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Urinalysis Continued

The Microscopic Exam

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Microscopic Exam Background

Introduction

A microscopic examination is a procedure to determine if cells, crystals, casts, and microorganisms are present in the urine. If performed manually, the examination begins by placing about 10 milliliters of urine in a glass tube, then centrifuging the contents for about 5 minutes. 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 surveyed 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; 400X) indicates the sample may be contaminated.

Renal tubular epithelial cells (RTEs) originate from the walls of the nephron tubules in the kidney, including the distal and proximal 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).

Squamous Cells
(400 X)

Squamous epithelial cells in urine

Renal Tubulars Cells
(400 X)

Renal tubular epithelial cells in urine

Transitional Cells
(400 X)

Transitional epithelial cells in urine

Red blood cells in high numbers (> 5 five per HPF) indicate bleeding along 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.

Red Blood Cells (RBCs)
(400 X)

Red blood cells (RBCs) in urine

White Blood Cells (WBCs)
(400 X)

White blood cells (WBCs) in urine

Crystals Found in Urine

Crystals appear in the urine when particular substances become too concentrated, and they aggregate to form larger solids, often due to dehydration. Dehydration, the overconsumption of certain foods, changes in urine pH, or certain medicines can cause crystals to form.

The accumulation of crystals can cause stones that block the urinary tract passageways (kidney stones), urinary tract infections (UTIs), and kidney infections.

Substances that often combine to form crystals include calcium oxalate, uric acid, struvite (triple phosphate crystals), cystine, bilirubin, and calcium carbonate.

Urine Crystals that are Often Present in Small Numbers

Calcium Oxalate Dihydrate Crystals
(400 X)

Calcium oxalate dihydrate crystals in urine

Calcium Oxalate Monohydrate Crystals
(400 X)

Calcium oxalate monohydrate crystals in urine

Uric Acid Crystals
(400 X)

Uric acid crystals in urine

Struvite Crystals
(400 X)

Struvite crystals in urine

Urine Crystals that Indicate Pathology and Should Not be Present

Cystine Crystals
(400 X)

Cystine crystals in urine

Bilirubin Crystals
(400 X)

Bilirubin crystals in urine

Calcium Carbonate Crystals
(400 X)

Calcium carbonate crystals in urine

Cholesterol Crystals
(400 X)

Cholesterol crystals in urine

Casts Found in Urine

Casts are relatively large cylindrical structures, each having a matrix made of glycoproteins (Tamm-Horsfall proteins). The epithelial cells of the nephron tubules secrete the matrix glycoproteins, especially if the urine pH is low, urine concentration is high, or the 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.

Hyaline Cast
(400 X)

Hyaline cast in urine

Red Blood Cell Cast
(400 X)

Red blood cell cast in urine

White Blood Cell Cast
(400 X)

White blood cell cast in urine

Fatty Cast
(400 X)

Granular cast in urine

Granular Cast
(400 X)

Granular cast in urine

Waxy Cast
(400 X)

Fatty cast in urine

Microorganisms Found in Urine

Microorganisms are usually not in the urine. Their presence, even in lows numbers, indicates a bacterial, fungal, or parasitic infection of the urinary tract (kidney, ureters, bladder, and urethra).

Bacteria (Cocci) and WBCs
(400 X)

Bacterial cocci in urine

Bacteria (Rods) and WBCs
(400 X)

Bacterial rods in urine

Fungi (Yeast Cells) and WBCs
(400 X)

Yeast cells (fungi) in urine

Parasites (Trichomonas vaginalis)
(400 X)

Trichomonas vaginalis (parasites) in urine

Microscopic 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 to a 15 ml conical tip centrifuge tube.

Seal the centrifuge tube with a screw cap.


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.


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.


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.


Remove Urine Supernatant

Use a transfer pipette to withdraw the urine supernatant (top portion) from the centrifuge tube, leaving the urine sediments at the bottom of the tube.

Place the supernatant in a small beaker so that it can be discarded appropriately.


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.


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.

Microscopic 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).

Urine Sediment Identification Images

Show Cells

Squamous Cells
(400 X)

Squamous epithelial cells in urine

Renal Tubulars Cells
(400 X)

Renal tubular epithelial cells in urine

Transitional Cells
(400 X)

Transitional epithelial cells in urine

Red Blood Cells (RBCs)
(400 X)

Red blood cells (RBCs) in urine

White Blood Cells (WBCs)
(400 X)

White blood cells (WBCs) in urine
Show Crystals

Urine Crystals that are Often Present in Small Numbers 

Calcium Oxalate Dihydrate Crystals

(400 X)

Calcium oxalate dihydrate crystals in urine

Calcium Oxalate Monohydrate Crystals

(400 X)

Calcium oxalate monohydrate crystals in urine

Uric Acid Crystals

(400 X)

Uric acid crystals in urine

Struvite Crystals

(400 X)

Struvite crystals in urine

Urine Crystals that Indicate Pathology and Should Not be Present

Cystine Crystals

(400 X)

Cystine crystals in urine

Bilirubin Crystals

(400 X)

Bilirubin crystals in urine

Calcium Carbonate Crystals

(400 X)

Calcium carbonate crystals in urine

Cholesterol Crystals

(400 X)

Cholesterol crystals in urine
Show Casts

Hyaline Cast
(400 X)

Hyaline cast in urine

Red Blood Cell Cast
(400 X)

Red blood cell cast in urine

White Blood Cell Cast
(400 X)

White blood cell cast in urine

Granular Cast
(400 X)

Granular cast in urine

Waxy Cast
(400 X)

Waxy cast in urine

Fatty Cast
(400 X)

Fatty cast in urine
Show Microorganisms

Bacteria (Cocci) and WBCs
(400 X)

Bacterial cocci in urine

Bacteria (Rods) and WBCs
(400 X)

Bacterial rods in urine

Fungi (Yeast Cells) and WBCs
(400 X)

Yeast cells (fungi) in urine

Parasites (Trichomonas vaginalis)
(400 X)

Trichomonas vaginalis (parasites) in urine

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References /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