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README.md

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----
-license: cc-by-4.0
----
+This README file was generated on 03-11-2023 by David Bouget.
+Last updated: 03-11-2023.
+
+--------------------
+GENERAL INFORMATION
+--------------------
+1. Title of Dataset: AeroPath
+2. Publication and DOI: "AeroPath: An airway segmentation benchmark dataset with challenging pathology". https://arxiv.org/abs/2311.01138
+3. Contact Information
+     Name: Erlend F. Hofstad
+     Institution: Medical Technology Department, SINTEF Digital, Trondheim
+     Email: erlend.hofstad@sintef.no
+     Website: https://www.sintef.no/en/all-employees/employee/erlend.hofstad/
+
+
+4. Contributors: Karen-Helene Støverud, Haakon Olav Leira, Erlend F. Hofstad, Andre Pedersen, David Bouget, and Thomas Langø.
+5. Kind of data: computed tomography angiography (CTA) scans and binary annotation masks, all stored as NifTI files (*.nii.gz).
+
+6. Date of data collection/generation: .
+7. Geographic location: Trondheim, Norway.
+8. Funding sources: the Ministry of Health and Care Services of Norway through the Norwegian National Research Center for Minimally Invasive and Image-Guided Diagnostics and Therapy (MiDT) at St. Olavs hospital, Trondheim University Hospital, Trondheim, Norway. The research leading to these results has in addition received funding from the Norwegian Financial Mechanism 2014-2021 under the project RO- NO2019-0138, 19/2020 “Improving Cancer Diagnostics in Flexible Endoscopy using Artificial Intelligence and Medical Robotics” IDEAR, Contract No. 19/2020.
+
+
+9. Description of dataset: 
+General description and ethics approvals: The dataset contains 27 computed tomography angiography
+(CTA) scans, acquired using the Thorax Lung protocol at St. Olavs hospital (Trondheim, Norway). The included patients (nine women), aged 52 to 84 (median 70), were all undergoing diagnostic tests for lung cancer and had a wide range of pathologies including malignant tumors, sarcoidosis, and emphysema.
+
+
+---------------------------
+SHARING/ACCESS INFORMATION
+---------------------------
+
+1. Licenses/Restrictions:CC-BY 4.0 (See license.md).
+2. Recommended citation: See citation recommended at https://github.com/raidionics/AeroPath.
+
+
+---------------------
+DATA & FILE OVERVIEW
+---------------------
+1. File List: 
+README.md
+license.md
+ └── 1/
+        └── 1_CT_HR.nii.gz
+        └── 1_CT_HR_label_airways.nii.gz
+        └── 1_CT_HR_label_lungs.nii.gz
+ .
+ .
+ .
+ └── 27/
+        └── 27_CT_HR.nii.gz
+        └── 27_CT_HR_label_airways.nii.gz
+        └── 27_CT_HR_label_lungs.nii.gz
+
+---------------------------
+METHODOLOGICAL INFORMATION
+---------------------------
+1. Description of sources and methods used for collection/generation of data:
+Dataset statistics
+Overall, the CT scan dimensions are covering [487 : 512] × [441 : 512] × [241 : 829] voxels, and the trans-axial voxel size ranges [0.68 : 0.76] × [0.68 : 0.75] mm2 with a reconstructed slice thickness of [0.5 : 1.25] mm.
+
+Annotation procedures
+The annotation process for generating the ground truth was performed in three steps. First, the largest components (i.e., trachea and the first branches) were extracted based on a region growing, or a grow-cut method. Due to leakage, the region growing method did not yield satisfactory results in all cases. Therefore, for certain cases, the grow-cut method in 3D Slicer was used instead. In the second step, BronchiNet was employed to segment the smaller peripheral airways. In the third and final step, the segmentations were refined manually. Bronchial fragments and missed segments were connected, before false positives and fragments that could not be connected based on visual inspection were removed. All manual corrections were performed using the default segment editor in 3D Slicer. The manual correction was performed by a trained engineer, supervised by a pulmonologist. Finally, all annotations were verified on a case-by-case basis by a pulmonologist. The final annotations from the AeroPath segmentation included on average 128 ± 56 branches per CT scan.

license.md

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+
+       2. Patent and trademark rights are not licensed under this
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+       3. To the extent possible, the Licensor waives any right to
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+Section 3 -- License Conditions.
+
+Your exercise of the Licensed Rights is expressly made subject to the
+following conditions.
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+  a. Attribution.
+
+       1. If You Share the Licensed Material (including in modified
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+            a. retain the following if it is supplied by the Licensor
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+                 i. identification of the creator(s) of the Licensed
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+                    attribution, in any reasonable manner requested by
+                    the Licensor (including by pseudonym if
+                    designated);
+
+                ii. a copyright notice;
+
+               iii. a notice that refers to this Public License;
+
+                iv. a notice that refers to the disclaimer of
+                    warranties;
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+                 v. a URI or hyperlink to the Licensed Material to the
+                    extent reasonably practicable;
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+               retain an indication of any previous modifications; and
+
+            c. indicate the Licensed Material is licensed under this
+               Public License, and include the text of, or the URI or
+               hyperlink to, this Public License.
+
+       2. You may satisfy the conditions in Section 3(a)(1) in any
+          reasonable manner based on the medium, means, and context in
+          which You Share the Licensed Material. For example, it may be
+          reasonable to satisfy the conditions by providing a URI or
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+          reasonably practicable.
+
+       4. If You Share Adapted Material You produce, the Adapter's
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+
+
+Section 4 -- Sui Generis Database Rights.
+
+Where the Licensed Rights include Sui Generis Database Rights that
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+
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+
+For the avoidance of doubt, this Section 4 supplements and does not
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+Rights include other Copyright and Similar Rights.
+
+
+Section 5 -- Disclaimer of Warranties and Limitation of Liability.
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+  c. The disclaimer of warranties and limitation of liability provided
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+     possible, most closely approximates an absolute disclaimer and
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+
+
+Section 6 -- Term and Termination.
+
+  a. This Public License applies for the term of the Copyright and
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+     this Public License, then Your rights under this Public License
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+
+  b. Where Your right to use the Licensed Material has terminated under
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+       1. automatically as of the date the violation is cured, provided
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+
+       2. upon express reinstatement by the Licensor.
+
+     For the avoidance of doubt, this Section 6(b) does not affect any
+     right the Licensor may have to seek remedies for Your violations
+     of this Public License.
+
+  c. For the avoidance of doubt, the Licensor may also offer the
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+
+  d. Sections 1, 5, 6, 7, and 8 survive termination of this Public
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+
+Section 7 -- Other Terms and Conditions.
+
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+  b. Any arrangements, understandings, or agreements regarding the
+     Licensed Material not stated herein are separate from and
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+
+
+Section 8 -- Interpretation.
+
+  a. For the avoidance of doubt, this Public License does not, and
+     shall not be interpreted to, reduce, limit, restrict, or impose
+     conditions on any use of the Licensed Material that could lawfully
+     be made without permission under this Public License.
+
+  b. To the extent possible, if any provision of this Public License is
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+
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