Summer 2008 Research Fellowships
This was an 8 week program running from June 23th through August 15th, 2008.
The application process is now closed.
2008 Research Report
You can access last year's and previous year's Research reports below:
Summer 2007 Research Fellowships
We have successfully completed our 2007 summer research program in Biology and Information Technology. We had an amazing year this year! Interns included 2 high students and 12 undergraduates mostly from local universities, but from as far away as Puerto Rico. After the 8 week course, summer scholars presented their accomplishments at two workshops on August 15th and August 16th.
High School Students:
Two high school students participated in the program as a part of Apprentice Researchers (AR) program.
Wei Wu - The goal of her apprenticeship was to gain exposure to university research by participating in a research project under the mentorship of a graduate student. Her project, under the guidance of graduate student Nhat Vu, was 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. Here is her final presentation.
Miranda Kapin - Miranda’s project, under the guidance of Chris Banna, was 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. Here is her final presentation.
Undergraduate Students:
Mar-Iam Nieves (Polytechnic University of Puerto Rico) (mentor: Boguslaw Obara, faculty advisor: B. S. Manjunath) and Sadot Banuet (California State Univ. San Bernardino (CSUSB)) (mentor: Boguslaw Obara and Austin Peck, faculty advisor: B. S. Manjunath) are developing a search engine that queries databases and extracting information on a specific word relating to the biological images. Here is the final poster.
Sachithra Udunuwarage (CSUSB) (mentor: Emre Sargin, faculty advisor: B.S. Manjunath) and Steven Parker (CSUSB) (mentor: Alphan Altinok, faculty advisor: Ken Rose) are integrating currently developed image analysis tools to the graphical user interface for microtubule tracking/tracing. Here is the final poster.
Stephanie Perez (CSUSB) (mentor: Emin Oroudjev, faculty advisor: Leslie Wilson) is creating ground truth for microtubule traking and testing various microtubule tracing/tracking methods to improve the performance of the methods. Here is the final poster.
Matthew Strader (CSUSB) (mentor: Zhiqiang Bi, faculty advisor: B. S. Manjunath) is testing R-tree package, a data structure designed to index data with multiple dimensions, as a quicker alternative to the current search methods in the Cortina search engine. Here is the final poster.
Jose Freire (CSUSB) (mentor: Elisa Drelie Gelasca, faculty advisor: B. S. Manjunath) is 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. Here is the final poster.
Albert Garcia (CSUSB) (mentor: Nick Larusso, faculty advisor: Ambuj Singh) is creating ground truth for horizontal cells from 3-D confocal microscope retinal images. He will use the ground truth to compare with the probabilistic segmentation result using random walk. Here is the final poster.
Nicholas Navaroli (CSUSB) (mentor: Luca Bertelli, faculty advisor: B. S. Manjunath) develops a method for the segmentation of cone photoreceptors in cross section of retinal images based on Hough transform and fast marching. Currently work on segmenting benign/malignant breast cancer cells, using a nuclei detector followed by a segmentation technique (Max cut/ NCut/ Region Growing). Here is the final poster.
Ivan Villalba (Cal Poly) (mentor: Jiyun Byun, faculty advisor: B. S. Manjunath) is working on COS1 cell segmentation from light microscope images for analyzing cell live/death ratio. Here is the final poster.
Gabe Luna (UCSB) (mentor: Geoff Lewis, faculty advisor: S. K. Fisher) is studying transgenic rats expressing various rhodopsin mutations which causes retinal degeneration similar to Retinitis Pigmentosa in humans. Here is the final poster.
Jonathan Okerblom (Allen Hancock College) (mentor: Erkan Kiris, faculty advisor: Stu Feinstein) is studying abnormal phosphorylation of Microtubule Associated Protein tau, which has long been associated with Alzheimer¡¯s disease and related dementias. More specifically, he is working on effects of combinatorial tau phosphorylation upon microtubule binding, and the regulation of dynamic instability in vitro. Here is the final poster.
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