Accurate Kidney Stone Analysis



Paul Jannetto, Ph.D.

Associate Professor of Laboratory Medicine and Pathology
Director, Clinical and Forensic Toxicology, Clinical Mass Spectrometry, and Metals Labs
Division of Clinical Biochemistry
Mayo Clinic, Rochester, Minnesota



Hello, I‘m Paul Jannetto, the co-director of the Metals Laboratory at Mayo Clinic, where kidney stone analysis is performed. In this month’s "Hot Topic," I will highlight our AI-augmented (artificial intelligence- augmented) kidney stone test and discuss the proper procedures for collecting and processing kidney stones to provide accurate, cost-effective, and timely analysis of the stones. I hope you enjoy this month’s Hot Topic, and I want to personally thank you for allowing Mayo Clinic the opportunity to be a partner in your patient’s health care.


I have nothing to disclose.

Kidney stones

At Mayo Clinic Laboratories, we have a long history of providing accurate and rapid kidney stone analysis. Our lab analyzes more than 90,000 kidney stones per year. Today, I am here to update you on our AI-augmented kidney stone test and the proper procedures for collecting and processing kidney stones to provide accurate, cost-effective, and timely analysis of patients’ kidney stones.

Kidney stones are quite common in the worldwide population. In the United States, it is estimated that 1 out of 10 people will develop a kidney stone during their lifetime. Epidemiology also indicates that the incidence of kidney stones is increasing.  

If you have ever had a kidney stone, you realize the trauma and pain they can cause. I cannot stress enough that the proper handling and labeling of kidney stone samples is critical to accurate stone composition analysis. 

Given the irretrievable nature of the stone, we have one chance of obtaining an accurate compositional analysis. Hence, we must take all the utmost precaution to ensure that the information is not lost. Each step of the analytic process is key to ensure the accuracy of the data. 

Thus, kidney stones should be given the same procedure policies as surgical specimens to ensure that proper identification and analysis are maintained. Information about the stone can easily be lost if the specimens are not labeled or are labeled incorrectly.

Clinical importance of kidney stone analysis

After the passage or surgical removal of the kidney stone, accurate analysis of the urinary stone composition is the most crucial laboratory diagnostic procedure for the treatment and recurrence prevention in the stone-forming patient.

The causes of kidney stones are complex, resulting from a combination of genetic, dietary, and lifestyle factors. From the lab’s point of view, we can aid in determining the cause by careful examination of the urine and stone constituents. Information about the stone composition is used in both medical and surgical interventions.

Kidney stone analysis (KIDST)

Proper analysis of stone collections begins with proper collection, handling, and labeling of kidney stones.

Although it is difficult for a patient to know exactly when a stone will pass, the odds of collecting the stones are increased when patients properly filter their urine. Our lab has seen many unique and sometimes odd ways that patients will attempt to collect their stone. To help our clients simplify the process, Mayo Clinic Laboratories offers a collection kit with a filter, vial, and detailed instructions for patients and lab personnel on how to collect kidney stones. 

Clients can order kits by logging in to, selecting the Customer Service page, and from there, selecting the Supplies page. Alternatively, orders may be placed by calling customer service at 1-800-533-1710. 

After the stone is collected, clean any blood or foreign material from the stone with deionized water. 

Afterwards, dry the stone at room temperature (approximately 24 hours) on a tissue or towel and send the entire stone in a screw-capped plastic container that is labeled properly. 

Make sure to indicate the source of the stone also (e.g., urine, kidney, or bladder).

The kidney stone must be clean and dry for accurate analysis

Stones need to be clean and dry before analysis. The analytical method by which we determine the composition absolutely requires the stone to be clean and dry. Excess water in the stone will cause a major interference in the composition analysis and can totally obscure our results. Excess blood and tissue can cause a false determination that the stone is proteinaceous and mask the true composition of the stone. Therefore, we require that all kidney stones be clean and dry before analysis. 

Currently, about 50% of the kidney stones arrive like the stone in the left picture. This forces our lab to spend extra time drying the samples before analysis, which will result in a delayed turnaround time. 

Kidney stone analysis (KIDST)

Current guidelines state that kidney stone analysis should be performed using modern methods like infrared spectroscopy or X-ray diffraction. At Mayo Clinic, we use Fourier transform infrared spectroscopy, or FTIR, which is considered to be the reference method.

