2007 Internship Projects

group photo of the 2007 interns

A total of 12 undergraduates from the universities below and 2 local high school students participated in the 2007 summer internship program.

Polytechnic University of Puerto Rico
California State University, San Bernardino
California Polytechnic Institute
Allen Hancock College
University of California, Santa Barbara

2007 Research Report

Projects

Studying Abnormal Phosphorylation of Microtubule Associated Protein Tau

Mentor

Stu Feinstein (faculty advisor), Erkan Kiris

Student Interns

Jonathan Okerblom
​Allen Hancock College

Abstract

Studying Abnormal Phosphorylation of Microtubule Associated Protein Tau — which has long been associated with Alzheimer's disease and related dementias 

Final Poster 

Develop a Method for the Segmentation of Cone Photoreceptors in Cross Section of Retinal Images Based on Hough Transform and Fast Marching

Mentor

B.S. Manjunath (faculty advisor), Luca Bertelli

Student Interns

Nicholas Navaroli
California State University, San Bernardino

Abstract

Final Poster 

Creating Ground Truth for Horizontal Cells from 3-D Confocal Microscope Retinal Images.

Mentor

Ambuj Singh (faculty advisor) , Nick Larusso

Student Interns

Albert Garcia
California State University, San Bernardino

Abstract

Final Poster​

Developing an Evaluation Method for Various Segmentation Algorithms to Assess the Performance of the Segmentation Algorithms

Mentor

B.S. Manjunath (faculty advisor), Elisa Drelie Gelasca

Student Interns

Jose Freire
Jose Freire
California State University, San Bernardino

Abstract

Developing an Evaluation Method for Various Segmentation Algorithms to Assess the Performance of the Segmentation Algorithms by Comparing the Segmentation Results to the Manually Obtained Segmentation through the Implemented Quality Evaluation Measures. 

Final Poster

Testing R-tree package — a data structure designed to index data with multiple dimensions

Mentor

B.S. Manjunath (faculty advisor), Zhiqiang Bi

Student Interns

Matthew Strader
Matthew Strader
California State University, San Bernardino

Abstract

​Final Poster

Creating Ground Truth for Microtubule Tracking and Testing Various Microtubule Tracing/Tracking Methods to Improve the Performance of the Methods

Mentor

Leslie Wilson (faculty advisor), Emin Oroudjev

Student Interns

Stephanie Perez
Stephanie Perez
California State University, San Bernardino

Abstract

Final Poster​

Integrating Currently Developed Image Analysis Tools to the Graphical User Interface for Microtubule Tracking/Tracing

Mentor

B.S. Manjunath (faculty advisor), Ken Rose (faculty advisor), Emre Sargin, Alphan Altinok

Student Interns

Sachitra Udunuwarage
Sachithra Udunuwarage and Steven Parker
California State University, San Bernardino

Abstract

Final Poster

Developing a Search Engine that Queries Databases and Extracting Information on a Specific Word Relating to the Biological Images

Mentor

B.S. Manjunath (faculty advisor), Boguslaw Obara, Austin Peck

Student Interns

mar-iam nieves
Mar-Iam Nieves​
Polytechnic University of Puerto Rico
Sadot Banuet
California State University, San Bernardino

Abstract

​Final Poster

Ground Truth for Evaluating an Automated Program to Segment Nuclei in the Inner Nuclear Layer of the Retina

Mentor

Chris Banna

Student Interns

miranda kapin
Miranda Kapin (high school student)

Abstract

To provide ground truth for evaluating an automated program to segment nuclei in the inner nuclear layer of the retina. Miranda started by learning the different layers of the retina. Next, she progressed to enucleating the eye, sectioning the eye, and finally applying antibodies to visualize the different layers of the retina. She then watched and learned how the images were taken on a laser scanning confocal microscope. To provide the ground truth, Miranda painstakingly outlines nuclei after nuclei within the inner nuclear layer of retina from 10 images. She then repeated the process a second time. The ground truth will then be compared to the ground truth created by others on the same data set and used to compute intra-person errors and inter-person errors. This will provide the range of error that an automated program needs to achieve in order to be useful.

Final Presentation

Image Segmentation using Graph Cuts and to Apply the Algorithm to Segment Retinal Layers in Confocal Images

Mentor

Nhat Vu

Student Interns

Wei Wu (high school student)

Abstract

​To learn about image segmentation using graph cuts and to apply the algorithm to segment retinal layers in confocal images. Starting with little knowledge of image processing, Wei quickly learned fundamental concepts such as 2D Fourier transforms, image filtering, and high dimensional feature spaces. Using the Matlab programming environment, she applied these concepts to define edge weights for graph cuts, having only minimal programming experience before the apprenticeship program. By the conclusion of the program, Wei successfully applied graph cuts to segment images based on intensity and color.

Final Presentation