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Anatomy, Embryology and Physiology Low-poly models for a 3D atlas of human embryos Reggie Schildmeijer Department of Anatomy, Embryology & Physiology Academic.

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Presentation on theme: "Anatomy, Embryology and Physiology Low-poly models for a 3D atlas of human embryos Reggie Schildmeijer Department of Anatomy, Embryology & Physiology Academic."— Presentation transcript:

1 Anatomy, Embryology and Physiology Low-poly models for a 3D atlas of human embryos Reggie Schildmeijer Department of Anatomy, Embryology & Physiology Academic Medical Centre Amsterdam Amsterdam, October 2014

2 F.H. NetterT.R. Olson; W. Pawlina From three layers to human being Pearson Education, Inc., publishing as Benjamin Cummings 0.4 mm

3 Anatomy, Embryology and Physiology

4 CS 23, 56 days: 28 mm CS 08, 18 days: 1.5 mm

5 Anatomy, Embryology and Physiology Teaching embryological development 3D Atlas of human embryology –Bernadette de Bakker, PhD student –True-to-nature and comprehensible –For students, by students –3D digital series of embryonic development –Interactive, e.g. an app

6 Anatomy, Embryology and Physiology Alignment From embryo to model Amira Microscopic data days 42 – 1063 sections Amira Segmentation Amira Reconstruction Modelling Blender

7 Anatomy, Embryology and Physiology Alignment From embryo to model Amira Microscopic data Amira Segmentation days Amira Reconstruction 42 – 1063 sections Modelling Blender

8 Anatomy, Embryology and Physiology Why Blender? Blender feels easiest for the pure raw modelling needed Constant development Great community Lots of tutorials The simplest answer: open source

9 Anatomy, Embryology and Physiology Knowledge driven modelling With Blender we: –Create smooth models avoiding shrinkage –Reduce the polygon count selectively –Remove artefacts in models –Solve certain issues with more ease Computer is not human –Algorithms do what they’re supposed to do –Algorithms aren’t embryologists

10 Anatomy, Embryology and Physiology Create a smoother model days; Aorta

11 Anatomy, Embryology and Physiology Reduce the polycount days; Aorta 17k vertices85k vertices

12 Anatomy, Embryology and Physiology Remove or fix artefacts days; Aorta 85k vertices17k vertices

13 Anatomy, Embryology and Physiology Certain issues are easier with Blender days; Aorta Single modelEight models

14 Anatomy, Embryology and Physiology Knowledge driven modelling With Blender we: –Create smooth models avoiding shrinkage –Reduce the polygon count selectively –Remove artefacts in models –Solve certain issues with more ease Computer is not human –Algorithms do what they’re supposed to do –Algorithms aren’t embryologists

15 Anatomy, Embryology and Physiology Modelling techniques A variety of techniques –Box modelling –Sculpting –Boolean –Bsurfaces –Skin –Shrinkwrap

16 Anatomy, Embryology and Physiology The Boolean cut (1/4) days; Neural tube

17 Anatomy, Embryology and Physiology The Boolean cut (2/4) days; Neural tube Actually four different parts Hindbrain Midbrain Forebrain Spinal cord

18 Anatomy, Embryology and Physiology The Boolean cut (3/4) days; Neural tube Add a plane on the border Duplicate this plane (and invert faces for the second) Duplicate model Boolean plane A on model A Boolean plane B on model B Spinal cord Hindbrain Midbrain Forebrain

19 Anatomy, Embryology and Physiology The Boolean cut (4/4) days; Neural tube Spinal cord Hindbrain

20 Anatomy, Embryology and Physiology Bsurfaces (1/3) days; Liver

21 Anatomy, Embryology and Physiology Bsurfaces (2/3) days; Liver Add a new object Clear the vertices Use the grease pencil to drawn on surface

22 Anatomy, Embryology and Physiology Bsurfaces (3/3) days; Liver Add surface using Bsurfaces add-on

23 Anatomy, Embryology and Physiology Skin modifier (1/3) days; Lung arteries

24 Anatomy, Embryology and Physiology Skin modifier (2/3) days; Lung arteries Add a new object Clear the vertices Place single vertices

