About Sam Anzaroot (Me):
I am an undergraduate computer science student (Junior) at Queens College of the City University of New York, previously from Hofstra University. I hope to graduate by August 2010. I've lived my whole life in Brooklyn, New York which has some people scratching their heads about my decision to spend a summer in a college town in Texas.
I'm a bit of a science nerd (miming pushing nerdy glasses up toward eyes ala Conan O'Brien) and have an interest in the intersection between science and computation, which I guess is why I'm working in the Brain Networks Lab this summer. I'm also a freelance web designer, developer, and programmer. You can see some of my work at samanz.com. and I can be contacted at sja4343@cs.tamu.edu
I am also a really big New York Mets Fan, obvious from the cap I'm always walking around with. And despite their most recent track record, they are the best team in baseball, and are not choke artists (I'm talking to you Cole Hamels, who definitely reads this webpage).
Weekly Informational Bulletins:
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Week One: The Summer Begins
So, yeah.. summer in Texas. Right. So there I was, standing in a completely foreign place after coming off the most interesting puddle-jumping turboprop...More..
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Week Two: The Week After Week 1
Hi Y'all! Here is where I inform you of what I did this week. I got my prototype working better then before and sat through Donghyeop's actual dissertation defense...More..
The "Brains" of My Project:
The Brain Networks Lab houses a really amazing machine called the Knife-Edge Scanning Microscope (KESM). This incredible device has the ability to scan complete organs (like brains) from small animals (like rats) at a really high resolution and the result is incredibly large amounts of data in the form of image stacks. Despite the immense size of the data, the data has to be released to the public, and effective methods of distributing large quantities of three-dimensional data do not exist. My time at Texas A&M will be spent trying to solve this problem.
I've created a method of releasing this data which is an implementation of a google-maps like interface which can be zoomed in and out for each layer of the data. The different layers can be overlaid on top of the current layer in order for users to view a fly-through of the data in three-dimensions. I've also created a method of adding three-dimensional annotations to the data.
Deliverables:
- For latest code: Git Repository
- Released code: Viewer.zip
- Paper as PDF
- Poster as Powerpoint
My Abstract
The purpose of this research is to discover and implement methods of allowing public access to high-resolution volumetric datasets such as those obtained from the Knife-Edge Scanning Microscope (KESM), as well as effective methods of annotating such data.
The KESM is designed to image complete organs from small animals, and the resulting scans produce large amounts of data in the form of high-resolution image stacks. The main goal of this project is to provide a way of allowing users to easily browse the images in three dimensions in a relatively low-resolution format while maintaining the ability to view interested regions in high-resolution using a lightweight web interface.
The secondary goal of the project is to allow annotation of the data with domain information, a problem exacerbated by the requirement of allowing the annotation of three-dimensional structures using just an image stack. The project aims to use only the standard web tools of CSS, HTML, and JavaScript to view and annotate the data to ensure that a wide user base can access the application. The results of this research include the creation of a public JavaScript application that can view volumetric image stack data, and an annotation system that seeks to maximize the ability to annotate three-dimensional structures using the data viewer.
My Mentors (aka Smart People):
An undergraduate research student is like a wondering ghost without advisors and mentors. My two mentors are Dr. Yoonsuck Choe and Dr. John Keyser. Both are amazingly brilliant and you can read more about them on their websites.
Graduate Students who help me in the lab currently include: Huei-Fang Yang, Timothy Mann, David Mayerich, Daniel Miller, Donghyeop Han, and Jae Rock Kwon.