Considerations for Purchasing a Microscope at a Wastewater Treatment Facility

Published On: July 10, 2023

When considering the maintenance of your car, do you wait until it’s on fire before taking it to the shop? Of course not! We are taught from a young age that we need to check the oil and tire pressure in order to keep the car in good condition. Monitoring the tiny details is how we prevent small issues from becoming big problems. In wastewater, this same concept applies. Like the dip stick in your car, there are many tools available to wastewater operators to assess plant health. Some of these tools include pH, dissolved oxygen, temperature, and settling. One of the most useful tools available for the last fifty years has been to monitor the smallest component of treatment, the microbial community. It is one of the best ways to identify and proactively correct issues within the plant before effluent quality is impacted.

Unfortunately, the use of microscopes to asses the microbial community, or bugs, is not widely incorporated in today’s assessments of plant health by operators. This happens for a number of reasons. Emerging technologies and monitoring systems often overshadow the power of the microscope at newer facilities. At older facilities, it is likely that a corroded microscope from the 70s is sitting on a shelf somewhere. Because of its age, its unusable, and your facility may not want to purchase another one for fear of it being equally as unused.

Adding a new microscope to your facility may sound like a simple task until the prices, features, and optional components stop you in your tracks. When a given microscope can cost anywhere from 200 to 60,000 dollars, have a magnification from 2x to 2,000x, cameras ranging in resolution from 0.3 to 30 megapixels, or have options like oil immersion and phase contrast, its no wonder its difficult to decide what works best for a wastewater application. In order to identify which microscope is best suited to your facility, there are a few key considerations.


In most wastewater applications, the bugs we examine are not the bugs performing the biological treatment. It is a rare scenario that it is necessary to have a microscope capable of identifying a bacterium that is only 0.5 micrometers. It is common, however, to assess plant health on the type and abundance of indicator bugs like protozoa and metazoa in your sample.

For most analyses that include checking the floc density/size/shape and the presence of indicator bugs, total magnification of equal to or less than 400x is sufficient. Total magnification is made up in two parts, the magnification of the eyepiece and the magnification of the objective. For example, a 10x eyepiece and a 40x objective gives a total magnification of 400x. Microscopes often come with a set of objectives ranging from 4 to 100x. Objectives that are 100x are commonly used for more advanced analyses and typically require oil immersion. These objectives are used for observing the small details of cell shapes, septa, and consumed material, but isn’t essential to assess plant health.

Lens Quality

Like a camera, the quality of the glass used in the construction of the objectives can dramatically impact the clarity on the microscope. Identifying indicator bugs don’t require high-quality objectives. Most objectives from reputable brands are sufficient for these tasks. High-quality objectives are used for tasks such as identifying the type of filamentous bacteria, whereas standard objectives are adequate for distinguishing between filamentous bacteria or other fibers.


For the considerations discussed above, most any microscope could become a useful tool. When considering a camera for a microscope, that’s where decisions from facility to facility will vary the most. Because the microbial community at every facility is different and changes based on plant conditions, it is often useful to create reference photographs during facility events such as the week before a biomass die off. This allows operators to compare their findings to historic facility events and preemptively act to avoid impacts to effluent quality.

I have taken photos using everything from my phone to fully integrated HD cameras. The role of a microscope-mounted camera is to capture photos and video of what is in the sample, and requirements will vary based on intended use. For instance, if the camera will only be used for capturing images for senior operators to assist with identification of indicator bugs, then a basic 2 MP camera is sufficient. If educational material will be generated from the photos and videos taken from the microscope, then a higher resolution camera would be required.

Microscope Head

I have been seeing a trend towards microscopes that do not have eyepieces, but instead have one large screen to view the samples. Which kind of head a microscope has will come down to personal preference and whether or not it includes a camera. Trinocular heads are the traditional way to include eyepieces to view the sample as well as a dedicated port to attach a camera. Trinocular heads and the screened microscopes require the least amount of work to transition from looking at the sample with your eyes to taking a photograph. Based on the detail of identifications being done, either may work. However, when fine detail is required, trinocular heads are best. The human eye has an equivalent megapixel count of over 500, which is far greater than any microscope camera. So, when fine details need to be seen, it is best to use your eyes.

For microscopes without cameras, or ones that seldomly use cameras, a binocular or monocular microscope is ideal. The tri, bi, or mono are in reference to the number of eyepieces on the microscope head (3, 2, or 1, respectively). For binocular or monocular microscopes, eyepieces can easily be swapped out for a camera, but are difficult-to-impossible to look through the eyepiece while the camera is mounted.


The stage is the platform in which the slide rests and is easily overlooked when considering the bells and whistles for your microscope. The sample slide is placed on the stage and can either be held down by clips, moved around by hand, or moved mechanically by the stage. Selecting which type of stage to use should be based on the anticipated use of the microscope. For cursory viewing of the indicator bugs or floc shape, any stage will work. Mechanical stages, however, are most common on wastewater microscopes. Mechanical stages are used to systematically move across the sample. This becomes critical at higher magnifications as well as when performing counts on the abundance and types of indicator bugs present in the sample. When selecting a microscope, a mechanical stage, or the option to attach one, should not be overlooked.


In my experience, inexpensive microscopes have been perfectly capable to perform the analyses I have required at wastewater facilities. I have chosen to use microscopes that have cost 20 times less than others simply because they were better suited for what I needed. In general, most of the microscopes I have seen that are actively being used in facilities range from about 800 to 3,000 dollars. The considerations listed above are what drive the user experience of the microscope. By assessing what the anticipated use of the microscope will be and the features is should include, most microscopes that check all the boxes should be a pleasant experience and an incredibly powerful tool for your facility.

If you would like to learn more about microbiology in wastewater, join us August 16th for our upcoming webinar. 

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