Observing Kindey Stone Under Microscope Guide

Observing Kindey Stone Under Microscope

Kidney stones are a typical problem worldwide, and their treatment is very expensive. Passing stones is supposedly one of the most painful experiences a person can go through. And looking at a kidney stone under the microscope can help you determine what they look like up close.

Collecting samples of kidney stones will not be as easy as the earlier experiments, and often this type of observation is done in laboratories. But there are a few things you can do to increase your chances of observing a kidney stone.

Before we head on to the observation, let us first know more about these stones that cause illnesses to the human body.

What is a Kidney Stone?

A kidney stone is a solid mass or crystal that can be as little as a grain of sand to the size of a golf ball and, in some cases, even bigger. You may not even realize you have a stone if it is small. Even tiny stones can cause excruciating agony when they pass through your urinary system. Fluid passing through the kidneys (urine) carries small stones out of the body. But if a stone gets stuck along the way, it can cause serious problems.

Kidney stone formation happens urine contains too much mineral and not enough water. The minerals crystallize and form a solid mass. Uric acid is one type of mineral that causes kidney stones to develop. Other minerals that can form kidney stones include calcium, oxalate, and phosphate.

Scanning electron micrograph of a kidney stone
Credit: Kidney stone, SEM. Kevin Mackenzie, University of Aberdeen. Attribution 4.0 International (CC BY 4.0)

How Do People Get Kidney Stone?

Human kidney stone forms when urine contains too much mineral and not enough water. The minerals crystallize and form a solid mass. Uric acid is one type of mineral that can form kidney stones. Other minerals that can form kidney stones include calcium, oxalate, and phosphate.

There are several reasons why a person might have too much of these minerals in their urine. Some people inherit a tendency to form kidney stones. Diet, weight, and how active you are also play a role in whether or not you’ll form kidney stones.

People who drink too much soda or coffee, eat a high-protein diet, or don’t drink enough fluids are more likely to get kidney stones. Not drinking enough fluids can cause urine to become very concentrated and increase the likelihood of stones forming. Obesity also puts people at risk of developing kidney stones.

What are the Symptoms of Having Kidney Stones?

A stone can be present in the kidney for years without being detected. When it begins to move or grows large, though, you may have symptoms. The following are signs of a human kidney stone:

  • Lower back or side pain. This pain might start as a dull ache that comes and goes. It can also become severe, resulting in an emergency visit.
  • Vomiting and nausea
  • Pain when urinating
  • Blood in urine
  • Fever or chills
  • Unable to urinate
  • Smelly and cloudy urine
  • Feeling the need to urinate often

Smaller stones may not cause pain or other symptoms. These “silent stones” pass out of your body in your urine.

What are the different types of kidney stones?

There are four types of kidney stones:

  • Calcium stones – The most common type of kidney stone, accounting for about 75% of cases. They are usually made up of calcium combined with oxalate or phosphate.
  • Uric Acid Stones –  These form when there is too much uric acid in the urine. Uric acid is a waste product made when the body breaks down protein.
  • Struvite Stones –  These stones are made up of a combination of magnesium, ammonium, and phosphate. They form in response to an infection in the urinary tract.
  • Cystine stones  – The least common type of kidney stone, accounting for about 2% of cases. Cystine is a naturally occurring amino acid.

Observing Kidney Stones Under the Microscope

different types of kidney stones using Scanning electron micrograph
Source: Research Gate

Observing kidney stones under the microscope reveals an interesting world of microscopic images. You will need the following to start your observation:


To observe a kidney stone, you will need the following items:

  • microscope slides
  • coverslips
  • specimen jar or container
  • immersion oil
  • slide labels
  • sample specimen for observation
  • Electron and stereo microscope

MUST-READ: Light Microscope vs Electron Microscope


Before you begin to observe your kidney stone, there are a few things you need to do first:

  • Kidney stone specimens can b sourced from laboratories, hospitals, clinics, or the national kidney foundation. If you are unable to get a specimen from these places, you can also try to get it from your local water treatment plant.
  • Once you have obtained a specimen, make sure to clean it well and remove any attached kidney tissues. Place the stone on a microscope slide and add a drop of immersion oil. The immersion oil will help to make the stone visible.

