hoa-tools 1.0.4__py3-none-any.whl → 1.0.6__py3-none-any.whl

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"
+}

hoa_tools/data/metadata/metadata/S-21-46_brain_complete-organ_19.57um_bm18.json

@@ -0,0 +1,240 @@
+{
+  "name": "S-21-46_brain_complete-organ_19.57um_bm18",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [7629, 7629, 7537],
+    "voxel_size_um": 19.57,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-21-46/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-21-46",
+    "age": 68,
+    "sex": "F",
+    "weight": 168.0,
+    "height": 69.0,
+    "cause_of_death": "Sepsis with high-dose catecholamine therapy",
+    "date_of_death": null,
+    "medical_history": "Generalised tumour disease with disseminated metastatic, small cell neuroendocrine carcinoma of the colon with cardiorespiratory failure with air embolism. Sepsis with fulminant intestinal necrosis and hepatic necrosis. neuroendocrine carcinoma of the colon with diffuse hepatic metastasis. After right hemicolectomy. ileus. ED of an endoluminal Sepsis in fulminant intestinal necrosis and hepatic necrosis. ED of a NEC of the colon with diffuse hepatic metastasis. After right hemicolectomy. acute deterioration with decrease of the peripheral oxygen saturation and unmeasurable blood pressure. Transfer to IST. Sepsis with high-dose catecholamine therapy. with hepatic metastasis. Hemicolectomy and port implantation performed (11.06.2021). During the night of 23-24.06.2021 acute deterioration with decrease of the peripheral oxygen saturation and unmeasurable blood pressure.",
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2022-07-23",
+    "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": 6.0,
+    "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": 7537,
+    "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-21-46, 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"
+}