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Being Fully Digital: Perspective of a Dutch Academic Pathology Laboratory

Yet the existing infrastructure was not suitable for primary diagnostics. Additionally slides requiring multi-focal planes, e.g. cytology slides could not be digitized. But as the old equipment had to be replaced in 2015 anyway, Prof. Paul van Diest and his team decided that it was time to take digitalization one step further: to go completely digital. This required a complete new setup both of hardware, as well as a high efficient workflow system for primary digital diagnostics. It needed to offer the possibility to implement image analysis/artificial intelligence and securely link scanned slides to patient cases containing all information about a patient’s diagnostics and treatment.

The first requirement for such an ambitious project was extremely reliable high throughput slide scanners to cope with an average of 800 slides per day and 120 slides/hour in peak hours. Besides speed, the ability of scanning multiple planes was mandatory to include cytology slides in the digital workflow. An additional scanner was required for 2 × 3 slides and fluorescence. A very potent PACS system and an image analysis software were also mandatory for full digitization of all processes. The choice fell on the Sectra AB PACS system and 4 Hamamatsu NanoZoomer scanners: 3 NanoZoomer-XR for high-throughput in the daily routine and a NanoZoomer-RS for non-standard sized slides and fluorescence.

It took Nikolas Stathonikos, IT manager of the Pathology Department, and his co-workers 6 months to setup the new system and integrate it in the existing infrastructure. They had to make several new connections between the new hardware and software, and the existing LIMS and pathology reporting system to establish a smooth workflow.

When everything was ready, the scanners fulfilled their workload satisfactorily. Taking into account scanning and handling time, the NanoZoomer-XR scanners were able to scan 43 slides per scanner in 1 h. Yet it became apparent that the scanners were not able to scan all slides using their standard scan profile. To ensure a fully automatic workflow, the scanner can choose now between 10 different scan profiles based on the barcode information of each slide, for differently stained routine slides, special stains, fatty tissue, fluorescence, etc.

During the first time working with the new systems, it appeared that the image quality was not sufficient for digital diagnosis in some fields, especially gastrointestinal biopsies, brain tumour and breast cancer. Optical slices were too thick, blurring nuclear detail. By making the gamma adjustable in the PACS system and switching from 4-μm-thick to 3-μm-thick sections as work around, these problems were overcome.

Now, after two years of working with the new system the team in Utrecht reviewed their experience with the new system and workflow so far. It was concluded that as a consequence of going fully digital, the turnaround time, especially of complex cases, had considerably decreased, in some cases by up to 2 days.

Most of the pathologists found image quality good enough for digital diagnosis. Only in the fields of paediatrics, haemopathology and neuropathology people deemed the digital slides insufficient. Consequently, these critical cases are still diagnosed under a microscope. There are ways to improve the required image quality, either scanning in higher resolution or Z-stacks leading to longer scan times and more storage. Another possibility is the implementation of machine-learning algorithms. One of our future projects is to include these in the digital workflow.

Other open issues are Z-stack scanning for including cytology in the digital workflow, full switch to DICOM format to arrive at a vendor-independent future-proof archive and the full integration of WSIs in the hospital information system, allowing even patients to see their own images through the patient portal of the UMC Utrecht.

For more information see Histopathology 2019, 75, 621–635. DOI: 10.1111/his.13953

* Note: NanoZoomer-XR is CE marked under EU’s In Vitro Diagnostics Directive (IVDD) for in vitro diagnostic use.
NanoZoomer-XR is Research Use Only in US. For other countries, please consult with Hamamatsu.
NanoZoomer-RS is Research Use Only.

The NanoZoomer line-up and medical device regulatory status varies across countries. For more information, please contact your local Hamamatsu sales representative.