hoa-tools 1.0.3__py3-none-any.whl → 1.0.5__py3-none-any.whl

hoa_tools/data/metadata/metadata/S-20-28_kidney_VOI-07_2.5um_bm05.json

@@ -0,0 +1,224 @@
+{
+  "name": "S-20-28_kidney_VOI-07_2.5um_bm05",
+  "dataset_type": "zoom",
+  "voi": "VOI-07",
+  "data": {
+    "shape": [3838, 3838, 4674],
+    "voxel_size_um": 2.5,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/S-20-28/kidney/2.5um_VOI-07_bm05/"
+  },
+  "sample": {
+    "organ": "kidney",
+    "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": "S-20-28",
+    "age": 84,
+    "sex": "M",
+    "weight": 179.0,
+    "height": 96.0,
+    "cause_of_death": "COVID-19",
+    "date_of_death": null,
+    "medical_history": null,
+    "diabetes": null,
+    "hypertension": null,
+    "smoker": null
+  },
+  "scan": {
+    "date": "2021-07-07",
+    "beamline": "BM05",
+    "energy": 81.0,
+    "current_start": 193.77,
+    "filling_mode": null,
+    "n_frames": 6000,
+    "n_ref": 3,
+    "n_dark": 0,
+    "latency_time": 0.005,
+    "exposure_time": 0.05,
+    "subframe_time": 0.05,
+    "n_subframes": 1,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 5,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": null,
+    "filters": ["Al 0.51mm", "Mo 0.24mm", "SiO2 16mm rods 4x4mm"],
+    "scintillator": "LuAG:Ce 250um",
+    "optic": "Zoom",
+    "optic_magnification": 2.53,
+    "distance_source_sample": null,
+    "distance_sample_detector": 1440.0,
+    "sensor_name": "PCO edge 4.2 CLHS",
+    "sensor_mode": "FFM",
+    "sensor_roi_x_size": 2048,
+    "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-20-28_kidney_VOI-07_2.5um_bm05",
+    "target_dataset": "S-20-28_kidney_complete-organ_25.0um_bm05",
+    "translation": [1116.9538224099058, 995.7478961899947, 1441.6615499699556],
+    "rotation": -8.200277228877324,
+    "scale": 0.10000055301467928
+  },
+  "citation": {
+    "title": "Zoom (VOI-07) at 2.5um of the kidney of donor S-20-28, 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": 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",
+      "Rui Xian",
+      "Sebastian Marussi",
+      "Theresa Urban",
+      "Willi Wagner"
+    ]
+  },
+  "metadata_version": "1.1"
+}

hoa_tools/data/metadata/metadata/S-20-28_kidney_complete-organ_25.0um_bm05.json

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

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-01_2.5um_bm05.json

@@ -44,7 +44,7 @@
     "n_dark": 0,
     "latency_time": 0.006,
     "exposure_time": 0.06,
-    "subframe_time": null,
+    "subframe_time": 0.06,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-01_6.5um_bm05.json

@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-01b_6.5um_bm05.json

@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-02_2.5um_bm05.json

@@ -44,7 +44,7 @@
     "n_dark": 0,
     "latency_time": 0.006,
     "exposure_time": 0.06,
-    "subframe_time": null,
+    "subframe_time": 0.06,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-02_6.5um_bm05.json

@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-03_2.5um_bm05.json

@@ -44,7 +44,7 @@
     "n_dark": 0,
     "latency_time": 0.006,
     "exposure_time": 0.06,
-    "subframe_time": null,
+    "subframe_time": 0.06,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-03_6.5um_bm05.json

@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-04_2.5um_bm05.json

@@ -44,7 +44,7 @@
     "n_dark": 0,
     "latency_time": 0.007,
     "exposure_time": 0.07,
-    "subframe_time": null,
+    "subframe_time": 0.07,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_VOI-04_6.5um_bm05.json

@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

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

@@ -44,7 +44,7 @@
     "n_dark": 0,
     "latency_time": 0.006,
     "exposure_time": 0.06,
-    "subframe_time": null,
+    "subframe_time": 0.06,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

