One compliant system for your WSI files, staining SOPs, tissue specimen metadata, peer review workflows, and long-term archiving — replacing the shared drives and spreadsheets your lab depends on today.
The Problem
Most histopathology labs manage critical data in a patchwork of tools never designed for compliant scientific data management. These gaps create regulatory risk, retrieval failures, audit exposure, and data loss.
Whole slide images — SVS, NDPI, CZI, JP2, TIFF — live on shared drives with no searchable metadata. Images from 18 months ago cannot be reliably found or linked back to specimen records.
Histopathology data supporting IND, NDA, or 510(k) submissions must meet 21 CFR Part 11. Every annotation, observation, and sign-off must be attributable, time-stamped, and tamper-evident. Most systems fail this test.
GLP histopathology requires formal, documented peer review. Most labs communicate this by email and shared drives — creating audit trail gaps that regulators notice.
Tissue block inventory, staining protocols, animal metadata, study records, and business contracts live in different systems — or on paper. The searchability and integrity of the complete study record is compromised.
GLP archives must be maintained for the lifetime of a product. Histopathology image volumes are enormous and growing, and the tools most labs use today were not designed for perpetual, compliant archiving.
Staining SOPs, processing protocols, and equipment calibration records exist in separate repositories. There is no mechanism to enforce or document which SOP version governed a specific study.
Solutions
Every major challenge a histopathology lab faces has a specific answer in CERF. This table maps the most common pain points directly to the CERF features that address them.
| Histopathologist Pain Point | How CERF Addresses It |
|---|---|
| Image data scattered across drives with no searchable metadata | Centralized file management with configurable thumbnail previews, metadata tagging, and semantic search across all image files. Folders display visual thumbnail grids for fast image browsing. Relationships between files, studies, and contributors are immediately clear. |
| No audit trail on image annotations or slide reviews. Hard to trace and compare versions | Every action by every user captured in CERF's immutable, computer-generated audit trail — including image views, annotations, and file access events. Version history makes side-by-side comparison of any two versions straightforward. |
| Peer review sign-off not documented compliantly | PKI-based digital signatures with formal review and approval workflows — the only commercial ELN using the U.S. government's Digital Signature Algorithm (DSA). Every record is cryptographically bound to its signer. |
| Tissue specimen metadata disconnected from images | Histology-specific "Tissue Sample" resource type allows association of appropriate, specialized metadata directly with image files. Image thumbnails can now appear in structured tables alongside specimen metadata, or as thumbnails in linked folders. |
| No structured way to associate images with study data in a single view | CERF 6 Tables now support image thumbnails in cells — allowing specimen registries where each row contains the microscopy image, metadata, and linked pathology report or other assets in a single auditable notebook entry. |
| Staining protocols and SOPs not version-controlled | Full SOP and controlled document management — version history, approval workflows, and read-acknowledgment tracking. SOPs can be directly linked to notebook templates. |
| Long-term archiving of massive image datasets | CERF's database architecture supports perpetual archiving; no record is ever deleted without administrator authorization. Network file links allow large WSI files to remain on high-capacity storage while remaining fully indexed and annotated in CERF. |
| File format incompatibility with WSI workflows | Native viewing and indexing for JP2 (JPEG 2000), PSD, SVS, NDPI, CZI, TIFF, DICOM, and many others. Convenient previews can be used to represent any type of file you work with, no matter how specialized. Highly specialized formats can also be passed to external viewers via round-trip integration. |
| Shared network drives with no access control | Granular role-based access control at the project, study, notebook, and individual record level. Large files kept externally can be richly annotated in CERF so significance and provenance are clear. |
| Compliance for multi-study CRO environments | Complete data isolation between studies and clients. Multi-site architecture with access and visibility adjustable instantly. Guest role restrictions prevent unauthorized file download. |
CERF 6 — New in 2026
CERF 6 introduces the first set of features designed specifically for histopathology and digital pathology workflows. These additions build on CERF's existing compliance infrastructure to address the data management challenges unique to pathology labs.
CERF 6 introduces a dedicated "Tissue Sample" resource type with pre-configured metadata fields aligned to histopathology workflows: specimen ID, tissue type, organ, staining method, processing protocol, animal or patient identifier, study number, and more — linked directly to your images and records.
