GEO 391

DIGITAL METHODS IN PALEONTOLOGY

 

This is a seminar/hands-on course for graduate students interested in working with and publishing CT data.  This class will provide a forum for students to become experts on cranial osteology in the course of exploring the technical issues of acquiring, designing, manipulating, authoring, and publishing digital content.  This is a project-based course, where students will work towards publishing a CT data set.

 

Goals for CT data projects:

·      Understand CT scanning technology

·      Process images to appropriate resolution and dimensions

·      Generate all three slice planes from given data

·      Build animations for each plane

·      Provide images with anatomical labels and slice numbers in an appropriate size, color, and font

·      Determine sources and ranges of error

·      Document all protocols and methods

·      “Show and tell” sessions including discussions of morphology

·      Written anatomical description of project specimens

·      'Publish' results on Web and CD-ROM

 

SOFTWARE LIST:

·      VGStudioMax

·      ImageJ

·      QuickTime

·      Adobe Photoshop

·      Adobe Illustrator

·      IrfanView

·      Microsoft Word/ Excel

 

Grading is based on assignments and the final project.  All work must be delivered on time.

Students must obtain an Individually Funded (IF) account to use the CIT MMLab.

WARNING: Never put your trust in technology.  All students are responsible for providing storage media and backing up work. 

 

Setting up an IF storage account:

http://www.utexas.edu/its/account/

Read the introduction, follow steps.  You’ll need a UNIX account for storing and transferring files.  You may set your own disk quota.  You are charged per megabyte.

 


MEETING SCHEDULE

 

MEETING 1

·      Overview of course

·      Past and future of CT

·      Intro to facilities: CIT, UTCT, and Vislab

·      Basics of CT and computer data and digital terminology (glossary)

·      Nuts and bolts—IF accounts, storage media, etc.

 

Assignment 1:

·      Set up IF account

·      Familiarize yourself with terminology

 

MEETING 2

·      Image processing of Tapir atlas data set

·      Introduction to basic image processing software

 

Assignment 2:

·      Finish processing Tapir atlas data set (3 QuickTime movies w/slices numbered)

·      Begin gathering references for anatomical labeling

 

MEETING 3

·      Review results of Tapir exercise

·      Discuss sources of error

·      Introduction to Adobe Photoshop

·      Receive project data sets and establish work groups

 

Assignment 3:

·      Begin processing project data sets – reslicing, leveling, numbering, and making animations

·      Begin writing methods section of your description

 

MEETING 4

·      Discuss Assignment 3

·      Data mining

·      Archiving data/How to burn a CD

·      Introduction to Adobe Illustrator

 

Assignment 4:

·      Label one slice

·      Begin gathering anatomical references

·      Write up methods section and reference list

·      Back-up image processing on CD, with contents file

 

 

MEETING 5

·      The Art of Labeling

·      Discuss database of anatomical terminology

 

Assignment 5:

·      Begin labeling

·      Record new labels in database

 

 

MEETING 6

·      Introduction to resources of the Vertebrate Paleontology Laboratory

 

Assignment 6:

·      Continue labeling

 

 

MEETING 7

·      Introduction to Computed Tomography, Part I

·      Show and tell labels

·      Work group reviews

 

Assignment 7:

·      Begin written anatomical description of specimen.

·      Continue labeling

 

MEETING 8

·      Introduction to Computed Tomography, Part II

·      Show and tell labels

·      Work group reviews

 

Assignment 8:

·      Continue labeling and writing description

 

 

SPRING BREAK—KEEP LABELING

 

 

MEETING 9

·      Introduction to 3D digital renderings

·      Show and tell labels

·      Work group reviews

 

Assignment 9:

·      Continue labeling and writing description

 

 

MEETING 10

·      Image processing for the web

·      Creating web pages

·      Show and tell labels

·      Work group reviews

 

Assignment 10:

·      Create web-sized animations for each slice plane

·      Continue labeling and writing description

 

MEETING 11

·      Applications of morphometrics to CT data

·      Show and tell labels and web-sized movies

·      Work group reviews

 

Assignment 11:

·      Continue labeling and writing description

 

MEETING 12

·      Assorted anatomical systems Part I

·      Show and tell labels

·      Work group reviews

 

Assignment 12:

·      Continue labeling and writing description

 

MEETING 13

·      Assorted anatomical systems Part II

·      Work group reviews

 

Assignment 13:

·      Continue labeling and writing description

 

MEETING 14

·      Project presentations, Part I

 

Assignment 14:

·      Continue labeling and writing description

 

MEETING 15

·      Project presentations, Part II

·      Turn in final project CD (including labeled images, web-sized movies, methods, label database, and written description)

 

 

_______________________________________________________________

Copyright 2001.

University of Texas High-Resolution X-ray Computed Tomography Facility

The University of Texas at Austin Center for Instructional Technologies