A guide for histopathology labs and research teams evaluating their digital pathology stack
Digital pathology promises faster workflows, better collaboration, and more consistent results. But delivering on that promise requires more than a scanner and a shared drive. It requires infrastructure and software that can handle some of the largest imaging files in preclinical research — reliably, securely, and at scale.
The technology that makes or breaks this transformation isn't the scanner. It isn't the image analysis tool. It's the image management system (IMS) — the platform that ties your entire digital pathology workflow together. Choose the right one, and every other investment in your stack gets more valuable. Choose the wrong one, and you'll spend years working around its limitations.
This article explains what an IMS actually is, how to evaluate the options, and what to look for based on your lab's specific workflows.
The reality of digital pathology transformation
Implementing a digital pathology solution involves a number of difficult choices. Deciding on the best software and hardware systems, and integrating your existing laboratory infrastructure into a cohesive, empowering workflow, is rarely straightforward. The choice of vendors and products shapes how your team collaborates, how studies get completed, and how compliant your data practices are, for years to come.
In theory, a complete digital pathology solution has four core components:
- Laboratory information management (LIMS/LIS) — the metadata and case management layer that contextualizes the images
- Slide scanning — digitizing glass slides into whole slide images (WSI)
- Image management — storing, organizing, streaming, and enabling review of those images
- Image analysis — automated detection, quantification, and AI-assisted interpretation
The catch: no single vendor in the preclinical segment offers a best-in-class solution across all four. In practice, labs source components from multiple vendors — a scanner here, an analysis tool there — and rely on the IMS to hold everything together.
That's what makes the IMS selection so consequential. It's not just another component. It's the connective tissue of your entire digital workflow.
Why labs get the IMS decision wrong… and what happens when they do
Most labs don't start their digital pathology journey with an IMS. They start with a scanner.
That's understandable. Scanners are tangible, immediate, and address a clear need: turning glass slides into digital files. But scanner purchases often come bundled with basic image storage and viewing software — an IMS-lite — that gets labs up and running quickly without forcing a harder conversation about long-term infrastructure.
Initially, this works. Small scanning volumes, a handful of users, and limited collaboration needs can all be managed with file sharing platforms or scanner-bundled software. But as slide volumes grow, as more stakeholders need access, and as workflows become more complex, the limitations compound:
- File sharing platforms (Dropbox, SharePoint, OneDrive) lack the ability to stream whole slide images, forcing users to download files that can run into tens of gigabytes. These platforms simply don't scale well because they lack many features necessary for minimum viable workflows, including image access controls, metadata capabilities, pathology-specific workflow tools — such as image viewing and annotations — and audit trails for regulated environments, to name a few.
- IMS-lite platforms (bundled with scanners or analysis tools) do stream images in web viewers, which is a meaningful improvement, but they tend to support only proprietary formats, promote vendor lock-in, and lack the security, compliance, integration, and collaboration features that growing labs need. They're accessories designed to sell hardware, not top-line software.
The result is a familiar pattern: labs invest in scanning capacity and analysis tools, then spend years fighting the limitations of the infrastructure designed to support them. Studies take longer. Collaboration is cumbersome. IT workarounds multiply. And when compliance requirements tighten, the gaps become urgent.
What looked like a low-cost interim solution becomes a drag on productivity — and eventually, an IT and data migration project that costs more than building on the right foundation from the start.
What a true enterprise IMS does
An enterprise-grade IMS is engineered specifically for the demands of digital pathology workflows. It provides three things that file sharing and IMS-lite platforms fundamentally cannot:
- Specialized IT infrastructure Whole slide images are the largest imaging files in medicine — from several hundred megabytes to tens of gigabytes per image, and trending toward terabytes for emerging modalities. Off-the-shelf storage and viewing solutions are not designed for this scale or access pattern. An enterprise IMS provides secure, compliant cloud-native and elastically scalable infrastructure for high-performance image viewing, analysis, storage, streaming, and archival — without requiring your internal IT team to build or maintain it.
- Integrations that make you vendor-neutral One of the most underappreciated functions of an enterprise IMS is interoperability. By connecting your scanners, LIMS, and image analysis tools through open APIs and validated integrations, the IMS insulates your workflows from the proprietary nature of any single vendor's ecosystem. Labs with a strong IMS foundation can switch or add scanners, plug in new analysis tools, and adapt to evolving workflows — without rebuilding from scratch. This is vendor neutrality in practice, and it's one of the most durable forms of risk reduction available.
- End-user tools that enable productive digital work Beyond IT infrastructure, an enterprise IMS provides the user-facing tools that make digital workflows possible: browser-based image viewing, annotation and markup tools, figure generation, collaboration and commenting features, role-based access controls, and reporting. These are the features that pathologists and scientists actually interact with every day — and their quality directly determines how much value your team extracts from digital pathology.
