Editors: Raymond D. Aller, MD, & Dennis Winsten
How a hospital lab stepped up its informatics training
July 2024—Earlier this summer, Danbury Hospital completed its first academic year using an integrated pathology informatics curriculum that introduced informatics exercises into seven of the pathology residency program’s 18 rotations. “The goal is for residents to learn informatics alongside the pathology workflows where they can apply it,” says Samuel Barasch, MD, medical director of cytopathology at the Danbury, Conn.-based hospital, part of the Nuvance Health Network.
“It’s easier for residents to understand the utility of the informatics skills and topics covered when they are related to other things they have to do, be that anatomic pathology or clinical pathology,” Dr. Barasch explains.
The pathology exercises are part of the Pathology Informatics Essentials for Residents curriculum, jointly developed by the College of American Pathologists, Association for Academic Pathology (formerly the Association of Pathology Chairs), and Association for Pathology Informatics. Dr. Barasch together with residency director Ramapriya Vidhun, MD, and chief resident Mikael Haeggstroem, MD (who is starting a pathology informatics fellowship at the University of Minnesota in August), began mapping the PIER exercises to various rotations in the hospital’s pathology residency program in January 2023. Dr. Haeggstroem had completed many of the residency rotations by the time the project started and was able to provide a resident’s perspective on which exercises would best fit each area.
The rotations include orientation to the laboratory’s hardware and software (initial rotation during the first year), lab management, anatomic pathology, blood bank, cytogenetics, chemistry, and immunology.
The three colleagues initially considered adding pathology informatics as a separate, dedicated rotation, as some other residency programs do, but decided against it. “The problem with having a separate rotation in informatics is what are you going to give up? Pathology residents have to learn a very broad set of topics,” Dr. Barasch says.
None of the seven rotations that incorporated informatics exercises needed to be extended as a result of the extra material. The amount of time required to complete the exercises varies, with some of the simpler ones requiring only 15 to 20 minutes, while more advanced exercises could exceed several days or weeks.
Because informatics plays an increasingly important role in automating manual lab-management workflows, more than half of the PIER pathology informatics exercises were integrated into the laboratory-management rotation, Dr. Barasch says. Even before the new PIER exercises were introduced, Dr. Barasch encouraged residents to attend a monthly lab information systems-focused meeting during their lab-management rotation to learn how lab managers work with the LIS team.
“I translate the goings-on in the LIS meeting for them so that they understand the importance of instrument interfaces and avoiding manual data entry in the laboratory,” he explains.
One of the simpler PIER informatics exercises added to the lab-management rotation tasks residents with familiarizing themselves with the pathology department’s data-backup policy and identifying when and how frequently data backups are performed, Dr. Barasch says.
In a more advanced exercise related to lab management, residents meet with medical records staff members in charge of locating and merging duplicate patient records. At the meeting, the staffers explain how duplicate patient records occur and affect patient care and how to prevent duplication.
In the anatomic pathology rotation, informatics exercises have been added for first- and second-year residents. First-year residents are required to use the LIS to enter orders for recuts and special stains—procedures they should already know how to accomplish, Dr. Barasch says. A second-year informatics exercise directs residents to follow a specimen from receipt through final report generation and observe how lab instruments interact with the LIS, among other tasks.
“This would involve spending some time in a histology lab to really understand the whole laboratory process and how it works through the LIS beginning from specimen receipt and accessioning,” Dr. Barasch notes.
The PIER exercises added to the blood bank rotation educate residents about the specialized barcoding used in blood banking for patient and blood unit identification. Another exercise focuses on how the LIS handles electronic crossmatch and the patient care efficiencies generated.
Test autoverification, which allows the LIS to autoverify some normal test results and release them to a patient’s record without verification from a laboratory scientist, is an important aspect of laboratory management, Dr. Barasch says. The team assigned exercises on this topic to the clinical chemistry rotation, a high-volume testing area. Residents are required to understand what types of results can be autoverified and what issues would prevent autoverification, he adds.
The cytogenetics and immunology rotations received the fewest informatics exercises. The cytogenetics rotation exercises relate to data privacy and include determining whether genetic data are being housed in the cloud and conducting a risk assessment of the location where genetic data are stored. Exercises for the immunology rotation focus on the use of middleware. These exercises could have been used in several rotations, but the team decided to add them to immunology to disperse the informatics workload, Dr. Barasch says.
