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Three Data Management Considerations for Digital Pathology

Digital pathology has a number of benefits over traditional microscopy. It allows for better management of data and therefore better security. It also minimizes human interaction, and thus human error, through automated quality control, image transfer, and data management. Digital slides can be organized easily, making search more effective. They can also be stored indefinitely and analyzed with algorithms that are accurate and objective.

However, digital pathology comes with its own challenges. Many of these revolve around data management, especially for multiplex immunofluorescence (IF) imaging, which generates whole-slide, high-resolution images in the form of digital slides. As we continue to shift towards digital, it’s essential for pathologists and researchers using multiplex IF to manage their data in a simple, organized way. We review three considerations to keep in mind when designing your data management system.

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1. Storage and access

Whole-slide imaging produces extremely high-resolution tissue images, which is useful for annotation and analysis, but presents problems for data storage. Whole slide scanners can produce terabytes or even petabytes worth of data in a year.

There are a couple different options when it comes to dealing with all this data. The simplest method is using hard drives or removable drives. These have the benefit of keeping data secure, but they can be unreliable and make it difficult to share data both within and outside your institution.

A repository hosted on a local area network (LAN) allows data to be accessed quickly and shared easily with members of the institution network. However, these types of systems require expertise to maintain, and data remains difficult to share outside your institution network. Plus, as you generate more and more data, your server space will need to grow in response.

Cloud storage is another option. Uploading your digital slides to the cloud ensures unlimited storage that is backed up on scalable servers. The greatest advantage of cloud storage is the ease with which you can share data globally. Using only cloud storage, however, can be slow, making it difficult to move large images into and out of the cloud.
A hybrid-cloud structure combines the best of both worlds. This type of system involves uploading data directly to a single enterprise-level network-attached storage (NAS), which is then backed up to the cloud. The hybrid-cloud system provides the infinite storage and collaboration capabilities enabled by the cloud, as well as the fast local access speeds offered by LAN.

DeploymentWhat Is It?BenefitsChallenges
Hard Drive or Removable DriveData directly saved to a local, transportable hard drive for local access
  • Easily transportable
  • Can open data in desktop software of choice
  • Inexpensive
  • Easy to lose hardware
  • Lack of inherent security
  • Drives are not reliable
  • Hardware needs expand with storage needs
  • No automated backup scheme
  • No traceability or auditability
Repository on LANData directly uploaded to series of enterprise-level Network Attached Storage devices for local access
  • Data easily shared with anyone on the institution network
  • Ability to quickly retrieve data
  • Can open data in desktop software of choice
  • Difficult to share data outside an institution
  • Requires building your own database
  • Hardware needs expand with storage needs
  • Requires expertise to maintain
CloudData directly uploaded to the cloud for access globally
  • Scalable storage
  • Easy to collaborate globally
  • Built-in data redundancy
  • High data availability
  • Data access is reliant on internet provider
  • Speed of access is reliant on internet provider
  • Lack of data isolation
  • Site requires knowledge of appropriate cloud security measures
  • Long upload and download times for large images
Hybrid-Cloud StructureData directly uploaded to a single enterprise-level NAS and backed up in the cloud for easy access both locally and globally
  • Scalable storage
  • Fast data access locally
  • Easy to collaborate both locally and globally
  • Built-in data redundancy
  • Design enables single hardware component (physical or virtual) on local network that does not have to expand with need
  • Data access is reliant on internet provider
  • Speed of access is reliant on internet provider
  • Lack of data isolation
  • Site requires knowledge of appropriate cloud security measures
2. Data security

While storing slides in the cloud is convenient, it can be vulnerable to data breaches if not properly secured. And security is crucial when handling sensitive patient data.

In the United States, the Health Insurance Portability and Accountability Act (HIPAA) has established security standards for the privacy and protection of electronic protected health information (ePHI). Many other countries have similar guidelines for protecting patient records. While digital slides on their own might not be considered PHI, associated patient metadata likely will be.

To ensure your data stays safe, make sure your storage platform keeps it securely encrypted — both “in-flight” as it’s transferred to cloud storage and “at rest” on the local repository in a hybrid-cloud system.

You should also make sure that you can control data access privileges for users. By choosing a platform that allows you to control data access for your study, you can be confident that it’s being handled appropriately.

3. Remote collaboration

Sharing digital slides was important before COVID-19, but the pandemic has greatly increased the need for remote collaboration tools. With researchers going into the lab only as necessary, your lab members may feel as far away as collaborators halfway across the world. As many users will need remote access, your data management platform should be able to scale up your user access in response to demand.

Another thing to keep in mind when working with multiple users is data integrity. Your platform should be logging user interactions throughout the digital slide life cycle to prevent possible data falsification.

Try our solution

To address these challenges, we recently launched Proxima™, the Spatial Biology Platform. Proxima enables secure, cloud-based data management and analysis tailormade for tissue images. Our platform seamlessly integrates with your existing laboratory workflows and connects your scanner to scalable, secure storage in the cloud. The system uses a hybrid-cloud structure, so users can access data locally and perform analysis with any desktop tissue analysis software.

Proxima workflow

Our parallel workflow allows simultaneous analysis of files by collaborators even in remote locations. Data can be synced from scanner to collaborative cloud in <1-min and is instantly available within studies on the Proxima cloud, providing the fastest path from slides to spatial analysis.

Discover how Proxima increases the speed of collaboration and biomarker discovery.

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