hoa-tools 1.0.4__py3-none-any.whl → 1.0.5__py3-none-any.whl

hoa_tools/data/metadata/metadata/LADAF-2020-27_heart_complete-organ_25.08um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_kidney_left_central-column_1.29um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_kidney_left_central-column_6.05um_bm05.json

@@ -81,13 +81,7 @@
       "Willi Wagner"
     ]
   },
-  "registration": {
-    "source_dataset": "LADAF-2020-27_kidney_left_central-column_6.05um_bm05",
-    "target_dataset": "LADAF-2020-27_kidney_left_complete-organ_25.08um_bm05",
-    "translation": [1015.647710639054, 1216.3270767034828, 906.143929656302],
-    "rotation": -0.09977031883926162,
-    "scale": 0.24122780183119433
-  },
+  "registration": null,
   "citation": {
     "title": "Zoom (central-column) at 6.05um of the kidney of donor LADAF-2020-27, scanned at ESRF on beamline BM05.",
     "contributors": [
@@ -206,5 +200,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2020-27_kidney_left_complete-organ_25.08um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 0,
     "n_dark": 400,
     "latency_time": 0.004,
-    "exposure_time": 0.04,
-    "subframe_time": null,
+    "exposure_time": 0.4,
+    "subframe_time": 0.04,
     "n_subframes": 10,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -200,5 +200,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2020-27_kidney_right_complete-organ_25.0um_bm05.json

@@ -0,0 +1,199 @@
+{
+  "name": "LADAF-2020-27_kidney_right_complete-organ_25.0um_bm05",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [2334, 2539, 3272],
+    "voxel_size_um": 25.0,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2020-27/kidney-right/25.0um_complete-organ_bm05/"
+  },
+  "sample": {
+    "organ": "kidney",
+    "organ_context": "right",
+    "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-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": "2021-04-04",
+    "beamline": "BM05",
+    "energy": 88.0,
+    "current_start": null,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.005,
+    "exposure_time": 0.007,
+    "subframe_time": null,
+    "n_subframes": 7,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": null,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": null,
+    "filters": ["SiO2 40mm rods 10x4mm", "Mo 0.24mm"],
+    "scintillator": null,
+    "optic": "DZoom",
+    "optic_magnification": null,
+    "distance_source_sample": null,
+    "distance_sample_detector": 3500.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "FFM",
+    "sensor_roi_x_size": 2042,
+    "sensor_roi_y_size": 3720,
+    "sensor_binning": null,
+    "pixel_size": 25.0,
+    "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 25.0um of the kidney 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"]
+      },
+      {
+        "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"]
+      },
+      {
+        "first_name": "Peter",
+        "last_name": "Lee",
+        "orcid": "0000-0002-3898-8881",
+        "roles": ["Conceptualization", "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",
+      "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/LADAF-2020-27_lung_left_FSC-A_2.51um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-A_25.25um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-A_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-B_2.51um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-B_25.25um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_FSC-B_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_2.45um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_6.05um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-01-upper-lobe-apical_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-02-lower-lobe-basal_2.45um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-02-lower-lobe-basal_6.05um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-02b-upper-lobe-apical_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-02b-upper-lobe-medial_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-03-upper-lobe-apical_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-03_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-03b-interlobular-fissure_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-04-upper-lobe-medial_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-04b-lower-lobe-basal-medial_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-05-lower-lobe-basal_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-05-upper-lobe-apical_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-06-lower-lobe-basal_2.45um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_VOI-06-lower-lobe-basal_6.05um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_lung_left_complete-organ_25.08um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_spleen_central-column_1.29um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_spleen_central-column_6.05um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-27_spleen_complete-organ_25.08um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 0,
     "n_dark": 400,
     "latency_time": 0.004,
-    "exposure_time": 0.04,
-    "subframe_time": null,
+    "exposure_time": 0.4,
+    "subframe_time": 0.04,
     "n_subframes": 10,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -200,5 +200,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_cerebellum-occipital_6.05um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_cerebellum_2.45um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_complete-organ_25.08um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_frontal_2.45um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_hippocampus_2.45um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_brain_hippocampus_6.05um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-01_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 40,
     "latency_time": 0.004,
-    "exposure_time": 0.04,
-    "subframe_time": null,
+    "exposure_time": 0.16,
+    "subframe_time": 0.04,
     "n_subframes": 4,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -190,7 +190,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -242,5 +242,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-01_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-02_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 40,
     "latency_time": 0.004,
-    "exposure_time": 0.04,
-    "subframe_time": null,
+    "exposure_time": 0.16,
+    "subframe_time": 0.04,
     "n_subframes": 4,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -190,7 +190,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -242,5 +242,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-02_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-03_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 40,
     "latency_time": 0.004,
-    "exposure_time": 0.04,
-    "subframe_time": null,
+    "exposure_time": 0.16,
+    "subframe_time": 0.04,
     "n_subframes": 4,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -190,7 +190,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -242,5 +242,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-03_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/LADAF-2020-31_heart_ROI-04_6.5um_bm05.json

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