25 Anatomy, Embryology and Physiology Skin modifier (3/3) days; Lung arteries Add skin modifier Add subsurf Scale the vertices with Ctrl+A

26 Anatomy, Embryology and Physiology Clipping (1/4) days; Vertebrae

27 Anatomy, Embryology and Physiology Clipping (1/4) days; Vertebrae

28 Anatomy, Embryology and Physiology Clipping (2/4) days; Vertebrae Clipping border view to peek inside

29 Anatomy, Embryology and Physiology Clipping (3/4) days; Vertebrae Select an area to shrinkwrap Store in vertex group

30 Anatomy, Embryology and Physiology Clipping (4/4) days; Vertebrae Add a shrinkwrap with the stored vertex group on the model it clips on

31 Anatomy, Embryology and Physiology Tools –Clipping border view –Make face –OpenGL render –Decimate Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

32 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things Alt+B

33 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

34 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

35 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

36 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

37 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

38 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

39 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

40 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

41 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

42 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

43 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

44 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

45 Anatomy, Embryology and Physiology Tools –Clipping border view –OpenGL render –Decimate –Make face Add-ons –F2 –Relax –LoopTools –Copy attributes The little things

46 Anatomy, Embryology and Physiology So... do we still have some issues? Please help!

47 Anatomy, Embryology and Physiology Decimate problem (1/3) days; Oral cavity & pharynx

48 Anatomy, Embryology and Physiology Decimate problem (2/3) days; Oral cavity & pharynx Something is looking off

49 Anatomy, Embryology and Physiology Decimate problem (3/3) days; Oral cavity & pharynx OH MY GOD! LOOK AT THAT MESH!

50 Anatomy, Embryology and Physiology Complexity! days

51 Anatomy, Embryology and Physiology Complexity! days

52 Anatomy, Embryology and Physiology

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58 Project leaders: Bernadette S de Bakker Antoon FM Moorman Scientific support: Kees H de Jong Roelof-Jan Oostra Karel de Bree Joris Maarleveld Photography assistance: Berrie Meijer Olga JGB de Bakker Scientific annotation and research projects: ICT & Amira support: Jaco Hagoort Jan M Ruijter Bouke A de Boer Jan G Zegers Ramon MW Fincken Modeling: André C Linnenbank Reggie Schildmeijer Patrick Stroombergen Pjotr M de Weert Berend Bakker Dennis C van Etten Jordy Kalle Jasper Gieskens Rehan Rana Pepijn van der Linden Yoobin Kim Jeroen Pouw Richard Pesch Robin Molenaar Guido Lens Kirsten Aben Babette Bais Claudia Berends Clara Besselink Hjalmar Boon Fatima Bounif Ikram el Bouyahyaoui Charlotte Buijs Marieke Buijtendijk Man-Wai Chan Kaye de Cuba Shosha Dekker Jason van Genderen Maryam Ghariq Charlotte Hafkamp Noortje Hagemeijer Iris Harmsen Laurien Hassing Eden Hodde Dieuwertje Hoornstra Bas Hulstein Babette de Jong Jeroen Kruidenier Laura Kuil Tarik Lachkar Sonja Levy Ramona Linschoten Berrie Meijer Soufiane El-Merbouh Robel Michael Francisco Noyola Marcel van der Poel Robert Post Marjolein Seinen Zaid Al-Shaibani Maxime Slooter Daniël Smidt Fabienne Stubenrouch Denise Torenstra Tyas Veldhuis Isabelle de Vries Moritz Warmbrunn Sander van Wieringen Merel de Witte Sitaya Zomer

59 Anatomy, Embryology and Physiology Contact 3D Atlas of Human Embryology - Lite –iPad, iOS 7+, free download –Features two complete stages Prof. Dr. A.F.M. Moorman Reggie Schildmeijer


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