3D Morphology with Open-Source Software

3D Morphology with Open-Source Software. Day/time Wednesday, April 11, 8:00 AM – 12:00 PM.  Room: Texas 7, Organizer: A. Murat Maga, (University of Washington). Maximum attendance: 65 

Registration for this workshop is now closed. It has reached maximum capacity. 

Thanks to online and free repositories like MorphoSource, Smithsonian Institution Digitization Program, DigiMorph, Phenomes10K, and others, 3D specimen data are getting ubiquitous in anthropological sciences. Such wealth of data can open new venues for investigation whether questions are quantitative (measurements, shape analyses) or qualitative (detailed anatomical descriptions and interpretations based on 3D renderings). These repositories and 3D data should be particularly important and appealing for graduate students, as they offer convenient and free access to specimens and help democratize the field in the long run. While datasets are conveniently available online, the know-how to process and analyze them does not seemed to be widely disseminated in the community.

This workshop will use free, open-source 3D visualization tools to retrieve, process, visualize and measure specimen from online repositories, as well as custom data from imaging labs. Since processing and analysis of the volumetric data (e.g., CT and MR) is more challenging, the workshop will focus primarily on them. However, the software that we will use (3D Slicer) can handle 3D surface data (PLY/STL/VRML/OBJ), and we will cover pertinent topics.

In this half-day workshop, topics we cover will be:

1.     Introduction to 3D Slicer and 3D morphology (10-15 min)

2.     3D Data wrangling (format conversions) (15-20 min)

3.     Image segmentation and processing (60 minutes)

4.     3D visualization (still rendering and movies) (30 minutes)

5.     Obtaining measurements (recording landmark coordinates, distances, areas and volumes) (30 minutes)

6.     Break out session and Q&A (60 min)

While not mandatory, attendees are encouraged to bring their own laptops and data, so that they can follow along. 3D Slicer works on Windows, Mac and Linux. Sample data for workshop and step-by-step instructions will be posted on the github prior to the workshop. Participants are limited to a maximum of 20.

The workshop is designed for graduate students, junior faculty, anyone who wants to learn how to work with 3D specimen scans