Merge pull request #6601 from kostrykin/dev/dicom_3d

Add tutorial: Segmentation of Anatomical Structures in Medical 3-D Images

Author: kostrykin

faqs/galaxy/bulk_change_datatype.md

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+---
+title: Changing the data type of multiple datasets or collections
+description: This will set the data type for multiple datasets, collections, and the datasets therein. Does not change the datasets themselves.
+area: collections
+box_type: tip
+layout: faq
+contributors: [kostrykin]
+---
+
+1. Click on {% icon galaxy-selector %} **Select Items** at the top of the history panel ![Select Items button]({% link topics/galaxy-interface/images/historyItemControls.png %})
+2. Check {% if include.datasets_description %}{{ include.datasets_description }}{% else %}all the datasets and collections in your history you would like to change the data type for{% endif %}
+3. Click **{% if include.n %}{{ include.n }}{% else %}n{% endif %} of N selected** and choose **Change data type** 
+4. In the drop-down field, select {% if include.datatype %}`{{ include.datatype }}`{% else %} your desired data type {% endif %}
+  - tip: you can start typing the data type into the field to filter the dropdown menu
+4. Click the **OK** button

topics/imaging/images/dicom-anatomical-3d/axes.jpg

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+---
+destination:
+  type: library
+  name: GTN - Material
+  description: Galaxy Training Network Material
+  synopsis: Galaxy Training Network Material. See https://training.galaxyproject.org
+items:
+- name: Imaging
+  description: Image analysis using Galaxy
+  items:
+  - name: Segmentation of Anatomical Structures in Medical 3-D Images
+    items:
+    - name: 'DOI: 10.5281/zenodo.18225140'
+      description: latest
+      items:
+      - url: https://zenodo.org/records/18225140/files/PCIR_98890234_20010101_7.zip
+        src: url
+        ext: zip
+        info: https://zenodo.org/records/18225140

topics/imaging/images/dicom-anatomical-3d/mip_rainbow.mp4

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+---
+layout: faq-page
+---

topics/imaging/images/dicom-anatomical-3d/segm_aorticbif.mp4

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+
+# This is the bibliography file for your tutorial.
+#
+# To add bibliography (bibtex) entries here, follow these steps:
+#  1) Find the DOI for the article you want to cite
+#  2) Go to https://doi2bib.org and fill in the DOI
+#  3) Copy the resulting bibtex entry into this file
+#
+# To cite the example below, in your tutorial.md file
+# use {% cite Batut2018 %}
+#
+# If you want to cite an online resourse (website etc)
+# you can use the 'online' format (see below)
+#
+# You can remove the examples below
+
+@inproceedings{chougule2018clinical,
+  title={Clinical case study: spine modeling for minimum invasive spine surgeries (MISS) using rapid prototyping},
+  author={Chougule, VN and Mulay, A and Ahuja, BB},
+  booktitle = {2017 10th International Conference On Precision, Meso, Micro and Nano Engineering (COPEN)},
+  pages={96-102},
+  year = {2017},
+  url={https://www.researchgate.net/publication/323377607_Clinical_Case_Study_Spine_Modeling_for_Minimum_Invasive_Spine_Surgeries_MISS_using_Rapid_Prototyping}
+}
+
+@article{LimFat2011,
+  title = {The Hounsfield value for cortical bone geometry in the proximal humerus—an in vitro study},
+  volume = {41},
+  ISSN = {1432-2161},
+  url = {http://dx.doi.org/10.1007/s00256-011-1255-7},
+  DOI = {10.1007/s00256-011-1255-7},
+  number = {5},
+  journal = {Skeletal Radiology},
+  publisher = {Springer Science and Business Media LLC},
+  author = {Lim Fat,  Daren and Kennedy,  Jim and Galvin,  Rose and O’Brien,  Fergal and Mc Grath,  Frank and Mullett,  Hannan},
+  year = {2011},
+  month = sep,
+  pages = {557–568}
+}
+
+@inbook{Frangi1998,
+  title = {Multiscale vessel enhancement filtering},
+  ISBN = {9783540495635},
+  ISSN = {1611-3349},
+  url = {http://dx.doi.org/10.1007/bfb0056195},
+  DOI = {10.1007/bfb0056195},
+  booktitle = {Medical Image Computing and Computer-Assisted Intervention — MICCAI’98},
+  publisher = {Springer Berlin Heidelberg},
+  author = {Frangi,  Alejandro F. and Niessen,  Wiro J. and Vincken,  Koen L. and Viergever,  Max A.},
+  year = {1998},
+  pages = {130–137}
+}
+
+@inbook{Glsn2008,
+  title = {Robust Vessel Tree Modeling},
+  ISBN = {9783540859888},
+  ISSN = {1611-3349},
+  url = {http://dx.doi.org/10.1007/978-3-540-85988-8_72},
+  DOI = {10.1007/978-3-540-85988-8_72},
+  booktitle = {Medical Image Computing and Computer-Assisted Intervention – MICCAI 2008},
+  publisher = {Springer Berlin Heidelberg},
+  author = {G\"{u}ls\"{u}n,  M. Akif and Tek,  H\"{u}seyin},
+  year = {2008},
+  pages = {602–611}
+}
+
+@inproceedings{Biesdorf2015,
+  title = {3D segmentation of vessels by incremental implicit polynomial fitting and convex optimization},
+  url = {http://dx.doi.org/10.1109/ISBI.2015.7164171},
+  DOI = {10.1109/isbi.2015.7164171},
+  booktitle = {2015 IEEE 12th International Symposium on Biomedical Imaging (ISBI)},
+  publisher = {IEEE},
+  author = {Biesdorf,  Andreas and W\"{o}rz,  Stefan and von Tengg-Kobligk,  Hendrik and Rohr,  Karl and Schn\"{o}rr,  Christoph},
+  year = {2015},
+  month = apr,
+  pages = {1540–1543}
+}