It was another interesting week at the lab. I got to image samples that I segmented, fixed, washed, and placed on slides. It was a self-done project. In the previous week I described the segmenting-fixing-washing process but this week I learned the simple task of putting the samples on glass slides to use underneath a microscope. I found it to be a funny process considering they use nail polish in order to fix the sample to the slide.
After doing all that stuff though I finally got to use the microscope to see what my samples looked like. In this image, you can see my sample. The bright pink color is because the sample is being lit up with a laser. This laser is set to a specific wavelength and spectrum intensity, exciting the fluorescent tag(SiR-DNA) that I stained the cells with. This tag is highlighting the nuclei in the cell tissue. The wavelength of light being emitted by the laser and tag leads to the pink color.
After seeing this image I concluded I needed to use thinner simples. The high concentration of dots, nuclei, in the picture of the liver tissue suggests there was multiple layers of cells in the image, making it harder to do further analysis. So after realizing that, I prepared samples that were smaller, about 8-10 microns this time. And instead of using a gelatin slide, Anthony (PHD student) and I used poly-di lysine coated slides, to ensure that the sample stuck to the glass better when we stained and washed it. This might cause problems later when we end up using this procedure for STORM imaging techniques though. STORM is a new imaging technique that can produce higher resolution visualization of molecular structure, as well as biological interactions and processes. Because it is rather new, a few students in the lab, including Anthony who I work most with are trying to figure out the best procedure for using it.
I also have been doing a lot of computational stuff this week too. I am still working on my project from last week, in which I was designing a code to find the best x, y, z translations to align images through multiple rounds of imaging that might cause drift. This is a really computationally intense code. Every time I ran it, it would take hours to compute, and I often would wait and then just end up with an error, making it hard to see and adjust my work. Eventually, Anthony suggested that I could run my code in the Brown Super Computer server. I think I’m gonna try that next week.
The New England weather has been brutal this week. Recently its been raining almost every night. The storms haven’t been the bad part though, its the humidity they cause. I feel like I’ve been sweating all day everyday for the past week. I miss the Colorado dry air. One night I snapped a photo of the low clouds over the city. It kind of gives you an idea of how stifling the humidity has been.
Other than that, the Fourth of July was cool. I biked to Bristol, Rhode Island, which has the oldest Fourth of July festival in the nation, to see their parade. I also went to the water fire in Providence. It was a cool event, they lit fires in the middle of the river, and there was tons of people and street vendors throughout downtown. Sadly I forgot to grab pictures of all this.
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