5 Essential IT Preparations for Digital Pathology
By Isaac Huff | Apr 16, 2019
Organizations adopting digital pathology should carefully consider how it will more deeply intertwine their IT environment, laboratory instrumentation, and processes.
There’s no doubt that digital solutions have tremendous potential to transform the way your laboratory practices pathology - driving efficiencies, improving quality, and even unlocking insights that have previously been hidden in tissue. At the same time, capturing whole slide images generates tremendous volumes of data and injects new complexities into the laboratory workflow.
Organizations adopting digital pathology should carefully consider how it will more deeply intertwine their IT environment, laboratory instrumentation, and processes. Making the right preparations upfront will not only ensure a smoother transition to digital but also help to future-proof the investment. To help with your planning, here are 5 essential preparations that we regularly discuss with our clients.
Conversations about digital pathology quickly lead to the question of “which slide scanner?” Many factors can affect this decision, but speed is often the great unknown. Do you need to spend top dollar for a high-capacity model? Or can a productive workflow be built around a more entry-level unit? Do you have a technician who can be trained to operate the scanner quickly while still performing other duties? Or do you need a dedicated staff member?
Your pathologists and downstream customers have certain expectations about what time of day their slides will be ready to read. It doesn’t matter whether your scanner vendor tells you that a particular instrument can handle “x slides per day.” If you only have 1 hour between when slides are coverslipped and when they need to be read, then your scanner needs to complete the batch during that 1 hour. This becomes the lower-bound on your performance requirements. And if you are using cloud-based image viewing software, then the finished images also need to be uploaded to the cloud during that same hour! So, look for software features that can keep data flowing continuously throughout the scanning process rather than require a separate upload step after scanning completes.
Pay attention to the fact that most scanner vendors standardize their throughput calculations on slides with one 15mm x 15mm tissue area. If your slides have more, scanning will be slower!
Scanning at the highest possible resolution sounds great and seems like a safe choice. But it usually requires 3x more time and 2x more storage for every single slide moving through your digital pathology system. Is this worth it to your organization?
If your pathologists routinely work at 10x or 20x objective power and rarely go higher, then think about doing your WSI scanning at 20x. It is much more efficient for the organization to have pathologists request glass or request a re-scan of a specific slide at a higher power when necessary; however, don’t forget about the needs of future computational applications or research uses you may have planned. Do you want to pay that speed and storage penalty now? Or re-scan later when more powerful equipment is cheaper?
3. Talk to your IT team early about the demands of continuously pushing scanned images into a cloud-based system or an on-premises server.
WSI may quickly become the largest dataset your organization handles. This makes the flexibility of your storage expansion, WAN connectivity between facilities, and backup strategies paramount to ensuring technical roadblocks don’t derail wider adoption.
When determining whether to choose an on-premises solution or one hosted in the cloud, consider how Internet upload performance will affect the timing of your workflow. Many Internet connections asymmetrically favor downloads, and your WSI system may be competing for limited upload bandwidth with all other Internet activity happening in the organization. A typical 50Mbps fiber-optic Internet connection should be able to transfer 1 slide file in about 3 minutes. But, if your connections are already at 80% utilization before adding WSI, then it may take over 11 minutes to transfer that same file! In that worst-case-scenario, you may only be able to complete 5 slides per hour. This will not satisfy the needs of even the smallest pathology team. It can take months to install additional Internet capacity – so plan ahead.
Like the scanning throughput considerations above, don’t think about totals. Think about timing!
All of your slides should be barcoded as early in the workflow as possible, and you should avoid processes that require re-labeling. These introduce errors and create bottlenecks. If one of your instruments requires a proprietary barcode for its operation (for protocol selection, etc.), push your vendor for a more open solution. Focus your efforts on having barcodes that serve only as identifiers and can be shared across the laboratory systems.
There are many possible barcode formats, but each has tradeoffs related to physical size (“space” on printed labels is precious in most laboratories), reliability of reading, and the amount of data they can contain. The 2-D DataMatrix format is probably the right choice, and you should encode just enough information to fully represent the unique identity of the slide. This keeps the physical size of the barcode small, saving room for more human-readable information on the label.
Don’t get locked in if you can avoid it! If you rely on a slide ID number that only has meaning inside your LIS, for example, then every other system in your digital pathology workflow may require an electronic interface with it. This can be costly and makes the LIS vendor a potential obstacle in adopting new technologies, techniques, or instruments within the laboratory. If you ever want to change platforms, all of the barcodes on your stored slides may become useless!
5. Think about regulatory compliance, record retention policies, and the organization’s future goals.
These need to be developed in tandem with the technical and logistical aspects of a digital pathology initiative and are often the most difficult aspects. While workflow steps and instrumentation can be easy to standardize, these present as unique concerns and priorities for each organization. Here are some questions to help get started.
Is your digital pathology solution being implemented as a tool for primary diagnosis, secondary consult, telepathology, or research? Do you actually require an FDA-cleared product for your application? Can your plans fit into the framework of a laboratory-developed test (LDT)? If so, what validation protocol will be necessary, and who will be involved? How often will changes that require reverification be introduced? Will your laboratory medical director sign off directly or delegate this authority to another member of the organization? Do you have the necessary CLIA licenses for the locations where you intend to perform case sign-out?
Keep a clear focus on establishing the system-of-record, and make sure that it always receives the necessary data from ancillary systems.
If you are already storing glass to meet retention requirements, do you want to store digital images for the same time period? Think about the clinical relevance of the images in the near term, and the likelihood that they may need to be retrieved from archive 3 months, 6 months, 1 year, or 5 years in the future. Can your digital pathology system help you manage the full lifecycle of these images while also helping control the IT-related costs of storing them? Is your goal to use WSI for logistical and workflow improvements right now? Or, are you striving to build a library or bio-repository focused primarily on future value?
Not sure where to begin when it comes to your IT strategy? Connect with one of our experts, and let’s get started!