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

hoa_tools/data/metadata/metadata/FO-20-124_lung_upper_lobe_central-column_6.24um_bm05.json

@@ -0,0 +1,214 @@
+{
+  "name": "FO-20-124_lung_upper_lobe_central-column_6.24um_bm05",
+  "dataset_type": "zoom",
+  "voi": "central-column",
+  "data": {
+    "shape": [3836, 3836, 5772],
+    "voxel_size_um": 6.24,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/FO-20-124/lung-upper_lobe/6.24um_central-column_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "organ_context": "upper_lobe",
+    "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": "FO-20-124",
+    "age": 76,
+    "sex": "M",
+    "weight": null,
+    "height": null,
+    "cause_of_death": "Covid",
+    "date_of_death": null,
+    "medical_history": "Hospitalisation for 22 days; Mechanical ventilation yes for 22 days;BMI 30.5; Bacterial superinfection in the lower lobe",
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-06-01",
+    "beamline": "BM05",
+    "energy": 70.0,
+    "current_start": 191.508,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 1,
+    "n_dark": 40,
+    "latency_time": 0.002,
+    "exposure_time": 0.075,
+    "subframe_time": null,
+    "n_subframes": null,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": null,
+    "filters": [
+      "Al 3.5mm",
+      "Glassy carbon 135mm rods 27x5mm",
+      "Glassy carbon 48mm rods 12x4mm"
+    ],
+    "scintillator": null,
+    "optic": null,
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3675.0,
+    "sensor_name": null,
+    "sensor_mode": "FFM",
+    "sensor_roi_x_size": 2048,
+    "sensor_roi_y_size": 688,
+    "sensor_binning": null,
+    "pixel_size": 6.24,
+    "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": "FO-20-124_lung_upper_lobe_central-column_6.24um_bm05",
+    "target_dataset": "FO-20-124_lung_upper_lobe_complete-organ_26.38um_bm05",
+    "translation": [1458.0828171249836, 1481.3881248489947, 3446.299764664633],
+    "rotation": 2.0999028808032465,
+    "scale": 0.23654304721305994
+  },
+  "citation": {
+    "title": "Zoom (central-column) at 6.24um of the lung of donor FO-20-124, 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-2189449161",
+    "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/FO-20-124_lung_upper_lobe_complete-organ_26.38um_bm05.json

@@ -185,7 +185,7 @@
         "roles": ["Funding acquisition", "Investigation"]
       }
     ],
-    "doi": null,
+    "doi": "10.15151/ESRF-DC-2127908029",
     "author_list": [
       "The Human Organ Atlas Collaboration",
       "Claire Walsh",
@@ -204,5 +204,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-125_lung_complete-organ_26.38um_bm05.json

@@ -0,0 +1,208 @@
+{
+  "name": "FO-20-125_lung_complete-organ_26.38um_bm05",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [3927, 3927, 4474],
+    "voxel_size_um": 26.38,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/FO-20-125/lung/26.38um_complete-organ_bm05/"
+  },
+  "sample": {
+    "organ": "lung",
+    "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": "FO-20-125",
+    "age": 73,
+    "sex": "M",
+    "weight": null,
+    "height": null,
+    "cause_of_death": "Covid",
+    "date_of_death": null,
+    "medical_history": null,
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2020-06-01",
+    "beamline": "BM05",
+    "energy": 70.0,
+    "current_start": 195.313,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 0,
+    "n_dark": 0,
+    "latency_time": 0.002,
+    "exposure_time": 0.014286,
+    "subframe_time": null,
+    "n_subframes": 7,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": 702.0,
+    "filters": [
+      "Al 3.5mm",
+      "Glassy carbon 135mm rods 27x5mm",
+      "Glassy carbon 64mm rods 16x4mm"
+    ],
+    "scintillator": "LuAG:Ce 2000um",
+    "optic": null,
+    "optic_magnification": 1.077,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3675.0,
+    "sensor_name": null,
+    "sensor_mode": "FFM",
+    "sensor_roi_x_size": 2048,
+    "sensor_roi_y_size": 176,
+    "sensor_binning": null,
+    "pixel_size": 26.38,
+    "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 26.38um of the lung of donor FO-20-125, 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-2189451409",
+    "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/FO-20-129_lung_left_upper_lobe_VOI-01.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-01.2b_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-01_6.24um_bm05.json

@@ -51,7 +51,7 @@
     "n_scans": 38,
     "acquisition": "half",
     "z_step": 3.5,
-    "scan_time": 510.59999999999997,
+    "scan_time": 510.6,
     "filters": [
       "Al 3.5mm",
       "Glassy carbon 135mm rods 27x5mm",
@@ -210,5 +210,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-02.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-02_6.24um_bm05.json

@@ -51,7 +51,7 @@
     "n_scans": 13,
     "acquisition": "half",
     "z_step": 3.5,
-    "scan_time": 510.59999999999997,
+    "scan_time": 510.6,
     "filters": [
       "Al 3.5mm",
       "Glassy carbon 135mm rods 27x5mm",
@@ -210,5 +210,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-03.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-03_6.24um_bm05.json

@@ -210,5 +210,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-03b-bis_2.2um_bm05.json

@@ -44,7 +44,7 @@
     "n_dark": 0,
     "latency_time": 0.005,
     "exposure_time": 0.05,
-    "subframe_time": null,
+    "subframe_time": 0.05,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -201,5 +201,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-04-bis_6.5um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.0008,
-    "exposure_time": 0.008,
-    "subframe_time": null,
+    "exposure_time": 0.04,
+    "subframe_time": 0.008,
     "n_subframes": 5,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -201,5 +201,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-04.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-04_6.24um_bm05.json

@@ -210,5 +210,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-05.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-05_6.24um_bm05.json

@@ -51,7 +51,7 @@
     "n_scans": 22,
     "acquisition": "half",
     "z_step": 3.5,
-    "scan_time": 510.59999999999997,
+    "scan_time": 510.6,
     "filters": [
       "Al 3.5mm",
       "Glassy carbon 135mm rods 27x5mm",
@@ -210,5 +210,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-08.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-09.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-10.2_2.22um_bm05.json

@@ -206,5 +206,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-aa-bis_2.2um_bm05.json

@@ -201,5 +201,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-aa_0.65um_bm05.json

@@ -195,5 +195,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_VOI-sx20_6.24um_bm05.json

@@ -210,5 +210,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_complete-upper-lobe-bis_25.25um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 0,
     "n_dark": 400,
     "latency_time": 0.0005,
-    "exposure_time": 0.005,
-    "subframe_time": null,
+    "exposure_time": 0.05,
+    "subframe_time": 0.005,
     "n_subframes": 10,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -195,5 +195,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_left_upper_lobe_complete-upper-lobe_26.38um_bm05.json

@@ -204,5 +204,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/FO-20-129_lung_right_upper_lobe_core-biopsy_2.25um_bm05.json

@@ -200,5 +200,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }