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Microscopy is an Essential Technique in Veterinary General Practice.

Veterinarians, veterinary technicians, and veterinary assistants use microscopes to view blood and animal fecal samples or animal fluids. Our hospital most commonly uses microscopes to check fecal samples for parasites, diagnose skin conditions, take a closer look at urine samples (urinalysis), and other cytologies. Masses and tumors may require further investigation by taking a biopsy and sending it to our outside lab for full histopathology.

A cytology is the microscopic examination of cell samples. Cytology can be used to diagnose growths or masses found on the surface of the body, and also to assess bodily fluids, internal organs, and abnormal fluids that may accumulate, especially in the chest and abdomen. Cells can be collected using various methods including fine needle aspiration, skin scraping, impression smear, cotton-tipped swabs, or lavage. A biopsy is the surgical removal of a representative sample of tissue from a suspicious lesion. The most common biopsy techniques are punch biopsy,wedge biopsy, and excision biopsy. The tissue is then processed and is examined under a microscope via histopathology. Histopathology allows the veterinary pathologist to make a diagnosis, classify the tumor, and predict the course of the disease.

Reasons In-House Microscopy is Important

  • While our lab equipment is highly accurate, there is nothing more accurate than a well-trained human eye! We will often use various lab techniques to verify abnormal findings in bloodwork or urinalyses. 

  • They play an important role in the diagnosis and treatment planning of conditions that require immediate attention. For example, the identification of a skin mass as a mast cell tumor will determine how much tissue beyond the mass should be taken off to ensure complete removal and to prevent it from spreading.

  • While we do have the ability to send samples off to our outside laboratory, the diagnosis of certain conditions like Demodex sp. mange mites is best determined by the examination of fresh hair plucks or skin scrapings as these samples do not travel well to an outside laboratory.

Interesting VetMed Facts:

The focus of early veterinary microscopy was the diagnosis of diseases that were public health risks.

Example: the causative agent of Anthrax

Most Common Reasons We Use the Microscope


A urinalysis is a routine test that reports the physical and chemical properties of urine. It is used mainly to assess the health of the kidneys and urinary system, but it can also reveal problems in other organ systems, and is important for diagnosing metabolic disease such as diabetes mellitus. It is a valuable test in both healthy and sick animals and should be included in any comprehensive evaluation of a pet's health. Our laboratory uses the Abaxis UA and SA analyzers but routinely will also view urine sediment manually. After using a centrifuge to spin down a urine sample, the sediment from the bottom is collected, sometimes stained, and viewed under a microscope where we look for any irregularities with:

  • Cells​

  • Bacteria

  • Casts

  • Crystals

For more information about what information a urinalysis provides, please visit our urinalysis and urinalysis results pages.​

Skin and Ears

One of the chief problems seen in a small animal clinic is ear infections that diagnostically will include a good ol’ swab and look-see under the microscope for bacteria and yeast. Occasionally, these conditions could call for a culture and sensitivity test sent to the lab when they aren't responding to the normal treatments. 

In house Otitis Cytology Malassezia Staphylococcal Bacteria ear infection
Staphylococcal Bacteria
In house Otitis Cytology Pseudomonas Bacteria ear infection laboratory
Pseudomonas Bacteria

Ear swabs can also show the presence of ear mites. Other skin conditions like demodectic and sarcoptic mange need to have a "skin scrape" done. This test is able to get down into the pet's hair follicles and deeper into the skin where these external parasites reside. Sarcoptic mange, also known as scabies, is a condition that can affect humans too!

Ear mite Otodectes cynotis cat dogs rabbits itchy ears cytology
Ear Mite
Sarcoptic Mange sarcoptes scabies zoonotic diseas itchy ears cytology rabbit cat dog
Sarcoptic Mange
demodex mite demodectic mange itchy skin
Demodectic Mange

For more information on these parasites, please take a look at these pdfs provided by Companion Animal Parasite Council:


When your pet has a lump, we may perform a fine needle aspiration. We will use a needle to pull cells out of the lump to identify them. We can diagnose fatty lumps (lipomas) just by looking at the cells under the microscope, though we may send more complicated samples to the laboratory. Identifying tumors is vital in determining the course of treatment.

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Canine Mast Cell Tumor
Feline Oral Squamous Cell Carcinoma cancer cat histopathology
Feline Oral Squamous Cell Carcinoma
Fibrosarcoma in dogs histopath fine needle aspirate laboratory
Canine Fibrosarcoma
Fecal Testing
Fecal Floatation

One of the most common uses of the microscope in both the small and large animal realms is the fecal float. A diagnostic tool that takes a small fecal sample, mixes it with a special solution and then sits the resultant “poo-slurry” in a tube with a microscope coverslip on top, the fecal flotation test determines the presence of gastrointestinal parasites eggs. The CDC recommends testing for intestinal parasites several times a year since many of these parasites are "zoonotic" and can be passed on to people.

Once you’ve got the coverslip ready and on the slide, it’s then time to venture into the microscopic world of parasite eggs. The identification of different types of parasite eggs takes time and training. Not only can different parasites have different looking eggs (although not always the case, as in a group of roundworms in horses, cattle, and small ruminants called strongyles), but also different species of animals carry different types of parasites.  To view more information, click the name of the parasite listed under each species!

hookworm egg hookworms helminthiases Ancylostomiasis intestinal parasite infection zoonotic disease
Hookworm Eggs
coccidia canine Cystoisospora spp coccidiosis intestinal parasite single-celled
whipworm egg whipworms parasitic worms fecal float laboratory Trichuris trichiura
Whipworm Egg
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Guinea Pig Rabbit Mouse Rat Small Animal
Exotic Small Animals:
  • Coccidia

  • Hookworms

  • Pinworms

  • Roundworms

  • Stomach worms (Obeliscoides cuniculi)

  • Tapeworms

Panther Chameleon Reptile Exotic.png
Emerald Tree Boa Snake Exotic
  • Coccidia

  • Giardia

  • Hookworms

  • Pentastomes (Tounge worms)

  • Pinworms

  • Roundworms

  • Tapeworms

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Parasite Prevalence Maps

Be sure to check out the interactive prevalence maps on Companion Animal Parasite Council's website! They collect data from Idexx and Antech laboratories and have organized it down to the county level!

Informative Links
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