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

hoa_tools/data/metadata/metadata/LADAF-2021-17_colon_complete-organ_20.025um_bm18.json

@@ -0,0 +1,245 @@
+{
+  "name": "LADAF-2021-17_colon_complete-organ_20.025um_bm18",
+  "dataset_type": "overview",
+  "voi": "complete-organ",
+  "data": {
+    "shape": [7501, 7501, 9610],
+    "voxel_size_um": 20.025,
+    "gcs_url": "n5://gs://ucl-hip-ct-35a68e99feaae8932b1d44da0358940b/LADAF-2021-17/colon/20.025um_complete-organ_bm18/"
+  },
+  "sample": {
+    "organ": "colon",
+    "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": "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": "2024-01-16",
+    "beamline": "BM18",
+    "energy": 109.0,
+    "current_start": 195.380036,
+    "filling_mode": "7/8 multibunch",
+    "n_frames": 12000,
+    "n_ref": 10,
+    "n_dark": 3,
+    "latency_time": 0.0012,
+    "exposure_time": 0.048,
+    "subframe_time": 0.012,
+    "n_subframes": 4,
+    "scan_type": "zseries",
+    "scan_range": 360.0,
+    "n_scans": 27,
+    "acquisition": "half",
+    "z_step": null,
+    "scan_time": 635.384538,
+    "filters": [
+      "Sapphire 5mm",
+      "Sapphire 5mm",
+      "Silver 0.2mm",
+      "Glassy carbon 20mm"
+    ],
+    "scintillator": "LuAG:Ce 2000um",
+    "optic": "DZoom",
+    "optic_magnification": 0.33694889147738527,
+    "distance_source_sample": 178000.0,
+    "distance_sample_detector": 20000.0,
+    "sensor_name": "Iris15",
+    "sensor_mode": null,
+    "sensor_roi_x_size": 2528,
+    "sensor_roi_y_size": 512,
+    "sensor_binning": [2, 2],
+    "pixel_size": 20.024,
+    "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 20.025um of the colon 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": "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/LADAF-2021-17_heart_ROI-01_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-01_6.5um_bm05.json

@@ -195,7 +195,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -261,5 +261,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2021-17_heart_ROI-02_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-02_6.5um_bm05.json

@@ -195,7 +195,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -261,5 +261,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2021-17_heart_ROI-03_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-03_6.5um_bm05.json

@@ -195,7 +195,7 @@
       {
         "first_name": "Philippe",
         "last_name": "Chaffanjon",
-        "orcid": null,
+        "orcid": "0000-0002-7954-2798",
         "roles": ["Funding acquisition"]
       },
       {
@@ -261,5 +261,5 @@
       "Willi Wagner"
     ]
   },
-  "metadata_version": "1.0"
+  "metadata_version": "1.1"
 }

hoa_tools/data/metadata/metadata/LADAF-2021-17_heart_ROI-04_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-05_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-06_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-07_6.36um_bm18.json

@@ -43,8 +43,8 @@
     "n_ref": 3,
     "n_dark": 100,
     "latency_time": 0.003,
-    "exposure_time": 0.03,
-    "subframe_time": null,
+    "exposure_time": 0.12,
+    "subframe_time": 0.03,
     "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-2021-17_heart_ROI-1.1_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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/LADAF-2021-17_heart_ROI-1.2_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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/LADAF-2021-17_heart_ROI-3.1_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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/LADAF-2021-17_heart_ROI-4.1_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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/LADAF-2021-17_heart_ROI-4.2_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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/LADAF-2021-17_heart_ROI-4.3_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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/LADAF-2021-17_heart_ROI-5.1_2.256um_bm18.json

@@ -44,7 +44,7 @@
     "n_dark": 100,
     "latency_time": 0.008,
     "exposure_time": 0.08,
-    "subframe_time": null,
+    "subframe_time": 0.08,
     "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"
 }