Week 2

First of all, some updates on my project, 2-photon zebra fish neural image segmentation. As I have mentioned in last week’s blogger, I have tried a couple simple algorithms, like simple thresholding and watershed. Here is the results of them:


Fig 1: Thresholding results. 

  1. Thresholding (Fig 1). This algorithm is easy to understand, and is usually used as a preprocessing step.
  2. Watershed. It is a commonly used segmentation algorithm. Intensity of image is considered to be height in the topography. As water is flooded into the topography, different catchment basins are separated when different flooded regions started to merge.Here, this algorithm is implemented in two different ways:

    1. Thresholding; generating the distance map based on the binary image; applying watershed to the resulting distance map. (Fig 2)
      2. Fig 2: Distance map (left) and watershed segmenting results (right).
      Fig 3: Image imposed with regional minima (left) and watershed segmenting results. 
    2. Thresholding; based on the binary image, impose regional minima to wherever the binary image is zero; applying watershed to the resulting image. (Fig 3) .
  1. Watershed-based neutrosophic approach.
    Classic watershed is very sensitive to noise, leading to over segmentation. In order to solve this problem, a watershed-based neutrosophic approach is proposed. In this method, neutrosophy is applied to image processing by defining a neutrophic domain, which is described by three subsets. According to the results in the paper [1], this method is more robust to noise. I've implemented this method in matlab, but may need more time to adjust parameters.
     
Besides projects, I had a chance to shadow Dr. Schwartz's surgery on Thursday morning. That was my first time to shadow a surgery. Several things were impressing to me. First, the surgery was to remove a brain tumor. In order to do that, they used endoscope and a needle to drill a hole to the brain through nose and then got rid of the tumor through the hole. In this way, surgeons don't have to open the brain to remove the tumor. This can greatly reduce the risk of infection during surgery, and it's  also good for recovery. Second, real-time MRI guidance is used in the surgery. Third, several persons cooperated to complete the surgery. Forth, the preparation before the surgery took much more time than I thought. 




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