On Work and Summer Vacation

San Joaquín campus
San Joaquín campus

As the summer progresses, and my final weeks creep up on me, I’ve come to realize that I haven’t talked specifically about work very often in this space. It calls back memories of freshman year of college, where you’re making friends and exploring your new life, and you post pictures of people and places and all of the fun you’re having on Facebook, and your mom or dad or some relative comments “Haven’t seen any books yet!”

For the record, I think one of the first pictures I took at Drexel was a selfie in my lab coat and goggles, making a goofy face, holding my calculator, and was sent to my parents with the caption, “First day of school!” Am I doing college right?? 🙂 And while the hectic Drexel schedule can try to chase you down and grab hold of your sanity some days, I wouldn’t trade my education here for anything. I really like school, and I always have. More generally, I really enjoy learning new things. TH and I were talking about this the other night: about learning something new everyday. As small as that “something” may be, it keeps life interesting. It’s a topic that’s come up with my friends that studied abroad here in Santiago last term, and ended with us all agreeing that we want to be people who keep taking classes, practicing a skill (or a few), and traveling when possible to experience new ways of life. Between classes and the opportunities that co-op has afforded me, Drexel has opened a lot of doors. If you’re curious about the co-op model, an op-ed written by President Fry was recently published.

The beginning of my co-op started with a lot of scripted learning: reading textbooks, doing practice problems, working through coding tutorials. It was a crash course in material that I had not yet seen in my time at Drexel. The material will come up in the next few terms, but I haven’t progressed that far yet in my plan of study. My daily life in the lab was an exercise in self-motivation and organized thought. My first month six weeks were spent studying: I filled a large portion of my notebook and renewed the textbooks time after time. And while I don’t feel like I’m anywhere close to an expert in solid mechanics, I learned something, and am able to put my current work into context and explain the general framework of the project.

My day to day in the office consists of processing images and visualizing data, along with some research on the side regarding the potential clinical applications of the process we are developing. As a reminder, the project I’m working on aims to quantify volumetric strain in the lungs to give clinicians the ability to see a colored, three dimensional map of lung strain. My professor oversees a few different projects, and I work closely with my friend NV, who has graduated from PUC and has been working on the project for just about a year. NV graduated with a degree in Structural Engineering, and has been writing the code for the image registration and analysis that I have been using. I consider him my supervisor. My coding skills are very basic, but NV has been very patient and has been teaching me as problems arise.

My main tasks now revolve around processing thoracic CT scans. Through a series of steps, we compare two sets of images from the same patient on the same day: one taken with a held expiration, and the other taken with a held inspiration. Before I go further, here’s some vocabulary you should know:

Segmentation  a three dimensional model of some portion of an image
Registration  a process that tracks the change between two images of the same subject; specifically, tracking points from expiration to inspiration
CT scan  an image set acquired by combining a series of x-ray views: these x-ray views are packaged like slices of bread in a loaf, where each “cut” is a slice, and the entire image set is the combination of the cuts
Python  an open source coding language

Using ITK-SNAP, a software application used to segment medical images in three dimensions, I create a model of each separate lung in both inspiration and expiration. These models are called segmentations. ITK-SNAP has an auto-segmentation feature that makes my life a lot easier! Some images are better suited for auto-segmentation than others, and require more manual touching up following the initial segmentation. This can be likened to “painting” a mask over each cut. I iterate through each image, touching up the layers. Once all of the layers are complete, they are aligned and filled in to make an image of just the areas that were painted.

Following segmentation, I perform image registration and generate results files using a combination of commands issued in the computer terminal, followed by running a Python script written by NV. There are few intermediate steps, but the most important thing to understand is that registration quantifies the change from expiration to inspiration, then, using finite element analysis, we are able to calculate the volumetric strain at a large number of points in the lung. The computer stores this in a file as data, and using Paraview software, I am able to visualize the results: creating an image that shows the data in a three-dimensional lung map. Once in Paraview, I can manipulate the data and create cuts to show the inner structures in various planes, model both the full inspired lung as well as the fully expired lung, and create videos that show the progression of the hot spots of volumetric strain.

As I may have mentioned earlier, the university is closed in February. Since my time here is so short, however, I will be working three out of the four weeks of the month. Today is my first day alone in the office, and it’s very quiet! I don’t love the fact that I’m here working while everyone is off enjoying summer break, but it is what it is, and I’m grateful to have the third week of February off to take a break. While I’m here, I’ll be processing new image sets in order to build our database and working towards my goal number of images in order to fully disconnect from work for vacation. For my final three weeks of work, I plan to write a report detailing my work here while it also serves to instruct the student who will take over my job when I leave.

Some exciting news though! My aunt surprised me a few weeks ago and is able to visit the third week of February! I couldn’t be happier, and I’m looking forward to sharing a little bit of my life here in Santiago with her. We’ll be traveling to San Pedro de Atacama for a few days that week, so keep an eye out for plenty of pictures!

My daily life continues to be happy and relaxed. I’m getting back into running, found a great park nearby to workout in, and go to yoga classes twice a week. My roommates, also, are great. I love football, so we had friends over, they watched the Super Bowl with me last night, we ate typical gringo|American food, and they cheered and sang Chilean fight songs for the team. And the Patriots won!! I’m a New England girl, what can I say.

Good luck in Week 5 to everyone at Drexel, and to all those hearing back about B-round on Wednesday!

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