We're a little crazy, about science!

A unique figure design

Over the past few weeks I’ve been hard a work making a new visualization for some of the data I’d recently processed. This again is for the project I won an award for (here), and while I’m not trying to brag, I’m super proud of how it came together. It was the first time I tried to do something like this and not only did my main-PI give me his approval it sounds like a lot of people from the lab were impressed with this as well. Unfortunately, I can’t quite give away what I did or how I did it, but I can share some of this.

For awhile now I’ve been stuck trying to work with this data I collected last year. It’s been a whole lot of work and a ton of effort on my part to get the data processed and analyzed, but I’ve been steadily chipping away at it. One of the last hurdles I finally cleared about a week ago (here). Well I got all the code written, the data made sense, I’ve validated all of the stuff I’ve done, and it was time to take the next step, which was create the figure to showcase my beautiful newly processed data. Sometimes that’s easier said than done, but I had a great idea for the visualization that I figured would be pretty impressive if I could pull it off.

The inspiration came from 3D models of the brain and long story short, I found some software (called fieldtrip, a MATLAB toolbox) that had a bunch of stuff including 3D models of brains, heads, etc. that I wanted to implement into my visualization. That was the easy step, now I had a basis for what I wanted to use, but I had to somehow force my data into this premade thing and I had no idea how to do that! More importantly, I’m now working in 3D space and the coordinate system could be anything (turns out it wasn’t!) so placing the markers I needed to place may have been a challenge.

Over the last weekend I got my code all together and hammered away at making.. something, anything! A lot of what we’re doing with figures is subjective, I mean the style I like may not be what you like, the way I think something makes the most sense, you may think is completely confusing. Sort of like my blog, I read it and it makes sense to me, there is a logical progression here (if you squint hard enough anyway), but there my thoughts so they are easy for me to follow, your mileage may vary.

The short version is that I figured out the coordinate system. Thank you fieldtrip for using something that made sense, for those interested they used talairach coordinates. Once I figured that out, I was clear to force my data into this visualization. Which I did. It was surprisingly easy, like 10 lines of code or less easy. Then came the hard part…

Once I had everything figured out, which I can only do on a very specific computer because I had to download a lot of other things to get it to work properly and I’m too lazy to do it with all the computers I use, I spent the next four hours adjusting things. Literally I played with the transparency, the colors, the size of my markers. I played with the color for the 3D model, the lighting, basically if it could be adjusted I tinkered with it. In fact, if I’m being honest I am still playing around with it to get it exactly how I want it to look.

There are a few things I still need to figure out, namely how I want to finish this off and my main-PI brought up some good points in the lab meeting today about how I could overlay the data we’re showing. I’ll definitely be sharing the figures here once the paper is published because I’m really proud of how they came out and my main-PI was incredibly supportive of them. I was originally worried that because they were so unique he was not going to think it was a good way to show the data, but he was super happy with how they came out!

The rest of the lab was equally impressed and I actually had a few people who wanted a copy of the code so they could do the same thing themselves. So today’s post is another day where I did something very cool, but yet again I cannot share any of it because it’s still a work in progress and I need to publish it before we can share. But trust me, once that happens everything will be shared! I don’t want anyone else to have to go through what I did to make this!

I will say this though. I hated this project. I didn’t agree with the experimental setup and I still think it could’ve been done better with more planning. I did learn a lot from this project and that’s probably more of the point than anything else. Working with this dataset has been incredibly challenging, not because working with EEG data is challenging (I mean it is, but that’s not the only issue), the dataset had a lot of noise in it that couldn’t be removed so I had to work with the noise instead of against it.

Like I said, I’ve learned a whole lot on this project and even if I’m not super excited about the science I did here, I am happy that I got a lot out of it. I should probably clarify that last bit, I love the science, I do, it’s just not what gets me excited and over the summer I’ve had the chance to really work on two different projects that make me really excited to be working on. The distinction is important to me. I’m glad I did this experiment, like I’m happy to be part of all the stuff I do. This experiment in particular has taught me more than I ever thought I could learn during my PhD and I’m only to the (about) half-way marker. So while I still don’t like it, I’m glad I got to be the one to do it.

As I slowly inch towards the end of the second year of my 365 days of academia project, I’m realizing that while I still have a long way to go, I’ve already come very far. Learning sneaks up on you like that, but I’ve written about that before (here). Now that I’m FINALLY wrapping up this project I can focus on my PhD stuff and I cannot wait! I’ve actually got some good news about all that too, but that’s a post for another day!

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