Anatomic pathology goes paperless at Stanford Health Care

Stanford Health Care has launched a software system that streamlines the pathologic examination of tissues and body fluids, from collection to reporting results.

- By Kimberlee D'Ardenne

Pathology results are reported to physicians and patients more quickly now that Stanford Health Care has launched the Beaker AP system.  
Komsan Loonprom/

All pathology orders at Stanford Health Care are now fully digitized, allowing for faster results, ease of tracking and greater patient safety.

Since 2015, Stanford Health Care has been using a software system, Epic System’s Beaker CP, to track the analysis of bodily fluids such as blood and urine (CP refers to clinical pathology). Last month, it rolled out Beaker AP — AP as in anatomic pathology — to track the collection and examination of tissues and fluids at the cellular level by pathologists.

Beaker AP streamlines everything about pathology at Stanford Health Care, including automatic reporting of data to the Stanford Cancer Institute Research Database; monitoring the location and identity of tissue samples; and simplifying communication between treating physicians, pathologists and patients.

“Beaker AP improves patient safety because after collection, the status and location of samples are immediately visible and trackable as the sample goes through its many stops in a complex organization like Stanford Health Care,” said Ann Folkins, MD, an associate professor of pathology who helped lead the project to install the system.

The Beaker AP rollout has been years in the making because of the complexity of pathology at Stanford Health Care. Every sample removed during a procedure is examined by the multisite Stanford Clinical and Anatomic Pathology laboratory. The anatomic pathology division receives more than 90,000 cases a year, with tissue specimens or entire organs coming from the network of hospitals and clinics that make up Stanford Health Care and Stanford Medicine Children’s Health. The lab also receives requests for expert review from medical facilities across the country.

Mapping the journey

To prepare for the rollout, the anatomic pathology division mapped the various paths along the journey that a tissue sample takes, beginning with collection from a patient until the time it is reviewed by a pathologist.

“For each area of the lab, we looked at how we did things and wrote out the steps. We evaluated all our workflows and asked if there was anything we should change,” said Christina Kong, MD, a professor of pathology and vice chair for clinical affairs. “We did this at a time when it was very challenging to add more on top of our normal workload.” The lab was already in the process of preparing for the Beaker AP rollout when the COVID-19 pandemic hit and led to unforeseen stresses on the system and staff.

Beaker AP went live Nov. 6, 2022, and by the end of the first week, things were running smoothly, according to April Young, director of lab operations for anatomic pathology.

“Considering how big of a go-live this was — all sites were affected, and we had hundreds of people on site from Epic and Stanford Health Care information technology for support — the collaboration was impressive. We were able to address all major issues so quickly,” she said.

Tracking tissue samples

Before Beaker AP was implemented, many physicians wrote out their orders for pathology tests by hand. Once the sample and accompanying papers arrived at the lab, orders had to be entered into the software system previously used by the anatomic pathology division.

Now, each sample is tagged with a unique barcode linking it to the patient. In Beaker AP, that barcode acts like a FedEx shipping number.

Surgeons or treating physicians can send orders directly to pathology in the same Epic software environment that has hosted electronic medical records at Stanford Health Care since 2008. This feature is expected to speed turnaround times by eliminating the need to transcribe and confirm handwritten orders.

Pathology reports are also electronically linked to any related tests performed on the same sample, which benefits physicians and patients alike.

About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit

2024 ISSUE 1

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