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

@@ -220,5 +220,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

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

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 40,
     "latency_time": 0.002,
-    "exposure_time": 0.02,
-    "subframe_time": null,
+    "exposure_time": 0.08,
+    "subframe_time": 0.02,
     "n_subframes": 4,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -184,7 +184,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -236,5 +236,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_brain_complete-organ_25.33um_bm05.json

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

hoa_tools/data/metadata/metadata/S-20-29_heart_ROI-03_6.5um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.0015,
-    "exposure_time": 0.015,
-    "subframe_time": null,
+    "exposure_time": 0.06,
+    "subframe_time": 0.015,
     "n_subframes": 4,
     "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/S-20-29_heart_VOI-01_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/S-20-29_heart_VOI-02_2.5um_bm05.json

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

hoa_tools/data/metadata/metadata/S-20-29_heart_VOI-04_6.5um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.0015,
-    "exposure_time": 0.015,
-    "subframe_time": null,
+    "exposure_time": 0.06,
+    "subframe_time": 0.015,
     "n_subframes": 4,
     "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/S-20-29_heart_VOI-05b_6.5um_bm05.json

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

hoa_tools/data/metadata/metadata/S-20-29_heart_complete-organ_19.89um_bm18.json

@@ -195,7 +195,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -248,5 +248,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_heart_complete-organ_25.25um_bm05.json

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

hoa_tools/data/metadata/metadata/S-20-29_kidney_VOI-01_1.4um_bm05.json

@@ -81,13 +81,7 @@
       "Willi Wagner"
     ]
   },
-  "registration": {
-    "source_dataset": "S-20-29_kidney_VOI-01_1.4um_bm05",
-    "target_dataset": "S-20-29_kidney_complete-organ_25.38um_bm05",
-    "translation": [489.54624300094076, 568.0944131981872, 640.6147383414886],
-    "rotation": 177.50261493690053,
-    "scale": 0.055159223169650606
-  },
+  "registration": null,
   "citation": {
     "title": "Zoom (VOI-01) at 1.4um of the kidney of donor S-20-29, scanned at ESRF on beamline BM05.",
     "contributors": [
@@ -201,5 +195,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_kidney_VOI-01_6.5um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.001,
-    "exposure_time": 0.01,
-    "subframe_time": null,
+    "exposure_time": 0.05,
+    "subframe_time": 0.01,
     "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/S-20-29_kidney_VOI-02_6.5um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.001,
-    "exposure_time": 0.01,
-    "subframe_time": null,
+    "exposure_time": 0.05,
+    "subframe_time": 0.01,
     "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/S-20-29_kidney_VOI-03_6.5um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.001,
-    "exposure_time": 0.01,
-    "subframe_time": null,
+    "exposure_time": 0.05,
+    "subframe_time": 0.01,
     "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/S-20-29_kidney_complete-organ_25.38um_bm05.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 0,
     "latency_time": 0.0007,
-    "exposure_time": 0.007,
-    "subframe_time": null,
+    "exposure_time": 0.07,
+    "subframe_time": 0.007,
     "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/S-20-29_lung_left_ROI-2.1_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 200,
     "latency_time": 0.007,
     "exposure_time": 0.07,
-    "subframe_time": null,
+    "subframe_time": 0.07,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -195,7 +195,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -262,5 +262,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_lung_left_ROI-3.1_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 200,
     "latency_time": 0.007,
     "exposure_time": 0.07,
-    "subframe_time": null,
+    "subframe_time": 0.07,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -201,7 +201,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -268,5 +268,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/S-20-29_lung_left_ROI-5.3_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 200,
     "latency_time": 0.007,
     "exposure_time": 0.07,
-    "subframe_time": null,
+    "subframe_time": 0.07,
     "n_subframes": 1,
     "scan_type": "zseries",
     "scan_range": 360.0,
@@ -201,7 +201,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -268,5 +268,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }