Urinalysis Lab Simulation
The Microscopic Exam
Table of Contents ►
- Background Information
- Introduction
- Cells Found in Urine
- Crystals Found in Uriner
- Casts Found in Urine
- Microorganisms Found in Urine
- Exam Procedures
- Transfer Urine to Centrifuge Tube
- Place Tube in Centrifuge
- Adjust Centrifuge Settings and Start Rotor
- Remove Centrifuge Tube
- Remove Urine Supernatant
- Transfer Sediment to a Glass Slide
- Prepare Slide for the Microscope
- Exam Results
- Terms of Use
- References and Attributions
Background Information
Introduction
A microscopic examination analyzes spun-down (centrifuged) urine sediment under a microscope to identify:
- Cells,
- Crystals,
- Casts, and
- Microorganisms.
To manually prepare a urine sample, about 10 mL of urine is placed in a centrifuge tube and spun for 5 minutes. This packs the suspended particles into a concentrated sediment at the bottom of the tube.
A small portion of the sediment is placed on a glass slide and flattened with a coverslip.
The glass slide is then moved to a microscope stage and examined for suspended components.
Cells Found in Urine
Squamous epithelial cells - line the distal end of the urethra and cover the inner surface of the vagina. A high number (>20 per High-Power Field (HPF); 400X) indicates that the sample may be contaminated.
Renal tubular epithelial cells (RTEs) originate from the walls of nephron tubules in the kidney, including the proximal and distal convoluted tubules and collecting ducts. Two or more cells per HPF indicate damage to the renal tubules.
Transitional epithelial cells line the interior of the ureters, bladder, and a portion of the urethra. More than a few cells per HPF indicates a possible urinary tract infection (UTI).
Epithelial Cells in Urine Sediment
High numbers of red blood cells (>5 per HPF) indicate bleeding in the urinary tract or prostate. Possible causes for urinary tract bleeding are kidney infection or disease, urinary tract infections (UTIs), kidney or bladder stones, and kidney injury.
White blood cells (most commonly neutrophils) above 5 cells per HPF indicate a possible bacterial urinary tract infection (UTI) or inflammation of the urinary tract or kidneys.
Blood Cells in Urine Sediment
Crystals Found in Urine
Crystals form in urine when dissolved substances become too concentrated to stay in solution. Dehydration, diet, certain medications, and urine pH all affect crystal formation, and crystals can also form as a specimen cools after collection. Each crystal type tends to form at a characteristic pH: uric acid, calcium oxalate, and cystine crystals form in acidic or neutral urine, while struvite and calcium carbonate crystals form in alkaline urine.
Small numbers of the more common crystals usually have no clinical significance. Larger numbers can indicate a higher risk of kidney stones (renal calculi), which may block the urinary tract and increase the risk of infection. Struvite crystals, for example, often accompany a UTI caused by urease-producing bacteria.
Laboratories report crystals by type and grade them semi-quantitatively (none, rare/few, moderate, or many) rather than giving an exact count.
Urine Crystals that are Often Present in Small Numbers
Several pathologic crystals are not normally found in a healthy person’s urine. Their presence usually indicates an underlying disease, an inherited metabolic disorder, or a toxic exposure.
1. Cystine Crystals appear as clear, perfect hexagonal (six-sided) plates. They are a hallmark sign of cystinuria, a rare genetic metabolic disorder where the kidneys cannot reabsorb certain amino acids, leading to severe and recurrent kidney stones.
2. Bilirubin Crystals are dark-yellow or reddish-brown clumps of fine needles or granules. Bilirubin is processed by the liver. The presence of crystals in urine indicates that waste is backing up into the bloodstream due to a liver disorder or a bile duct obstruction.
3. Cholesterol Crystals appear as clear, flat rectangular plates with notched corners. Their appearance in the urine indicates severe renal disease, such as nephrotic syndrome, or significant damage to the renal lymphatic system.
4. Calcium oxalate monohydrate crystals look like tiny dumbbells or ovals. A sudden, heavy presence of these crystals is heavily associated with ethylene glycol (antifreeze) poisoning, which causes acute kidney failure.
Urine Crystals that Indicate Pathology and Should Not be Present
Casts Found in Urine
Casts are relatively large, cylindrical structures that form inside the nephron tubules and take the shape of the tubule lumen. Their matrix is a glycoprotein called Tamm-Horsfall protein (uromodulin), which is secreted by the epithelial cells of the thick ascending limb of the nephron loop. Casts form primarily in the distal convoluted tubules and collecting ducts, where this protein gels and traps any cells or debris present, especially when urine pH is low, urine concentration is high, or urine flow rate is low. Because of their large size, casts are typically viewed at 100X.
The most common type of cast, the hyaline cast, consists primarily of matrix glycoproteins. They often appear in the urine in low numbers due to stress, dehydration, or strenuous exercise and are usually not concerning.
In comparison, casts containing erythrocytes, leukocytes, epithelial cells, or fat indicate kidney disease or infection and should not be present in the urine. Granular and waxy casts probably result from the degeneration of cellular casts, and are also associated with kidney disease or infection.
Casts in Urine Sediment
Microorganisms Found in Urine
Microorganisms are not normally present in urine collected from the bladder. Small numbers of bacteria or yeast often come from contamination by skin or vaginal flora, especially in a sample that is not a clean catch. Larger numbers, particularly when accompanied by white blood cells, indicate a bacterial or fungal infection of the urinary tract (kidneys, ureters, bladder, or urethra). Trichomonas vaginalis is a sexually transmitted parasite of the genital tract that is often found in urine samples.
Microorganisms in Urine Sediment
Exam Procedures
Transfer Urine to Centrifuge Tube
First, mix the freshly collected urine sample to re-suspend the solid components.
Transfer about 10 mL of urine into a 15 mL conical-tip centrifuge tube.
Seal the centrifuge tube with a screw cap.
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Place Tube in Centrifuge
Place the urine-filled tube in an empty slot in a centrifuge rotor bucket.
Arrange other fluid-filled centrifuge tubes to balance the rotor assembly.
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Adjust Centrifuge Settings and Start Rotor
Turn on the centrifuge using the push toggle switch.
Adjust the rotor speed to 1,500 rpm and the time to 5 minutes.
Start the centrifuge rotor. The outward force generated by the spinning rotor will move any suspended particles to the bottom of the tube.
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Remove Centrifuge Tube
Remove the urine-filled tube from the centrifuge.
Place the centrifuge tube in one of the open slots in a holder rack.
Remove the screw cap from the top of the centrifuge tube.
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Remove Urine Supernatant
Use a transfer pipette to withdraw the urine supernatant (top portion) from the centrifuge tube, leaving the urine sediment at the bottom.
Place the supernatant in a small beaker for appropriate disposal.
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Transfer Sediment to a Glass Slide
Draw a small volume of the urine sediment into a transfer pipette from the centrifuge tube.
Squeeze a drop from the transfer pipette onto the surface of a glass slide.
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Prepare Slide for the Microscope
Spread the sediment into a thin, transparent layer by placing a coverslip on top of the sample droplet.
Move the glass slide to the microscope stage so the sediment can be examined.
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Exam Results
Examine Urine Sediment
Position the microscope's 40X objective over the coverslip and examine three fields of urine sediment for cells, casts, crystals, and microorganisms.
Use the images below to identify and record the structures seen in the urine sediment.
For each type of structure, record your findings as the average number seen per HPF (High Power Field; 400x).
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Urine Sediment Identification Images
Terms of Use
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References and Attributions
General
The University of Utah - Urinalysis
Cells
Labpedia - Urine Analysis: Microscopic Examination and Interpretations
Oxford University Press - Cells in the Urine Sediment
National Library of Medicine (NIH) - Urinalysis
The University of Wisconsin School of Pharmacy - Urinalysis Interpretation
Crystals
Illinois State Veterinary Medical Association - Urinalysis Made Easy
Kidney Support and Protection - Can You Prevent Kidney Stones
Medical News Today - Urine Crystals
National Kidney Foundation - Kidney Stones
NIH National Library of Medicine - Urinary pH and Stone Formation
Casts
Cornell University College of Veterinary Medicine - Casts
Lincoln Memorial University - Urinalysis
Oxford University Press - Casts in the Urine Sediment
Renal Fellow - Granular and "Muddy Brown" Casts
Renak Fellow - Waxy Casts
University of California (San Francisco) - Urinary Casts
Microorganisms
Clevand Clinic - Urinary Tract Infections