The case against building in-house
When labs recognize the limitations of their current setup, some IT departments explore building an internal image management solution. It's worth addressing this directly: it rarely goes well.
In-house IMS development projects are consistently more expensive and slower to deliver than commercial alternatives — and they produce less value. They require specialized software engineering talent that most lab IT teams don't have, and they become ongoing maintenance obligations that pull resources from core laboratory priorities. More importantly, they tend to plateau: without a dedicated product team continuously investing in the platform, in-house solutions fall further and further behind commercial products in features, security, and performance.
Highly specialized, commercial IMS platforms have been maturing for more than a decade. The investment required to replicate — let alone exceed — their capabilities in-house is substantial and difficult to justify. The better question is not "can we build this?" but "what could we be doing with those resources instead?"
IMS needs by use case
Not all digital pathology workflows are created equal. The right IMS for a high-throughput toxicologic pathology CRO looks different from the right IMS for a spatial biology research team. Here's what each major use case demands.
Toxicologic pathology (ToxPath)
Nonclinical toxicologic pathology — assessing the safety and efficacy of biologics before human trials — generates some of the largest slide volumes in all of pathology. A single study can produce thousands of slides, translating to petabytes of data when digitized. The IT demands are significant: elastic storage, high-throughput ingestion, and fast streaming are baseline requirements.
But the regulatory requirements may be even more demanding. Toxpath workflows conducted under GLP (Good Laboratory Practice) require validated systems, complete audit trails, strict access controls, and data integrity standards — including compliance with 21 CFR Part 11 for electronic records. Not every IMS is built to meet these standards, and the gap between a compliant and a non-compliant system is not bridgeable through configuration alone.
At the software level, toxicologic pathologists need highly efficient viewing tools: fast keyboard navigation, robust slide sorting and filtering, seamless study-level organization, and the ability to move through large numbers of slides without friction. Integration with LIMS platforms — particularly for primary read workflows — is often essential.
Spatial biology and multiplex immunofluorescence (mIF)
Multiplex immunofluorescence imaging captures protein expression at the cellular level across dozens or even hundreds of fluorescent channels. Individual mIF images routinely run from a few gigabytes to hundreds of gigabytes — and unlike brightfield imaging, they require high-precision pixel types (16-bit or 32-bit) to accurately capture marker intensities.
Collaborating on files of this size is notoriously difficult. Most file sharing platforms either limit file size or become impractical to use. Many image viewers don't support the multi-channel visualization these datasets require. An IMS built for spatial biology workflows must handle extremely large, complex images natively — streaming them in the browser, supporting multi-channel rendering and manipulation, and integrating with the analysis tools that researchers depend on.
CROs and pathology service providers
Contract research organizations and core pathology labs have among the broadest requirements of any IMS user. They serve multiple clients across multiple study types, which means they need to support a wide range of scanning platforms, imaging modalities, and regulatory environments simultaneously.
Collaboration is mission-critical: CROs need to present images and preliminary results to study sponsors, collect annotations and feedback, and deliver final data packages — all in a platform that sponsors can access without requiring them to install software locally. Security and data segregation between clients is equally important. And the ability to demonstrate compliance with GCP and GLP standards is often a prerequisite for winning and retaining clients.
Enterprise IT teams
For IT leaders, the value proposition of an enterprise IMS is straightforward: replace a fragmented, resource-intensive patchwork of network storage systems, proprietary software systems, manual processes, and shadow IT with a centrally managed, cloud-native platform.
Browser-based access eliminates the burden of deploying and updating client software across endpoints. Cloud infrastructure scales with data volumes without requiring procurement cycles or capital expenditure. And centralized access controls, single-sign-on, (SSO), 2FA, audit controls, logging, regular backups and encryption give IT teams the security and governance visibility they need — without requiring deep pathology domain expertise.
Evaluating an IMS: what to look for
The IMS evaluation process doesn't need to cover every possible vendor combination. It does need to cover the capabilities that will define your workflow for years to come. Here are the criteria that matter most.
Integration and interoperability Can the IMS connect to your existing scanners, LIMS, and analysis tools? Does it support open APIs that allow you to add new integrations as your stack evolves? Interoperability is the single capability that most determines your long-term flexibility.
Regulatory compliance If your workflows fall under GLP, GCP, or 21 CFR Part 11, the IMS must be validated for those standards — not merely configurable toward them. Ask vendors for their validation documentation, audit trail capabilities, and experience supporting regulated environments.
Scalability Where is your scanning volume today, and where will it be in three years? Can the IMS grow with you without requiring re-implementation or costly migrations? Cloud-native platforms have a significant advantage here over on-premises solutions.
