--What Is BioQUEST?


--First Review

|--Convince Me
|--Diffusion Laboratories
|--DNA Electrophoresis
|--Image Analysis
|--Interactive Calculus
|Problems in Biology
|--Investigative Cases
|and Case-Based
|Learning in Biology
|--Metabolic Pathways
|Construction Kit
|--Phylogenic Investigator
|--Real Time Data
|--Wading Bird
--Extended Learning
--Software Materials
--Support Materials

Image Analysis

Robert Blystone and Richard Cooper (Trinity University)
Screen Shots | System Requirements

The Image Analysis text module introduces students to the techniques of digital imaging analysis. Using the freeware program NIH-Image (found in the Support Archives folder) and the included images of starfish embryos in cleavage, students learn some techniques for estimating the size of an image, get a brief introduction to sampling theory, create a model of the "ideal" image, and learn to analyze their own images to find the ones that best fit their model. Below is an excerpt from the section on analyzing the raw data:

Of the 100 specimens in this raw dataset, which five best represent embryos
with 1 through 16 cells and the first four cleavage divisions?

Part of the Starfish Embryos dataset (8-cells)
(Actual images are larger)

Interesting challenge? We have to figure out how to sample our data. Our first step is to create some numbers so that embryos can be more accurately evaluated.

The analysis and measurement procedure is as follows:

  • Open each of the images.
  • Analyze > Options Select Area, Perimeter, Ellipse Major Axis, Ellipse Minor Axis
  • Analyze > Set Scale Units = micrometers; 0.77 pixels per micrometer
  • Options > Threshold
  • Analyze > Analyze Particles min particle = 200; max particle = 10,000; check all boxes; OK
  • Analyze > Show Results  File > Export (Save as measurements)

System Requirements

Macintosh or Power Macintosh

  • System 6.07 or later; System 7.1 or later for Power Macintosh.
  • 68030 processor or higher.
  • At least 8MB RAM, more recommended.
  • QuickTime 2.0 or later required to play the QuickTime movies.

BioQUEST@beloit.edu || http://bioquest.org