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

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-05_2.5um_bm05.json

@@ -0,0 +1,224 @@
+{
+  "name": "S-20-29_brain_VOI-05_2.5um_bm05",
+  "dataset_type": "zoom",
+  "voi": "VOI-05",
+  "data": {
+    "shape": [3833, 3833, 7312],
+    "voxel_size_um": 2.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/brain/2.5um_VOI-05_bm05/"
+  },
+  "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-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": "2021-07-07",
+    "beamline": "BM05",
+    "energy": 86.0,
+    "current_start": 193.386,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.006,
+    "exposure_time": 0.06,
+    "subframe_time": null,
+    "n_subframes": 1,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 8,
+    "acquisition": "half",
+    "z_step": 2.2,
+    "scan_time": 495.0,
+    "filters": ["Cu 0.24mm", "Mo 0.44mm"],
+    "scintillator": "LuAG:Ce 250um",
+    "optic": "Zoom",
+    "optic_magnification": 3.0,
+    "distance_source_sample": null,
+    "distance_sample_detector": 1440.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "rolling shutter",
+    "sensor_roi_x_size": 1152,
+    "sensor_roi_y_size": 1152,
+    "sensor_binning": null,
+    "pixel_size": 2.5,
+    "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_brain_VOI-05_2.5um_bm05",
+    "target_dataset": "S-20-29_brain_complete-organ_25.33um_bm05",
+    "translation": [2299.923381382527, 4319.065590687604, 4356.048334794111],
+    "rotation": 2.200106098825127,
+    "scale": 0.09869742825015558
+  },
+  "citation": {
+    "title": "Zoom (VOI-05) at 2.5um of the brain 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": "Rui",
+        "last_name": "Xian",
+        "orcid": null,
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Sebastian",
+        "last_name": "Marussi",
+        "orcid": "0000-0003-4537-210X",
+        "roles": ["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-1773960881",
+    "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",
+      "Rui Xian",
+      "Sebastian Marussi",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.0"
+}

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

@@ -0,0 +1,224 @@
+{
+  "name": "S-20-29_brain_VOI-05_6.5um_bm05",
+  "dataset_type": "zoom",
+  "voi": "VOI-05",
+  "data": {
+    "shape": [3844, 3844, 4176],
+    "voxel_size_um": 6.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/brain/6.5um_VOI-05_bm05/"
+  },
+  "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-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": "2021-07-04",
+    "beamline": "BM05",
+    "energy": 97.0,
+    "current_start": 197.3,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.0012,
+    "exposure_time": 0.012,
+    "subframe_time": null,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 12,
+    "acquisition": null,
+    "z_step": null,
+    "scan_time": null,
+    "filters": ["Cu 0.24mm", "Mo 0.68mm"],
+    "scintillator": "LuAG:Ce 1000um",
+    "optic": "DZoom",
+    "optic_magnification": 0.94,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3500.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "FFM",
+    "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": {
+    "source_dataset": "S-20-29_brain_VOI-05_6.5um_bm05",
+    "target_dataset": "S-20-29_brain_complete-organ_25.33um_bm05",
+    "translation": [2246.8169588007117, 3729.342032767995, 4174.079481003277],
+    "rotation": -0.000014268498315844556,
+    "scale": 0.25661326151056923
+  },
+  "citation": {
+    "title": "Zoom (VOI-05) at 6.5um of the brain 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": "Rui",
+        "last_name": "Xian",
+        "orcid": null,
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Sebastian",
+        "last_name": "Marussi",
+        "orcid": "0000-0003-4537-210X",
+        "roles": ["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-1773961429",
+    "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",
+      "Rui Xian",
+      "Sebastian Marussi",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.0"
+}

hoa_tools/data/metadata/metadata/S-20-29_brain_complete-organ_19.57um_bm18.json

@@ -0,0 +1,240 @@
+{
+  "name": "S-20-29_brain_complete-organ_19.57um_bm18",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [7621, 7621, 9080],
+    "voxel_size_um": 19.57,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-29/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-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": "2022-07-21",
+    "beamline": "BM18",
+    "energy": 72.0,
+    "current_start": null,
+    "filling_mode": "16 bunch",
+    "n_frames": 9900,
+    "n_ref": 3,
+    "n_dark": 40,
+    "latency_time": 0.002,
+    "exposure_time": 0.02,
+    "subframe_time": null,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "quarter",
+    "z_step": null,
+    "scan_time": null,
+    "filters": ["Sapphire 5mm", "SiO2 15mm block"],
+    "scintillator": "LuAG:Ce 2000um",
+    "optic": null,
+    "optic_magnification": 0.332,
+    "distance_source_sample": null,
+    "distance_sample_detector": 15000.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": null,
+    "sensor_roi_x_size": 512,
+    "sensor_roi_y_size": 512,
+    "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-20-29, 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-1773692859",
+    "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": "1.0"
+}