data": {
+    "shape": [3844, 3844, 6000],
+    "voxel_size_um": 6.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/heart/6.5um_ROI-01_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-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": "2022-02-28",
+    "beamline": "BM18",
+    "energy": 115.0,
+    "current_start": 198.608,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 40,
+    "latency_time": 0.0005,
+    "exposure_time": 0.06,
+    "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 0.65mm"],
+    "scintillator": null,
+    "optic": null,
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 10000.0,
+    "sensor_name": null,
+    "sensor_mode": null,
+    "sensor_roi_x_size": 2048,
+    "sensor_roi_y_size": 1392,
+    "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-2020-27_heart_ROI-01_6.5um_bm18",
+    "target_dataset": "LADAF-2020-27_heart_complete-organ_19.89um_bm18",
+    "translation": [2470.0572114047595, 1182.7326883341357, 2361.4308642516917],
+    "rotation": 12.499516949994963,
+    "scale": 0.32679465955015324
+  },
+  "citation": {
+    "title": "Zoom (ROI-01) at 6.5um of the heart of donor LADAF-2020-27, 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": "Alissa",
+        "last_name": "Parmenter",
+        "orcid": "0000-0002-9836-8932",
+        "roles": ["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": "Emer",
+        "last_name": "Burke O'Leary",
+        "orcid": "0000-0002-8831-8077",
+        "roles": ["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": "Kathleen",
+        "last_name": "Dollman",
+        "orcid": "0000-0002-5468-4896",
+        "roles": ["Investigation"]
+      },
+      {
+        "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": "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-1965462374",
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Alexandre Bellier",
+      "Alissa Parmenter",
+      "Brian Bay",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Elodie Boller",
+      "Emer Burke O'Leary",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Kathleen Dollman",
+      "Maximilian Ackermann",
+      "Olivier Palombi",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Philippe Chaffanjon",
+      "Rebecca Shipley",
+      "Simon Walker-Samuel",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.0"
+}