The residents—two for each of the four academic years—are instructed to complete the exercises for each rotation independently and seek help when needed, but “it’s a challenge to find the time to complete them, especially on busy rotations,” Dr. Barasch acknowledges. Therefore, he plans to seek feedback on time management and other aspects of the program from the supervising pathologists for the participating rotations.
“Maybe we’ll look at the program every year or every other year and have residents weigh in on the utility of doing it in this manner,” says Dr. Barasch. “I’d like to go through a process where we look at the exercises and re-evaluate whether or not some of them can be done in other rotations.”
–Renee Caruthers
Indica Labs offers new release of Halo software
Indica Labs has introduced version 4.0 of Halo, Halo AI, and Halo Link, which provide pathologists and researchers with artificial intelligence-powered image analysis in an open digital pathology ecosystem.
Version 4.0 expands integration of AI-based tools across the Halo platform. With Halo 4.0, users of Indica’s AI-powered image-analysis platform can leverage pretrained deep learning-based networks for precise, automated nuclear and membrane segmentation in brightfield and fluorescence. The networks come ready to deploy and can be customized via Halo AI.
A graphics processing units-driven viewer in Halo 4.0 provides smooth panning and zooming of highly multiplexed and extensively annotated images. In addition, those who use the Halo Link 4.0 platform for collaborative pathology will benefit from an updated image server that allows more time for review and analysis. Users can also view Halo interactive markups across even more modules in 4.0, including those designed for Advanced Cell Diagnostics’ RNAscope in situ hybridization detection system.
Halo 4.0 too offers customizable analysis outputs and the ability to view, sort, and filter slide metadata. New features and functionalities introduced in the software’s classifier workflow include enhanced classifier pipeline capability, queueing of training jobs, and a colorblind-friendly default pallet.
Indica Labs, 505-492-0979
Proscia partners with Nucleai
The digital and computational pathology solutions provider Proscia has partnered with Nucleai, a spatial artificial intelligence biomarker company that maps protein expression and cellular interactions within tissue samples to predict therapeutic outcomes.
The companies will work together to integrate Nucleai’s predictive biomarker technologies into Proscia’s Concentriq enterprise digital pathology solution and make them available as part of Proscia’s precision medicine AI portfolio.
“With the recent deployment of our technology to aid patient enrollment for an active [clinical] trial and the growing need for AI-powered biomarkers across trials and diagnostics, this partnership represents a significant step forward in deploying our solutions at scale,” said Nucleai CEO Avi Veidman, in a compay press statement.
The companies also announced that Nucleai has joined the Proscia Ready partner alliance, an interoperability-focused partnership to help diagnostic laboratories and life science organizations leverage digital pathology by accessing technology solutions from alliance members.
Proscia, 215-608-5411
ONC reports interoperability gains in U.S. hospitals
A recent data brief from the Office of the National Coordinator for Health Information Technology indicated that the proportion of hospitals reaching the federal agency’s bar for interoperability rose substantially from 2018 to 2023, but gaps in day-to-day data exchange remain.
According to the ONC, 70 percent of nonfederal acute care hospitals reported engaging in the four measured domains of electronic health information interoperability on a routine or sometimes basis. Of that group, 92 percent reported sending data, 87 percent receiving data, 84 percent querying data from outside their organization, and 78 percent integrating outside data into their records without manual entry.
“The 70 percent top line is an improvement from the 23 percent of 2014 and the 46 percent of 2018,” according to the data brief.
Genestack and CUNY partner to enhance genomics data
The Cambridge, United Kingdom-based bioinformatics firm Genestack and the City University of New York are collaborating on curating data for BioConductor open-source and open-development software for analyzing and interpreting genomic data.
Under the joint effort, Genestack will integrate its data-management platform with the BioConductor program, allowing researchers to more easily upload, organize, and annotate genomic data. Furthermore, “the streamlined data-curation process will enable researchers to easily share their curated data sets,” according to a Genestack press release.
“Our project aims to enhance the artificial intelligence/machine learning readiness of publicly accessible omics data, with a particular emphasis on enhancing metadata quality,” said Sehyun Oh, PhD, assistant professor, Department of Epidemiology and Biostatistics, CUNY, in the press statement.
CUNY is also working on the project with the University of Colorado, Northeastern University, Boston, and the University of Trento (Italy).
Dr. Aller practices clinical informatics in Southern California. He can be reached at [email protected]. Dennis Winsten is founder of Dennis Winsten & Associates, Healthcare Systems Consultants. He can be reached at [email protected].