hoa-tools 1.0.10__py3-none-any.whl

hoa_tools/data/metadata/metadata/LADAF-2021-17_liver_VOI-03_4.14um_bm18.json

@@ -0,0 +1,233 @@
+{
+  "name": "LADAF-2021-17_liver_VOI-03_4.14um_bm18",
+  "dataset_type": "zoom",
+  "voi": "VOI-03",
+  "data": {
+    "shape": [6482, 6482, 2048],
+    "voxel_size_um": 4.14,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2021-17/liver/4.14um_VOI-03_bm18/"
+  },
+  "sample": {
+    "organ": "liver",
+    "organ_context": null,
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": "n/a",
+    "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": "2023-09-24",
+    "beamline": "BM18",
+    "energy": 114.0,
+    "current_start": 197.329203,
+    "filling_mode": "7/8 multibunch",
+    "n_frames": 12000,
+    "n_ref": 1,
+    "n_dark": 3,
+    "latency_time": 0.003,
+    "exposure_time": 0.15,
+    "subframe_time": 0.03,
+    "n_subframes": 5,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 3,
+    "acquisition": "half",
+    "z_step": 7.0,
+    "scan_time": 1985.399629,
+    "filters": ["Sapphire 7mm", "Mo 0.44mm", "SiO2 5mm", "Glassy carbon 115mm"],
+    "scintillator": "LuAG:Ce 500um",
+    "optic": "Fixed x1",
+    "optic_magnification": 1.0,
+    "distance_source_sample": 177450.0,
+    "distance_sample_detector": 4000.0,
+    "sensor_name": "Iris15",
+    "sensor_mode": null,
+    "sensor_roi_x_size": 3500,
+    "sensor_roi_y_size": 2048,
+    "sensor_binning": [1, 1],
+    "pixel_size": 4.134,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1389",
+    "title": "HUB Proposal: Human Organ Atlas Hub (HOAHub)",
+    "proposers": [
+      "Peter Lee",
+      "Claire Walsh",
+      "Anastasia Yendiki",
+      "Maximilian Ackermann",
+      "Alexandre Bellier",
+      "Bernadette de Bakker",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Stijn Verleden"
+    ]
+  },
+  "registration": {
+    "source_dataset": "LADAF-2021-17_liver_VOI-03_4.14um_bm18",
+    "target_dataset": "LADAF-2021-17_liver_complete-organ_22.56um_bm18",
+    "translation": [4176.629900110747, 3598.4284167205337, 4224.396052732887],
+    "rotation": 0.9997671450011183,
+    "scale": 0.183510156140766
+  },
+  "citation": {
+    "title": "Zoom (VOI-03) at 4.14um of the liver 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": "Anastasia",
+        "last_name": "Yendiki",
+        "orcid": "0000-0003-1386-3828",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Andrew",
+        "last_name": "Cook",
+        "orcid": "0000-0001-5079-7546",
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Bernadette",
+        "last_name": "de Bakker",
+        "orcid": "0000-0003-0758-4064",
+        "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": "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", "Investigation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Jacob",
+        "orcid": "0000-0002-8054-2293",
+        "roles": ["Investigation"]
+      },
+      {
+        "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": "Stijn",
+        "last_name": "Verleden",
+        "orcid": "0000-0002-9656-5844",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      }
+    ],
+    "doi": null,
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Alexandre Bellier",
+      "Anastasia Yendiki",
+      "Andrew Cook",
+      "Bernadette de Bakker",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Joseph Jacob",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Stijn Verleden",
+      "Theresa Urban"
+    ]
+  },
+  "metadata_version": "1.1"
+}

