Fall term 1998
MWF 11:30 RCC 320 and/or CLS 158
R. Blystone, Ph.D. CLS 153 X7243 or rblyston@trinity.edu
Office hours MWF 9:00 to 10:00 am; M 1:30 to 4:00 pm; and F 2:30 to 4:30 pm

References:

Fortner, B. 1992. The Data Handbook. Spyglass: Champaign, IL.
Russ, J.C. 1995. The Image Processing Handbook, 2nd edition. CRC Press: Boca Raton, FL.
Shotton, D.(editor). 1993. Electronic Light Microscopy. Wiley-Liss: New York.
Starck, J.-L., F. Murtach, and A. Bijaoui. 1998. Image Processing and Data Analysis: The Multiscale Approach. Cambridge: New York.
Tufte, E.R. 1997. Visual Explanations. Graphics Press: Cheshire, CT.

Overview:

Biology data can come in many forms. One of the oldest forms is the image. A biological image can be as simple as a photograph of a flower or as complex as a CT scan of a turtle skeleton. Biological data can also be represented by numbers. The numbers could represent how many ground squirrels live in an area or the optical density readings of oxygen concentrations during an algal bloom. With digital computers it is possible to reduce images into numbers and numbers into images. This course will explore what can be done with biological images and numerical biological data using the digital computer as a tool.

Procedural Information:

The course is organized around doing things with the computer. Assessment of performance will revolve around doing short assignments. The assignments will be graded. There will be only one written exam - the final exam. The function of the final is for you to indicate your knowledge of all the techniques employed during the semester. The final will be worth 15% of the course grade. The course project will be worth 20%. The assignments will be collectively worth 65%. The course project is something that you and I agree should be done. I would suggest that by about October 15 you will have selected a project and that over a six week period you get the work done.

Performance:

Attendance is important. Your class attendance and participation will effect how I view your short assignment work. You may work individually, in pairs, or possibly in groups of three on the assignments and project. However, everyone must equally contribute to the progress of a multiple person group. And I expect a higher level of aggregate performance than I do from a solitary individual. Since this is a three credit hour course, I expect about ten hours a week of effort. Assignments will be graded on originality, execution, effort, and results. I would strongly encourage you to keep a lab notebook of the techniques you try. Just do not play on the computers. Several of the assignments will require you to turn in brief reports. Many of the assignments will require that you submit a visualization.

Week of August 24 August 31 Sept 07 Sept 14 Sept 21 Sept 28 Oct 05 Oct 12 Oct 19 Oct 26 Nov 02 Nov 09 Nov 16 Nov 23 Nov 30 Dec 07 12/15 Final at 8:30 am Tuesday

Topic, Activity, Assignment First class day: Skill inventory, introduction and overview. Assignment: Obtain at least four self-photographs depicting different stages of your life. The digital image: components, file type, introduction to Photoshop Assignment:: Working in pairs. Produce 1) a digital panorama image of campus or lab (rotate camera) and 2) a digital museum set (rotate specimen) Monday is Labor day. Building an image with numerical data, visualizing data. Assignment: Building a temperature gradient map. Optical Scanning and File & Database Management Assignment: Input "baby" pictures. Develop a file structure and data logs. Photoshop correct pictures. Morphing. Working in three and four dimensional space Assignment: Morph the baby pictures. Identify a set of camera lucida or similar drawings, digitize them, photo correct them, and morph them. Microscopy. How to set up a microscope. Köhler Illumination. Focus. Recording the microscope image. Assignment: Getting and displaying the best possible image. Three dimensional reconstruction: image capture, image enhancement, image convolution, image software. Assignment: Produce a serial image database and build a reconstruction. The binary image, erosion, dilation, particle separation, finding centers of mass, building image data tables exporting data into statistical packages, modeling. Assignment: Analysis of Compact Bone, testing a model. Friday is Fall Break day. Biasing data sets. Building better models. Assignment: Analysis of blood. From John Snow to Napoleon Bonaparte: The work of Edward Tufte Assignment: Finding good and bad illustrations of data display. The finer points of Image Enhancement: The work of John Russ. Assignment: The analysis of lung. The construction of a presentation. Finer points of PowerPoint. The rule of seven. Outputting ideas. Assignment: Constructing a PowerPoint presentation of biological data. Remote sensing and the lay of the land. Assignment: Analysis of topography and a virtual field trip. Friday is a Thanksgiving holiday. Biological microscopy revisited Assignment: Completion of project. Presentation of projects. Monday is the last class day. Wednesday is a Reading Day. Summaries, check in.