Learning Objectives

By the end of this activity, you will be able to:

  • Identify the different parts of the human kidney stone
  • Understand kidney stone formation
  • Observe a kidney stone using a microscope
  • What human kidney stone reveals

Preparing your microscope for observation:

You can use different types of microscopes for your kidney stone observation. The most common microscope used is the electron microscope. However, for this activity, we will be using a stereo microscope.

The following are the steps to prepare your microscope for observation:

  • Make sure that the microscope is in good working condition and that all of the lenses are clean.
  • Remove the eyepiece and place the microscope tube on the stage
  • Place a slide on the stage and secure it with the spring-loaded clips
  • Close the condenser diaphragm by turning the central knob clockwise
  • Move the substage mirror to its highest position by rotating the mirror adjustment knob
  • Open the field iris diaphragm by turning the knob on the right
  • Look through the eyepiece and focus the microscope using the coarse adjustment knob
  • If you are using a stereo microscope, adjust the interocular distance by turning the knobs on the sides of the microscope

Recording your observation

Depending on the type of kidney stone, the images you will observe under the microscope will vary widely. Typically the descriptions of the human kidney stone reveal:

  • Calcium stone – kidney stones made up of calcium oxalate and COD crystals appear to have jagged edges. Meanwhile, a calcium stone with COM crystals, which is more common will have a smooth appearance. Kidney stones made up of calcium oxalate, calcium phosphate, or a combination of these appear to be a brushite with little rosettes of thin sharp crystals.
  • Uric Acid Stone – this is the most common kidney stone. It appears to be pebble-like. It can be hard on the outside, but it has a softcore. It is usually made up of various uric acid and calcium oxalate monohydrates.
  • Struvite Stone – these stones are made up of a combination of magnesium, ammonium, and phosphate. They form in response to an infection in the urinary tract. Struvite kidney stones are the largest type of kidney stones.
  • Cystine Stone – The least common type and accounting for about 2% of cases. Cystine is a naturally occurring amino acid. These stones are compact, amber-colored, and are partially opaque.

When observing a kidney stone, it is important to take into account the following:

  • Size
  • Location
  • Shape
  • Surface features
  • Texture
  • Coloration

After you have recorded all of your observations, you can then begin to interpret what you have seen. Kidney stones can give us a lot of information about the patients’ health. By understanding how a kidney stone is formed and what it looks like, we can begin to piece together why the patient is having problems with their kidneys.

Kidney Stone Under Microscope FAQS

Kidney stone under electron microscope.
Credit to: Mount Allison University/ Murry Gans/ Kempf EK

There are a lot of questions that will come up after observing kidney stones under the microscope. Let us answer some of them.

Why Are Kidney Stones So Jagged?

Kidney stones are so jagged because of the way that they are formed. The stones are usually made up of a combination of different crystals. When these crystals combine, they form a kidney stone. As the stones grow, they will continue to add more and more crystals. This will cause the stones to become increasingly jagged.

On the other hand, some kidney stones are not jagged. This is because the different crystals that make up the stones have smooth edges.

Will a kidney Stone Float or Sink?

It all depends on the composition and how kidney stones develop. If the stone is made up of materials that are denser than water, then it will sink. If the stone is made up of materials that are less dense than water, then it will float.

Can you physically see a kidney stone without magnification?

It is possible to see a kidney stone without magnification, but it is not easy. The stones will usually be about the size of a grain of sand. Although there are stones that are bigger, it may need a procedure to remove them as it can block the ureter. Stones that are small enough to pass through the urethra can be seen by taking a sample of the urine and placing it on a slide looking at it under a microscope. If you are able to see the stone, it will look like a tiny white dot.


Observing kidney stones under a microscope gives startling images of jagged objects. These stones are formed when minerals, salts, and chemicals in urine clumped together or solidify. Smaller kidney stones are passed naturally, however, bigger ones get stuck in the tubes or the kidneys and this often leads to painful urination. When kidney stones are observed under the microscope, you will learn more about their composition.


Leave a Comment

Your email address will not be published. Required fields are marked *

Scroll to Top
Scroll to Top