hoa_tools/data/metadata/metadata/LADAF-2021-17_liver_VOI-08_4.14um_bm18.json

@@ -0,0 +1,233 @@
+{
+  "name": "LADAF-2021-17_liver_VOI-08_4.14um_bm18",
+  "dataset_type": "zoom",
+  "voi": "VOI-08",
+  "data": {
+    "shape": [6492, 6492, 3739],
+    "voxel_size_um": 4.14,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2021-17/liver/4.14um_VOI-08_bm18/"
+  },
+  "sample": {
+    "organ": "liver",
+    "organ_context": null,
+    "post_mortem_interval_hours": null,
+    "fixation_method": null,
+    "fixation_medium": null,
+    "organ_infilled": "n/a",
+    "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": "2023-09-25",
+    "beamline": "BM18",
+    "energy": 106.0,
+    "current_start": 194.355074,
+    "filling_mode": "7/8 multibunch",
+    "n_frames": 12000,
+    "n_ref": 1,
+    "n_dark": 3,
+    "latency_time": 0.003,
+    "exposure_time": 0.15,
+    "subframe_time": 0.03,
+    "n_subframes": 5,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 2,
+    "acquisition": "half",
+    "z_step": 7.0,
+    "scan_time": 1985.399505,
+    "filters": ["Sapphire 7mm", "Mo 0.44mm", "Glassy carbon 30mm", "SiO2 10mm"],
+    "scintillator": "LuAG:Ce 500um",
+    "optic": "Fixed x1",
+    "optic_magnification": 1.0,
+    "distance_source_sample": 177450.0,
+    "distance_sample_detector": 4000.0,
+    "sensor_name": "Iris15",
+    "sensor_mode": null,
+    "sensor_roi_x_size": 3500,
+    "sensor_roi_y_size": 2048,
+    "sensor_binning": [1, 1],
+    "pixel_size": 4.136,
+    "xray_magnification": null,
+    "technique": "Hierarchical Phase-Contrast Tomography (HiP-CT)",
+    "experiment_type": "Tomography"
+  },
+  "proposal": {
+    "proposal_number": "md1389",
+    "title": "HUB Proposal: Human Organ Atlas Hub (HOAHub)",
+    "proposers": [
+      "Peter Lee",
+      "Claire Walsh",
+      "Anastasia Yendiki",
+      "Maximilian Ackermann",
+      "Alexandre Bellier",
+      "Bernadette de Bakker",
+      "Paul Tafforeau",
+      "Danny Jonigk",
+      "Stijn Verleden"
+    ]
+  },
+  "registration": {
+    "source_dataset": "LADAF-2021-17_liver_VOI-08_4.14um_bm18",
+    "target_dataset": "LADAF-2021-17_liver_complete-organ_22.56um_bm18",
+    "translation": [5533.968756746199, 4879.181944985344, 8505.805038176819],
+    "rotation": -0.3000133236369433,
+    "scale": 0.18351091662536778
+  },
+  "citation": {
+    "title": "Zoom (VOI-08) at 4.14um of the liver 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": "Anastasia",
+        "last_name": "Yendiki",
+        "orcid": "0000-0003-1386-3828",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Andrew",
+        "last_name": "Cook",
+        "orcid": "0000-0001-5079-7546",
+        "roles": ["Investigation"]
+      },
+      {
+        "first_name": "Bernadette",
+        "last_name": "de Bakker",
+        "orcid": "0000-0003-0758-4064",
+        "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": "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", "Investigation"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Brunet",
+        "orcid": "0000-0002-8424-9510",
+        "roles": ["Data curation", "Investigation", "Software"]
+      },
+      {
+        "first_name": "Joseph",
+        "last_name": "Jacob",
+        "orcid": "0000-0002-8054-2293",
+        "roles": ["Investigation"]
+      },
+      {
+        "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": "Stijn",
+        "last_name": "Verleden",
+        "orcid": "0000-0002-9656-5844",
+        "roles": ["Funding acquisition"]
+      },
+      {
+        "first_name": "Theresa",
+        "last_name": "Urban",
+        "orcid": "0000-0002-0352-8180",
+        "roles": ["Data curation", "Investigation", "Software"]
+      }
+    ],
+    "doi": null,
+    "author_list": [
+      "The Human Organ Atlas Collaboration",
+      "Alexandre Bellier",
+      "Anastasia Yendiki",
+      "Andrew Cook",
+      "Bernadette de Bakker",
+      "Claire Walsh",
+      "Danny Jonigk",
+      "David Stansby",
+      "Guillaume Gaisne",
+      "Hector Dejea I Velardo",
+      "Joanna Purzycka",
+      "Joseph Brunet",
+      "Joseph Jacob",
+      "Maximilian Ackermann",
+      "Paul Tafforeau",
+      "Peter Lee",
+      "Stijn Verleden",
+      "Theresa Urban"
+    ]
+  },
+  "metadata_version": "1.1"
+}