User experience End-user adoption is often the determining factor in whether a digital pathology initiative succeeds. Request a hands-on evaluation with the people who will actually use the platform — pathologists, scientists, lab technicians — and weight their feedback heavily.
Security and access controls Role-based permissioning, SSO integration, encryption at rest and in transit, and audit logging are table stakes for any enterprise environment. For multi-client organizations like CROs, data segregation between studies and sponsors is equally critical.
Vendor stability and support An IMS is a long-term investment. Evaluate the vendor's track record, roadmap transparency, and support model with the same rigor you apply to the product itself.
Total cost of ownership License fees are visible. Migration costs, IT overhead, productivity losses from poor UX, and the cost of non-compliance are not. Build a realistic TCO model that includes implementation, training, integration work, and ongoing maintenance.
Want more details on this? Check out our IMS checklist.
How PathcoreFlow compares to other leading platforms
PathcoreFlow is an enterprise-grade IMS built specifically for the workflows described in this guide — with particular depth in toxicologic pathology, spatial biology, and CRO environments where compliance, collaboration, and integration demands are highest.
As you evaluate platforms, you'll likely encounter several alternatives. Below is a brief orientation to the most common comparisons.
PathcoreFlow vs. Proscia’s Concentriq
Proscia's Concentriq platform is primarily oriented toward clinical pathology and diagnostics workflows. Labs with a strong preclinical focus — particularly those working in toxicologic pathology or serving biopharma CROs — often find that Concentriq's feature set, support, development roadmap priorities, and compliance tooling doesn't map well to their requirements. PathcoreFlow is built for preclinical and translational workflows, with validated GLP compliance and deep LIMS and AI integration at its core. PathcoreFlow’s interface is lightweight and intuitive for scientists and pathologists, avoiding bloat and complexity overload.
PathcoreFlow vs. Glencoe’s OMERO Plus
OMERO Plus, Glencoe's commercial offering built on the open-source OMERO platform, appeals to research institutions that want an image management system for digital pathology, high content screening (HCS) and general microscopy. However, this flexibility comes with meaningful impacts on user experience as the platform is less refined for the digital pathology use case. Furthermore, there are significant implementation complexities: OMERO Plus requires significant IT resources to deploy, configure, and maintain, and the overall costs are higher. For labs that need a turnkey cloud solution with validated compliance for digital pathology out of the box, the overhead can outweigh the potential benefits. PathcoreFlow is optimized for preclinical pathology uses cases such as study management and review workflows built-in, offering comparable openness through its API without the implementation burden.
PathcoreFlow vs. Deciphex’s Patholytix Preclinical
Deciphex's Patholytix Preclinical platform focuses on toxicologic pathology workflows, while PathcoreFlow is well suited for the full gamut of preclinical pathology, which includes toxpath. Labs evaluating both platforms should look closely at integration breadth — particularly support for the full range of scanning platforms, analysis tools and digital pathology workflows across their organization — as well as the depth of compliance documentation and the maturity of collaboration features for multi-site or multi-stakeholder workflows.
PathcoreFlow vs. Indica Labs’ HaloLink
Indica Labs is best known for HALO, its widely used image analysis platform — and HaloLink is its image management companion, designed primarily to support HALO-centric workflows. For labs already running HALO, HaloLink offers a familiar environment. But that tight coupling is also its central limitation: HaloLink functions most naturally as an extension of the HALO ecosystem rather than as a standalone enterprise IMS. Labs that rely on multiple analysis platforms, or that anticipate adding new tools as their workflows evolve, often find HaloLink's interoperability and collaboration constraints become a bottleneck. PathcoreFlow is analysis-platform-agnostic by design, with validated integrations across a broad range of tools — including Visiopharm, HALO and others — making it a stronger fit for organizations that want flexibility in their analysis stack.
The bottom line on IMS platforms
Digital pathology is not a single purchase — it's a system. And like any system, it's only as strong as its foundation.
The IMS is that foundation. It determines which scanners you can use, which analysis tools you can integrate, how your pathologists and scientists experience their daily work, and whether your organization can meet its compliance obligations without heroic effort. Getting it right from the start — or correcting course if you've outgrown your current solution — is one of the highest-leverage decisions a lab can make.
If you're evaluating platforms, frustrated with your current solution, or simply trying to understand what a mature IMS should look like, we're happy to help.
Download the IMS Evaluation Checklist →
PathcoreFlow is Pathcore's enterprise image management system, built for the demands of preclinical and translational digital pathology. Pathcore serves histopathology labs, biopharma CROs, toxicologic pathology teams, and spatial biology researchers across North America, Europe, and globally.
