Best Digital Pathology Software for CLIA Labs

A digital pathology lab runs three systems. The scanner turns a glass slide into a whole-slide image. The image management system, which is what vendors mean by digital pathology software, stores that image, opens it for the pathologist and holds the case list, annotations and consults. The laboratory information system stays the record of the case: accessioning, blocks, slides, the signed report and the bill.

This page compares the middle system. What the AP LIS has to do once slides are scanned, such as tracking which slides are still glass, is covered in our pathology LIS comparison. Some LIS vendors now build a viewer in; the products here are bought on their own and connect to the LIS you have.

A cleared stack still has to be proven in your lab. CLIA asks a lab that introduces an unmodified FDA-cleared test system to show, before it reports patient results, that it performs as the maker says § 493.1253(b)⁠(1). A changed stack, such as another scanner, a different display or a tissue type outside the indications, puts the lab under § 493.1253(b)⁠(2): it sets its own performance specifications. Roche's labeling puts the same duty on the reader: “It is the responsibility of a qualified pathologist to employ appropriate procedures and safeguards to assure the validity of the interpretation of images” (Roche).

The College of American Pathologists publishes the method. Its guideline on validating whole slide imaging, updated in 2021, keeps the 60-case validation set from the 2013 original and recommends that agreement between the glass diagnosis and the digital one be above 95%. CAP says studies going past 60 cases did not improve agreement. CAP frames validation around each intended clinical use, so a lab reading both H&E surgical cases and IHC on screen should cover both. CAP's guideline page.

Every platform here runs image analysis inside the viewer: scoring a stain, counting cells or flagging a slide to read first. Most of it comes from partners. Proscia says 150 apps work with Concentriq, from makers such as Ibex, Mindpeak, Visiopharm and Aiforia; PathAI lists DeepBio, DoMore Diagnostics, Paige and Visiopharm; Sectra says 50+ pathology AI vendors are integrated with its platform.

An app being open inside a cleared viewer does not make the app cleared. Proscia says so in its own footnote: interoperability “does not confer diagnostic intended use”, and each app's status is set by its own maker (Proscia).

CLIA's retention rule is written for slides, not images. Histopathology slides are kept at least 10 years and cytology slides at least 5 years from the date of examination, and pathology blocks at least 2 years § 493.1105(a)⁠(7). A scanned slide still goes to the slide room. The full set of clocks is on our pathology LIS page.

That may change. CMS's proposed rule CMS-3478-P, published 8 October 2026, would add “digital images, digital data” to the items a lab must retain and add “and digital images” to the cytology and histopathology lines, so a lab would keep both the slide and its image. CMS gives the reason: either may be needed to trace an error behind a complaint or a quality problem. Comments are due 7 December 2026, and nothing changes before a final rule. Read the proposed rule.

Remote review rests on a CMS memo, not on the regulation. Memo QSO-23-15-CLIA, issued 11 May 2023, lets pathologists and other qualified staff review digital data, results and images away from the lab under the primary lab's certificate. CMS's own summary of its conditions includes these:

• The director of the primary lab is responsible for all testing under its certificate, remote work included.
• The primary lab is certified in the specialties and subspecialties of the work done remotely.
• Each remote reviewer is on the primary lab's Form CMS-209, the Laboratory Personnel Report.
• Reports should show the remote site location; a code in place of a home address is allowed if it is available on request.
• The primary lab keeps all documentation of the remote work and gives CMS a list of remote staff on request.

Cytology is the exception. Under the revised memo of 23 September 2025, anyone reviewing cytology slide images away from the certified lab has needed a separate CLIA certificate for that location since 23 March 2026 (the revised memo). The proposed rule would turn the rest into a defined “virtual access”, still excluding cytology.

Two of those conditions are software questions. The viewer should record who opened and signed each case, and from where, which supports the testing record CLIA asks for: the identity of the personnel who performed the test § 493.1283(a)⁠(4). And the report has to carry the remote site, so check where the LIS takes that field from. Confirm your setup with your CMS state survey agency or accreditor before the first remote case.

1. Show the FDA record. Which 510(k) covers the configuration you are quoting, and are our scanners and display models in its indications for use?
2. Scan, then open. Scan a slide with a barcode from our LIS and show it landing in the right case with no one typing a case number.
3. Show the log. Pull the record of who opened, annotated and signed out one case, with the time and place of each step.
4. Show the edition. For every algorithm in the demo, is it cleared, or research use only?
5. Restore a case. Bring back a case from the oldest storage tier and time it.
6. Leave in writing. How do we export every image and annotation in an open format if we change vendor? Images may have to outlive the contract by years.