This story appeared in the department’s 2025 annual report
The Department of Pathology, Microbiology, and Immunology made major progress in 2025 on installation of the new laboratory information system (LIS). The more than two years of work leading up to the launch of Beaker LIS will be worth it and is an important step forward for the department. The move was precipitated because Cerner CoPath was sunsetting, and many of the department’s legacy or older LIS systems were no longer modern or meeting the department’s needs.
Ben Swanson, MD, PhD, associate professor and medical director of the anatomic pathology division, said phase one of clinical content validation was completed in September on the Beaker LIS, which will be fully integrated with the Epic One Chart electronic medical record. The second validation phase should be completed by year’s end, he said, with the third and final phase complete early in 2026, followed by several months of staff training before the go-live date of June 6.
Phase one dealt mostly with test definitions, he said. “Say you draw a sodium level. What kind of tubes could be drawn from a line that the system would accept, or what is the billing code associated with sodium that would drop within our system?
“Our next phase will be clinical content validation phase 2. This is looking at and validating complex workflows. So examples of that would be coagulation that a clinical pathologist signs off, another straightforward example that’s complex is hematopathology including bone marrows, including peripheral blood smears as well as hematopathology cases, bone marrows that include flow cytometry as well as molecular or other ancillary findings. An example in surgical pathology that we would be reviewing would be a biopsy or a section that also has FISH testing or fluorescence in situ hybridization. Those are the types of things; there are dozens of complex workflows that we’re going to be working on both with our pathologists as well as our subject matter experts to look at. I think we’ll have a lot more people understanding what the work looks like in Beaker.
“We’re testing every combination and every possibility. We’re testing orders coming in, we’re testing results going out. We’re testing can we bill appropriately? Can we collect charges? We’re testing that things are linked. Let’s say somebody has a Pap smear. We need to make sure that’s linked to their HPV test. Many examples like that. We have to test the system, make sure it’s robust.”
Epic and Beaker have done this installation many times at many institutions, and that experience has informed the design of their base system, called Foundation. “As much as possible we want to stay with the base, with the Foundation system,” Dr. Swanson said. “But there are certainly many examples where we need customization. And that’s where we work really closely with our IT partners, our LIS partners, to make sure the software product meets our needs. Obvious examples of this would be our outreach business, our Regional Pathology Services. That’s a unique workflow that maybe not a lot of Epic/Beaker customers have presented to the company before. That’s where a lot of customization is happening.”
The months before the go-live date in June will be busy, too. “There’s going to be a lot of teaching, both to pathologists, to our support staff as well as to the hospital as large in how you work in Beaker, to our clinicians, to our providers, to our nurses,” he said. “There will be slightly different ways that they enter orders, print labels and send specimens, be it blood, be it tissue to our lab. And then on the pathologists and clinical pathology side, there will be significant changes in how we enter and report out data. Because we will be working in an entirely new computer system. So the last six months will be heavy on education and training. And also about understanding what the new workflows look like.”
Extra help will be available during the transition. “We’re going to have a command center,” he said. “We hope everything goes smoothly but there’s always bumps in the road. So there will be a command center to fix any pressing issues that need to be taken care of. We’re going to be working with our consultant as well as our Epic partners, and they will be working at our elbows the first couple of weeks to really make sure the transition to Beaker goes smoothly.”
In addition to the cutting-edge software system, they’re going live June 6 with an upgraded digital image management software (IMS) program. “It is equivalent in many respects to what is called a PACS system, PACS system in radiology. We are going with Sectra as our IMS. We have currently hired a consultant who will be helping us install the program and make sure that the connections are going live. We will continue to use our Leica GT450s for high-throughput scanning as well as the Leica CS2s for remote frozen sections. And that will be integrated with our Sectra system.”
They are also planning another change—going to a cloud-based storage system for digital images. “Much like we access things on OneDrive or if you have a Google account and there’s Google Drive, rather than keep our images on a computer server on campus or somewhere in the Omaha area, it will be going to the cloud. So we’re going to be upgrading our data storage to Microsoft Azure cloud storage, that’s part of our Sectra build.
“We’d have servers over at the 4230 building across Leavenworth to store our images, and it was quite expensive. So this is a cost-effective way. And this is where the field is headed, both within pathology as well as radiology.”
Dr. Swanson said one big advantage of the new IMS is that it will have direct connections to AI and machine learning algorithms. “So for instance if we want to start to scan let’s say breast cancers with R2, ER and PR, Sectra would be able to directly integrate to a third-party AI program that could help us quantitate. So rather than eyeballing, using standardized metrics but really using a computer program to be consistent and have better accuracy with what we call various biomarkers for tumors. Another exciting development that this will allow us to do is prescreening. So there are for example prostate cancer AI algorithms that will look at the biopsy before a pathologist gets to it and say I think there might be cancer here. Maybe you ought to look here first. And it’s just a way to help increase efficiency, increase patient safety so that no cancer is missed. There are lots of other tools, but that’s really our gateway into working with all of these computer programs that are coming down the pipeline.”