So, you finally got that scope, the pièce de resistance of your reefing gear. You put your beautiful eyes to the lens, eager to finally see what dinos are plaguing you. Maybe to check your phytoplankton culture. To just enjoy the amazing nature of The Microcosmos…or you would, if you could make out what that blob is. Why is it so blurry? Well, it’s gone now, so you don’t need to worry about it anyway.
What should you have done differently in this scenario? I wouldn’t know, I wasn’t there – but in this article, I will point out some things you should keep in mind while prepping samples, and some tools that might help you on your microscopy journey. I hope these will help you acquire your crisp, picture-perfect image for social media. You will get so many boys at reefing prom.
There are several tools and items that I have found myself using every time I do microscopy, besides the standard slides and coverslips:
- I use a couple of different types of glass dishes: a 125 mm (500 mL) dish, and small 35 mm petri dishes. These are good for isolating things before they go on a slide, or if you are using a dissecting (or digital) microscope, to hold samples for observation. Since the dishes can hold water and have a clear bottom, they are good for looking at samples that need to stay alive and/or go back in your tank (e.g. coral frags, crabs, even fish).
- I also regularly use forceps that came as part of a dentistry toolset. I like these because their tips are finer than feeding forceps. They are useful for sample manipulation in dishes and can be useful to hold or nudge coverslips if needed. They are also exceptional at pulling small patches or strands of algae or holding small objects in your aquarium.
- I have a small container of transfer pipettes; the little plastic ones with a bulb on one side that can take up to 1 mL, but larger ones exist too. I also use a 5 mL syringe with a large gauge (18G) needle – it can be a larger diameter needle (probably up to 14G?) but 18G was easily accessible to me. Transfer pipettes are great for general use, and I use them most often to transfer liquid. In some cases, I use the syringe since I can create a slightly more powerful ‘draw’ than the transfer pipettes and take up samples from sand or rocks more easily. However, since it’s still a metal tip, exercise a little caution not to pierce anything delicate (e.g. corals, CUC, yourself, etc.).
If you are using a digital or dissecting microscope, you are probably using a dish (or you should be). If you’re using a larger dish with a lot of water, remember that to get higher magnification you will need to bring the objective lens closer to the sample, so keep an eye on the water level. You do not want water to get inside your objective lens as this will ruin the clarity. Easy peasy.
If you would like to prepare a slide sample, all you need is a single drop – but not a big drop, or you will have trouble focusing…not a small drop or the water won’t spread enough, and you might crush your organism. How do you tell? Simple: Use your transfer pipette (or whatever device) to add a single drop on one side of your slide. Take your coverslip, and either with your fingers (try not to get too much oil on it) or with forceps, and place at an angle to your water drop – aim for roughly 45o – and let the water ‘adhere’ to the coverslip.
Slowly, gracefully, and with poise, lower the coverslip so that the liquid completely spreads under the coverslip, then release. DO NOT let it drop or you might get bubbles. If the liquid doesn’t reach the edges of the coverslip, you do not have enough liquid. You can fix this by trying to add water right next to the coverslip edge and having the capillary action draw the water under the coverslip. If you find that you are having trouble getting your organism into focus, or your coverslip is floating around and not sticking firm, VERY gently tap on the coverslip (the idea is to push out excess water without smooshing the delicate fragile organisms).
Use a pipette to draw up water that leaks out from the edges of the coverslip. If the coverslip is no longer floating on the water drop, you should be fine. You should always use a coverslip.
There are a couple of things you can try with your compound microscope to increase the “crisp” -ness, besides just using your fine-focus knobs on the side. You should be able to manipulate the light source in one or both ways: changing the intensity – usually a slider – and using the condenser-iris contraption thingy to increase or decrease the light beam. Incrementally increasing or decreasing the light intensity and closing/opening the condenser should visibly adjust the clarity of your image. You will notice some organisms might actually become sharper at low light intensity, but with the condenser wide open; each situation will be a bit different. I don’t usually find messing with anything else creates a dramatic change.
Other tips and considerations:
- You should clean your compound objectives at least once (or if they get dirty). Most lens-cleaner solutions and wipes should be acceptable. If you are looking for specialty wipes, look for wipes that are “anti-fog” and “anti-static.” If your objective can be unscrewed, clean both sides of the lens. This includes your ocular lens too!
- To make sure the scale is standardized in every image you can buy calibration slides that have lines denoting micrometer lengths. This will help keep the sense of scale the same in every image despite whatever microscope model or objective you use.
- For digital or stereo-microscopes, you can create different contrasts by using a black-white stage plate, which has a stark white side and a dark black side. The white side can help visualize pigmented or opaque objects, and the black side can help visualize transparent or semi-transparent organisms. Use both and see which one makes a prettier image.
- If you are having trouble focusing on an object or finding the focal plane on a compound, go to a lower objective and use that to focus first. It is best practice to start at the lowest objective (usually 5X or 10X) and make your way to the higher objectives.
- For some extra fun, you can buy various filters to alter the look and reveal different aspects of organisms. Darkfield is great for transparent or clear bodies, which most single-celled organisms are. If you are feeling ambitious, you can buy a polarizing filter and watch shells shine (as long as they’re made of a chemically crystalline structure).
And so dear reader, equipped with your powerful tool and these tidbits and highlights, I wish you success as you start your journey into microscopy. I would also like to highlight that this article is to serve as only a primer; there is a lot more you can know, and that there are plenty of more knowledgeable people out there that you can (more confidently) approach now that you have some context and knowledge. As you level up your skills, you can perhaps master microorganism identification. Perhaps you can make skin and gill scrapes a routine task for diagnosing your fish or detecting issues before they endanger your fish. This is only the start! or detecting issues before they endanger your fish. This is only the start!
Microscope FAQs
What’s a good make and model of microscope for general reef tank stuff?
The digital microscope suggested by Rich Ross in a previous article is a great digital scope. Omax, Swift, and Amscope are popular plug-and-play options, but even off-brand microscopes can suffice and plenty of ID groups use budget models. I would just pick one and start experimenting, but the answer to what is a good beginner microscope can vary, and can be the topic of its own article.
How can I take microscope pictures/video on my phone?
To take pictures on your phone, it would be easiest to purchase a “microscope phone adapter” and affix it to the ocular lens of your microscope. They are available online and come at a variety of price ranges; mine was ten dollars. There’s really nice ones that move in three dimensions if you need that. You can do it solely by hand too, but it will require practice since you will have to hold the phone at a very particular angle – but once you get it, this can be easy.
Will I be able to see bacteria with a microscope?
You can start making out bacteria shapes using oil immersion with a good quality 100X objective lens. I will add that it is impossible to ID bacteria by visuals alone (in this manner, anyway), especially with an unstained sample. Even when stained, there are only a couple of very general qualities we are able to determine – that’s how small they are.
What’s your favorite microorganism to view under the microscope?
I have become enamored by diatoms, thanks to the variety of colors, shapes, and patterns they come in. If you spawn any crabs or shrimp, the larvae are incredible to observe up close.
About the author
Shahab Younesi has been an aquarist since childhood and is a recently established reefkeeper. He has a master’s degree in biology and has been working in research laboratories for many years. He is a life-long marine biology enthusiast and passionate about the scholarly underpinnings of aquarium husbandry and aquaculture.
Main image: Diatoms as seen through a microscope. These species found in the Baltic Sea in northern Europe: Bacillaria paxillifera, Rhopalodia gibba, Tryblionella punctata
Leena Virta, Alf Norkko, CC BY-SA 4.0 https://creativecommons.org/licenses/by-sa/4.0, via Wikimedia Commons
