Week 1: Getting started

Time flies, and now it is the ending of the first week of our BME immersion term. As a student with Electrical Engineering background, I had never worked in a hospital before participating this immersion program. From my experience of the first week, I can say it will definitely be an unforgettable experience for me.

My clinical advisor is Dr. Schwartz in the Department of Neurological Surgery. He is among the nation’s leading neurological surgeons specializing in brain tumor and epilepsy surgery. Unfortunately, he is always working on surgery in OR these days, and I haven’t met with him since came here. However, I have tried schedule with him for shadowing his surgery next week to see the procedures and equipment involved in an open and/or interventional neurosurgery. I think that will really open my eyes, and that’s the point of our immersion program in the hospital. 

Dr. Schwartz also has a research group. His lab has pioneered new techniques in brain mapping in optical recording methods. In this week, I met with some research fellows in the group to get started in the project that I’ll be working on during the immersion program. They study epilepsy on zebra fish to investigate the cellular basis of epileptogenesis in the context of whole neuronal and supporting stromal cell networks. Specifically, they induce seizure in zebra fish, and then record the activation of neurons with 2-photon microscopy along time. My job is to write a script to automatically segment the neurons from 2-photon images, and quantify the activation of each neurons. In this way, we can investigate the propagation of epilepsy associated neurotransmitters in the brain on the cellular level.


During this week, I have read some literature to find out segmentation algorithms that will potentially work for this project. I started with the simple thresholding, but it can only detect half of the neurons. Then, I proceeded to use watershed transform, since these neurons have blurred edge, and watershed works very well with blurred edge. However, this algorithm is very sensitive to noise. As a result of that, there is a lot of over segmentation. In order to solve this problem, I find another algorithm based on watershed, but with more robustness to noise. I plan to figure out how this algorithm works, and implement it in MATLAB. 

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