Rich Hoff Immersion Week 6 - Bye NYC

This week I was able to wrap up my second project in Dr. Cesarman's lab. One member of the lab attempting to acquire image analysis data from immunohistochemistry-stained nuclei of lymphoma patient cells using a software called HALO. This was done with the intention of developing a scoring system for the gene expression of a particular histone mutation. He and Dr. Cesarman wanted me to develop a strategy for performing the image analysis and acquire some preliminary data for a large set of samples so that they could look for trends in the data that could be relevant to gene expression scoring. I figured out how to use the software and went through both slides acquiring and exporting the data for 200+ samples altogether with the optimized image analysis algorithm. Due to the amount of time it would take to process the large number of exported data files and acquire the desired, categorized summary statistics, I wrote a MATLAB code that would do the task for me, also categorizing by sample and gene expression score and saving all of the worked up data to a single spreadsheet. Normally when it comes to doing any kind of significant coding for data analysis, especially for image analysis studies, Dr. Cesarman's lab relies on external bioinformatics companies. Along with the spreadsheets for each set of 100+ samples, I provided them with the MATLAB code so that they can do the analysis themselves again in the future. I also provided them with the raw data files for each sample, a detailed protocol with screenshots detailing my HALO strategy and how to use the MATLAB code, a reference from the company that made HALO with additional instructions about using the specific main HALO algorithm that I was using, and a few side-by-side zoomed in pictures of some samples before and after analysis so that they can evaluate the quality of object (cell) detection using my HALO algorithm. I will receive some feedback this coming week after they go through the data and they will let me know if they have any questions. Perhaps her relationship with the Erickson Lab as well as my contributions to this image analysis project and her ongoing Kaposi sarcoma project with Dr. Erickson may lead to further collaborations with her in the future? Overall I would say that this has been a successful Immersion experience!

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