Microscopy Part 1: Show n' Tell

If I had time during undergrad to take a biology class there’s a high probability that I would have ended up double majoring in Electrical Engineering and something life sciences related. All of the classes I enrolled in served the sole purpose of meeting my department’s graduation requirements, which meant I could never explore other fields like Biology, Botany, Biochemistry, and so on. So after graduating, I enrolled in a few night time biology courses at a local community college. Besides the course content being fascinating, what continually kept me interested was the lab. Specifically, open lab on Saturdays when I could use the microscopes under no time constraint. I was able to prepare my own slides, experiment with staining techniques, and just explore.

The only sensation I know that reminds me of looking into a microscope is scuba diving. Scuba diving is an out of body experience, immediately your mind registers that you’re doing something impossible, breathing underwater. Once you adjust to this, you’re then captivated by the new world you just gained access to. It’s quiet, you can only hear your respirator, meanwhile, you’re buoyant, and met with the resistance of water all around you. You’re truly in an entirely new environment, every one of your senses is experiencing something brand new. That first glimpse into a microscope is very similar, you’re peering into a new world, every slide feels like you’re entering a new environment. Imagine placing a drop from a pond onto a slide, as you peer into the microscope you’re effectively miniaturizing yourself and “scuba diving” with microscopic organisms. It’s incredible.

I documented everything I saw in open lab, mostly prepared slides but I created my own slides too and experimented with staining techniques. Some of my favorite pictures are seen above at the beginning of this post. Some of the images are special because at that moment I had an epiphany where I connected classroom concepts to the structures of what I saw using the microscope. My bet is that early microscopists had a similar feeling when they saw the miniature world for the first time.

Recently I stumbled upon the subreddit r/microscopy that rekindled my fond memories of open lab. It’s a community of amateur microscopists sharing images, tips, and tricks. I dove into researching microscopes, how much they cost, tradeoffs, etc. After reading countless forum posts and watching videos (Microbehunter Microscopy on YouTube) I settled on an AmScope T490B-DK. It should serve me well in the long run while having the option for upgrades.

Keep an eye out for a Microscopy Part 2 follow up post where I’ll touch on some image processing pipelines I set up using Python and NextFlow. As a first step to familiarize myself, I’m thinking I will take a sample of blood from myself, throw it on a slide, stain/treat it if needed, and then have a pipeline set up so that I can hit “run” and an image will be captured, processed, transformed, analyzed, annotated, and its data pushed into a database. I’m looking forward to playing around with image processing techniques again, something I studied in undergrad. Through capstone projects, research positions, and coursework I developed predictive car tracking algorithms, tilt-shift post-processing algorithms, and object identification techniques.

P.S. For various reasons this is my favorite slide. It’s a slide prepared from a pear, most students have prepared this at some point so it’s frankly nothing special. What you see is a sclereid, it’s what gives that gritty texture to pears. You can read more about it on Wikipedia.