Presentation is loading. Please wait.

Presentation is loading. Please wait.

for a 3D atlas of human embryos

Published byHunter Nabb Modified over 9 years ago

Similar presentations

Presentation on theme: "for a 3D atlas of human embryos"— Presentation transcript:

1 for a 3D atlas of human embryos
Low-poly models for a 3D atlas of human embryos Reggie Schildmeijer Department of Anatomy, Embryology & Physiology Academic Medical Centre Amsterdam Amsterdam, October 2014 This presentation is about the creation of low poly models for a 3D atlas of human embryos. I’m not an embryologists, I am actually a game developer. So when I started working on this project I was in the same position as most of you are in right now.

2 From three layers to human being
And I had almost no knowledge of the subject. Embryology is really complex and difficult to understand. The examples on the right are recogniseable, they’re developed human bodies. But remember, it has to start somewhere, a single cell. On the left, at 16 days after conception, the embryo exists out of three layers. The blue one? That’s going to develop into the brain, the nervous system and the skin. The yellow one? That will form all the intestines. And what about the red one? Just everything else. As you might imagine, a lot of development has to take place in all three dimensions, and with 2D images it remains difficult to understand. This 16 day old embryo falls under Carnegie Stage 7, the earliest stage in development to be included in the atlas. 0.4 mm Pearson Education, Inc., publishing as Benjamin Cummings T.R. Olson; W. Pawlina F.H. Netter

3

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

5 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 The project is managed by Bernadette de Bakker, PhD student

6 From embryo to model Amira Alignment Amira Amira Blender Segmentation
Microscopic data 28-32 days 42 – 1063 sections Amira Amira Blender Segmentation Reconstruction Modelling

7 From embryo to model Amira Alignment Amira Amira Blender Segmentation
Microscopic data 28-32 days 42 – 1063 sections Amira Amira Blender Segmentation Reconstruction Modelling

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

9 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 Create a smoother model
28-32 days; Aorta

11 Reduce the polycount 85k vertices 17k vertices 28-32 days; Aorta

12 Remove or fix artefacts
85k vertices 17k vertices 28-32 days; Aorta

13 Certain issues are easier with Blender
Single model Eight models 28-32 days; Aorta

14 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 Modelling techniques A variety of techniques Box modelling Sculpting
Boolean Bsurfaces Skin Shrinkwrap Box modelling and sculpting really quick

16 The Boolean cut (1/4) 28-32 days; Neural tube

17 The Boolean cut (2/4) Actually four different parts Hindbrain Midbrain
Forebrain Spinal cord 28-32 days; Neural tube

18 The Boolean cut (3/4) 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 Hindbrain Midbrain Forebrain Spinal cord 28-32 days; Neural tube

19 The Boolean cut (4/4) Hindbrain Spinal cord 28-32 days; Neural tube
NOT BLOOD INSIDE JUST CALL IT HOLLOW Spinal cord 28-32 days; Neural tube

20 Bsurfaces (1/3) 51-53 days; Liver

21 Bsurfaces (2/3) Add a new object Clear the vertices
Use the grease pencil to drawn on surface 51-53 days; Liver

22 Bsurfaces (3/3) Add surface using Bsurfaces add-on 51-53 days; Liver

23 Skin modifier (1/3) 51-53 days; Lung arteries
All that blood has to get there somehow! 51-53 days; Lung arteries

24 Skin modifier (2/3) Add a new object Clear the vertices
Place single vertices All that blood has to get there somehow! 51-53 days; Lung arteries

25 Skin modifier (3/3) Add skin modifier Add subsurf
Scale the vertices with Ctrl+A All that blood has to get there somehow! 51-53 days; Lung arteries

26 Clipping (1/4) 51-53 days; Vertebrae

27 Clipping (1/4) 51-53 days; Vertebrae

28 Clipping (2/4) Clipping border view to peek inside
51-53 days; Vertebrae

29 Clipping (3/4) Select an area to shrinkwrap Store in vertex group
51-53 days; Vertebrae

30 Clipping (4/4) Add a shrinkwrap with the stored vertex group on the model it clips on Coinciding surfaces 51-53 days; Vertebrae

31 The little things Tools Clipping border view Make face OpenGL render
Decimate Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

32 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view Alt+B

33 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

34 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

35 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

36 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

37 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

38 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

39 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

40 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

41 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

42 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

43 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

44 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

45 The little things Tools Clipping border view OpenGL render Decimate
Make face Add-ons F2 Relax LoopTools Copy attributes Relax Bridge Make face Clipping border view

46 So... do we still have some issues?
Please help! Simplify Certain shapes take ages

47 51-53 days; Oral cavity & pharynx
Decimate problem (1/3) 51-53 days; Oral cavity & pharynx

48 51-53 days; Oral cavity & pharynx
Decimate problem (2/3) Something is looking off 51-53 days; Oral cavity & pharynx

49 51-53 days; Oral cavity & pharynx
Decimate problem (3/3) OH MY GOD! LOOK AT THAT MESH! 51-53 days; Oral cavity & pharynx

50 Complexity! 56-60 days

51 Complexity! 51-53 days

52

53

54

55

56

57

58 Scientific annotation and research projects:
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 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 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

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

Download ppt "for a 3D atlas of human embryos"

Similar presentations

1 WORKING WITH 2007 WORD Part 1 Developed October 2007 with lots of help from.

1 WORKING WITH 2007 WORD Part 1 Developed October 2007 with lots of help from.
16.1 Si23_03 SI23 Introduction to Computer Graphics Lecture 16 – Some Special Rendering Effects.