FTIR analysis

In the lab, we begin with a clean and dry stone. The kidney stone is then crushed into a powder and placed on top of a crystal. An infrared beam is passed through the crystal, interacting with the powdered kidney stone sample. During this interaction, the molecular bonds within the stone absorb some of the radiation, giving a unique spectrum as seen on the next slide. Every sample has a unique infrared spectrum, which can serve as a compound’s fingerprint.

Example of calcium oxalate monohydrate 

This is an example of a very common stone composition: calcium oxalate monohydrate. The infrared spectral analysis of the stone produces a unique pattern of absorption (fingerprint), which makes the composition identification relatively simple.

Common types of kidney stones

When we look at the types of kidney stones, we see the vast majority — approximately 74% — are calcium oxalate; followed by hydroxyapatite, a form of calcium phosphate; uric acid; struvite, which is magnesium ammonium phosphate; and brushite, another form of calcium phosphate.

Clinical significance

Accurate identification of the kidney stone constituents can help identify the underlying cause of the stone formation and direct appropriate treatment options to prevent the reoccurrence of stones. 

In the case of calcium oxalate stones, the recommended treatment might be to increase daily fluid intake and consider reduction in calcium intake. For hydroxyapatite stones, you might acidify the urine to increase calcium solubility, and for uric acid kidney stones, you might alkalinize the urine to increase uric acid solubility.

Clinical significance

In the case of magnesium ammonium phosphate or (struvite), the cause is an infection, so treatment would be appropriate antibiotics to treat the urinary tract infection. Sometimes we also can identify herbal or over-the-counter medications that can cause stones, like ephedrine or guaifenesin. In this case, the reduction or elimination of these substances would be recommended. 

Role for artificial intelligence

As you can see, kidney stone analysis is a manual and laborious process, where after stone collection, the stones must be cleaned, dried, crushed, and analyzed by FTIR spectroscopy. Previously, every FTIR spectra was manually reviewed by two different qualified technologists and then entered into the laboratory information system. 

Since accurate identification of kidney stone constituent is critical to identifying the underlying cause and proper treatment selection, Mayo Clinic has created and validated a suite of novel AI algorithms to help characterize the kidney stone FTIR spectra. Using the new AI-augmented kidney stone test, clinical staff can now send quality kidney stone FTIR spectra to a dedicated API, or application programming interface named RokkStar, and receive AI kidney stone composition interpretations in return. For common or easy spectra-like calcium oxalate that meet defined quality and accuracy criteria, these can be automatically released directly into the laboratory information system, while rarer or challenging spectra can be focused on by the technologist for review. Once reviewed by two qualified technologists, the results can then be released directly into the LIS system. In the end, the AI-augmented kidney stone test improves the accuracy and efficiency of the clinical workflow, so that patients get the correct results which directly impacts the treatment options to prevent future stone formation. 

Importance of a “dry stone”

As I mentioned before, wet stones can impact the FTIR spectra. This is an example of a wet stone. Water has a very strong UV absorbance, and the presence of water is masking the unique fingerprint of the stone composition, which is why kidney stones must be sent clean and dry.

What should your lab do if you receive a wet or dirty stone from the patient?

So, what should your lab do if you received a wet or dirty stone from a patient? Although the answer to this question may seem rather obvious, there are some special considerations to keep in mind when drying stones. Stones containing obvious blood should be rinsed with deionized water prior to drying. Drying wet stones must not be done at too high of a temperature. For example, struvite stones, which are typically yellow to brown stones that are composed of magnesium ammonium phosphate, if heated too aggressively can eliminate ammonia, thereby changing the composition. We recommend placing the stone on a filter paper at room temperature until dry. Once dry, the stone can be placed in the 10 mL tube provided in our collection kit.

Clean and dry

In summary, proper specimen handling is critical for accurate determination of kidney stone composition. This includes how you process your patients’ specimens prior to submitting them to Mayo Clinic Laboratories. By following the Kidney Stone Analysis Patient Collection Instructions and the Kidney Stone Analysis Packaging Instructions included in the Mayo Clinic Laboratories kit, you can improve the quality of the test results you receive.

Thank You

Thank you for your attention.


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This post was developed by our Education and Technical Publications Team.