Automated Extraction of Structures from Sketches of Biological Specimens

Authors

Jamie J. Schirf, Computer SciencesFollow

Date of this Version

5-2010

Comments

A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Masters, Major: Computer Science, Under the Supervision of Ashok Samal and Scott Gardner. Lincoln, Nebraska: May, 2010
Copyright 2010 Jamie Joseph Schirf

Abstract

The goal of this study was to develop automated techniques to extract biological structures from sketches of biological specimens. This will form the basis for a searchable database of information about the specimens. Having such a database enables researchers to efficiently search for specimens with particular qualities or identify unknown specimens.

After some preprocessing of the images, the important internal organs of the specimen are extracted using image analysis techniques. The shape, size, and organization of the organs are used to categorize and then to reorganize them in the image. Results using a large database of sketches of trematodes, in important class of parasites, show that we can extract the internal organs accurately.

Using the database, it will be possible to build an intelligent computer based image re- trieval (CBIR) system around it. As more data are added, this will prove to be of significance to researchers, practitioners, educators and indeed anyone researching such specimens.