16.1 Si23_03 SI23 Introduction to Computer Graphics Lecture 16 – Some Special Rendering Effects.
1 Bart Jansen Polynomial Kernels for Hard Problems on Disk Graphs Accepted for presentation at SWAT 2010.

1 Bart Jansen Polynomial Kernels for Hard Problems on Disk Graphs Accepted for presentation at SWAT 2010.
Box modeling technique working with sub-objects directly rendering primer.

Box modeling technique working with sub-objects directly rendering primer.
Reconstruction from Voxels (GATE-540)

Reconstruction from Voxels (GATE-540)
Computer Graphics An Introduction. What’s this course all about? 05/10/2014 Lecture 1 2 We will cover… Graphics programming and algorithms Graphics data.

Computer Graphics An Introduction. What’s this course all about? 05/10/2014 Lecture 1 2 We will cover… Graphics programming and algorithms Graphics data.
EZpak Office Clipart Starter Kit for Clinical Packaging office.ezpak.net.

EZpak Office Clipart Starter Kit for Clinical Packaging office.ezpak.net.
The go-to place for all our Extensive Reading needs

The go-to place for all our Extensive Reading needs
Compositing and Blending Ed Angel Professor Emeritus of Computer Science University of New Mexico 1 E. Angel and D. Shreiner: Interactive Computer Graphics.

Compositing and Blending Ed Angel Professor Emeritus of Computer Science University of New Mexico 1 E. Angel and D. Shreiner: Interactive Computer Graphics.
CS 352: Computer Graphics Chapter 7: The Rendering Pipeline.

CS 352: Computer Graphics Chapter 7: The Rendering Pipeline.
Modelling. Outline  Modelling methods  Editing models – adding detail  Polygonal models  Representing curves  Patched surfaces.

Modelling. Outline  Modelling methods  Editing models – adding detail  Polygonal models  Representing curves  Patched surfaces.
Geometric Probing with Light Beacons on Multiple Mobile Robots Sarah Bergbreiter CS287 Project Presentation May 1, 2002.

Geometric Probing with Light Beacons on Multiple Mobile Robots Sarah Bergbreiter CS287 Project Presentation May 1, 2002.
Employing e-Portfolios in Instructional and Co-Curricular Settings Jennifer Matthews, Senior Consultant Blackboard Inc April 13, 2005.

Employing e-Portfolios in Instructional and Co-Curricular Settings Jennifer Matthews, Senior Consultant Blackboard Inc April 13, 2005.
Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings The Language of Anatomy  Special terminology is used to prevent misunderstanding.

Copyright © 2009 Pearson Education, Inc., publishing as Benjamin Cummings The Language of Anatomy  Special terminology is used to prevent misunderstanding.
1 Perception, Illusion and VR HNRS 299, Spring 2008 Lecture 19 Other Graphics Considerations Review.

1 Perception, Illusion and VR HNRS 299, Spring 2008 Lecture 19 Other Graphics Considerations Review.
A Navigation Mesh for Dynamic Environments Wouter G. van Toll, Atlas F. Cook IV, Roland Geraerts CASA 2012.

A Navigation Mesh for Dynamic Environments Wouter G. van Toll, Atlas F. Cook IV, Roland Geraerts CASA 2012.
In the name of God Computer Graphics Modeling1. Today Introduction Modeling Polygon.

In the name of God Computer Graphics Modeling1. Today Introduction Modeling Polygon.
Copyright © 2008 Pearson Education, Inc. Publishing as Pearson Addison-Wesley Chapter 10: Computer Graphics Computer Science: An Overview Tenth Edition.

Copyright © 2008 Pearson Education, Inc. Publishing as Pearson Addison-Wesley Chapter 10: Computer Graphics Computer Science: An Overview Tenth Edition.
Preparing Data for Analysis and Analyzing Spatial Data/ Geoprocessing Class 11 GISG 110.

Preparing Data for Analysis and Analyzing Spatial Data/ Geoprocessing Class 11 GISG 110.
Week 11 - Thursday.  What did we talk about last time?  Image processing  Blurring  Edge detection  Color correction  Tone mapping  Lens flare.

Week 11 - Thursday.  What did we talk about last time?  Image processing  Blurring  Edge detection  Color correction  Tone mapping  Lens flare.

Similar presentations

Ads by Google