Health IT

Considerations for the anatomical pathology laboratory information system

Digital pathology encompasses the replacement of glass slides in the histology laboratory with digital slide images, as well as automated image analysis. Over the last decade, technological advances have led to improvements in digital slide scanner quality and a reduction in the cost of digital image storage. Because of this an increasing number of histology labs are now beginning to implement digital pathology to improve workflow efficiency and enable easier sharing of slides for collaboration or remote consultation.

The right IT capability

When considering how to transform and future-proof their practices for the introduction of digital pathology, lab managers and pathologists need to consider not only the slide scanners and other hardware required to ensure that digital slide images are suitable for clinical use, but also their supporting IT systems. The two main systems are the anatomical pathology laboratory information system (APLIS) and the digital pathology system (DPS). Most histology labs are already using an APLIS to manage the lab workflow and pathologist reporting. The DPS is required to manage the digital slide images, and usually offers features to support collaboration, case management and automated image analysis.

System integration

Key to the success of digital pathology implementation is integration between the APLIS and the DPS. This has been highlighted in reports by labs from a range of countries1. For example, a study from the Department of Pathology at the University Medical Center, Utrecht, The Netherlands, found that integration is needed to provide a better user experience2, while the Department of Pathology at the University of Pittsburgh Medical Center, USA, concluded that the integration of the DPS and APLIS “streamlined [the] digital sign-out workflow, diminished the potential for human error related to matching slides, and improved the sign-out experience for pathologists”3.

With integrated systems, communication via an interface is triggered by certain events in the workflow. For example, once slide preparation is completed in the APLIS, the interface passes patient, request, and slide details to the DPS, where a new case is created. Then, once the corresponding slides have been scanned into the DPS, they are automatically associated with the correct case. Without integrated systems, lab staff would be required to re-enter the patient and case details into the DPS, introducing the risk of human error.

Likewise, updates to request or patient details in the APLIS should be automatically communicated to the DPS, ensuring that case information in each system is synchronized. This dynamic communication between the two systems also eliminates the need for duplicate data entry.


Key to the success of digital pathology implementation is integration between the APLIS and the DPS.


With digital pathology, the pathologist’s reporting workflow is driven by cases assigned in APLIS, rather than slides on the workbench. When the pathologist opens a case to report in the APLIS, the digital pathology image viewer is automatically launched on a second screen. This means that the pathologist is presented with patient and request details from the APLIS on one screen, side by side with the corresponding slide images from the DPS on another screen. Without integrated systems, pathologists would need to search the DPS to find the correct images for each patient case at the time of reporting.

Given the importance of system integration in the transition to digital pathology, labs need to ensure that their APLIS is capable of interfacing with their chosen DPS. Interoperability and the use of technology standards are essential to ensure that systems are compatible. HL7 v2.x is the most widely used standard for exchanging clinical data between different systems4, so an interface designed using HL7 messaging provides a standardized and flexible platform. It is also important that the interface is bi-directional to ensure systems remain synchronized.

Specimen tracking and unique slide identification

Many labs are now introducing full specimen tracking systems into their APLIS to ensure that the patient’s specimen, including every block and slide created for the case, is uniquely identified through barcode labelling and tracked throughout the lab workflow. This is an essential foundation for labs to have in place in their APLIS before the introduction of digital pathology5. Without unique, barcoded slide labels the DPS is not able to identify every image as a single entity that belongs to the patient case.  It also means the pathologist can systematically review and track each slide for the case. The labelled slides must be of high quality to ensure accuracy of scanning and minimise barcode read error rates.


When moving to digital pathology, laboratories may also be considering the benefits of regional consolidation to reduce duplication of resources and benefit from economies of scale. For example, specimens may be processed in a central laboratory, and the scanned slides made available to pathologists based in different locations across a geographical region. In this case it is important to ensure that the APLIS supports a multi-site environment, i.e. multiple laboratories operating from a single laboratory system.

Remote pathologist reporting

Going digital may also open the possibility of remote reporting. If supported by the DPS and APLIS, pathologists can connect remotely from any location to view digital slides and create reports, facilitating off-site consultation or more flexible work arrangements.


An increasing number of histology labs are moving towards the adoption of digital pathology. To fully realise the benefits of going digital, labs need to ensure they have the right platform in place in their APLIS. The ideal LIS should:

  • enable unique slide identification, achieved through an APLIS specimen tracking system
  • be capable of interfacing to the lab’s chosen DPS to provide end-to-end synchronisation of both systems and eliminate duplicate data entry
  • support a multi-site installation to allow pathologists to work across different locations, if labs are moving towards regional consolidation
  • provide remote pathologist reporting functionality, if required

To fully realise the benefits of going digital, anatomical pathology labs need to ensure they have the right platform in place in their LIS.


1Filippo Fraggetta, Esther Diana Rossi, and Liron Pantanowitz (2018) Advocating a Laboratory Information System–Centric Approach to Digital Pathology. Archives of Pathology & Laboratory Medicine: April 2018, Vol. 142, No. 4, pp. 434-434.
2 Stathonikos, N., Veta, M., Huisman, A., & van Diest, P. J. (2013). Going fully digital: Perspective of a Dutch academic pathology lab. Journal of pathology informatics, 4, 15. doi:10.4103/2153-3539.114206. 3Guo H, Birsa J, Farahani N, Hartman DJ, Piccoli A, O’Leary M, McHugh J, Nyman M, Stratman C, Kvarnstrom V, Yousem S, Pantanowitz L. Digital pathology and anatomic pathology laboratory information system integration to support digital pathology sign-out. J Pathol Inform [serial online] 2016 [cited 2019 Jun 19];7:23.
5 Cheng, Chee Leong, Injecting Digital Pathology into the Diagnostic Laboratory – is it possible to Integrate Painlessly? Oct 2014


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