Browse folders of micrographs and WSI datasets visually. CERF 6 displays image-heavy file cabinets as labeled thumbnails with configurable sizes — exactly as you'd flip through a slide tray — dramatically improving image retrieval speed across large study archives.
CERF 6 adds native viewing and full-text indexing for JP2 (JPEG 2000) — the format used by most whole slide imaging platforms — and PSD (Adobe Photoshop). CERF 6 also adds support for a number of legacy formats you may still use. Store, view, annotate, and search these files within the compliant ELN without format conversion.
CERF 6 extends the CERF Table tool functionality to allow image thumbnails to be inserted directly into table cells. This enables pathologists to build image grids or lists where each row contains a visual preview of the micrograph alongside critical metadata and other related files.
A substantially refreshed UI with new light and dark themes, modern icon sets, and improved screen layouts, as well as customizable icon colors and sizes. New keyboard shortcuts for efficient multi-panel use. Designed to reduce visual fatigue during extended image review sessions.
TOTP-based MFA for CERF Desktop and Automation clients, compatible with Google Authenticator, Microsoft Authenticator, and Bitwarden. Configurable via Business Policy — required, optional, or disabled — to meet the tightest institutional security requirements.
Core Platform
The CERF 6 histopathology features are built on a compliance and data management foundation that has been proven in regulated research environments for over two decades.
The only commercial histology-focused ELN using the U.S. government's Digital Signature Algorithm (DSA). Every record carries an MD5 hash — making any unauthorized alteration immediately detectable. Cryptographically binding peer review sign-off to individual pathology records.
Annotate micrographs directly in CERF with comments, measurements, and callouts — stored as part of the versioned record. Every annotation is timestamped, attributed, and auditable.
Check files out to ImageJ, Photoshop, your preferred DICOM application, or any other external application — then return them to CERF with full version history and audit trail intact. The original file is never overwritten.
When an FDA inspector asks for all histopathology images from a specific compound, tissue type, or timepoint — CERF retrieves them in seconds, with complete metadata, lineage, and audit history attached.
Full approval workflows for staining SOPs, study protocols, and controlled documents. SOPs can be versioned, approved, and linked directly to notebook templates — including enforcement mechanisms that prevent sign-off before required SOPs are in place.
Control access at the project, study, notebook, and individual record level. Complete data isolation between studies and clients — critical for CRO environments managing multiple sponsors.
CERF's database architecture supports perpetual archiving. No record is ever deleted without administrator authorization. Built for the multi-decade retention requirements of GLP regulatory archives.
CERF automatically extracts embedded categorical metadata from your files and images, adding it to the database so that files can be precisely and instantly relocated years later with the advanced multi-parametric search tool.
Regulatory Compliance
CERF was designed from the ground up for use within regulated research environments. The compliance infrastructure is not an add-on — it is the foundation every feature is built on.
The most detailed compliance matrix offered by any ELN vendor — available at cerf-notebook.com. Requirement-by-requirement documentation of how CERF meets every provision of 21 CFR Part 11.
Designed for non-clinical safety study environments. Immutable audit trail, formal peer review documentation, and study data integrity controls aligned to GLP requirements.
Lab-Ally provides installation qualification (IQ) and operational qualification (OQ) documentation as part of the implementation process — supporting your validation requirements from day one.
Cloud, on-premises, or sealed LAN with no internet connection. CERF can be deployed on the infrastructure that meets your organization's security and compliance requirements.
Purchase CERF with the license that meets your needs and budget. Pay either a low annual SaaS fee per user, or purchase a perpetual license with a single one-time payment that allows you to use CERF forever.
CERF 6 supports full client operation on Windows, macOS, and Ubuntu Linux. New .MSI installer for Windows and full Debian-based Linux desktop support in the 2026 release.
CERF allows authorized admins to configure data access and visibility, individual user capabilities, and collaborative workgroups instantly — as well as monitor and export user activity, selected data, and search summaries.
CERF 6 allows for use of ink signature and user ID card images as a way to verify that every user is who they say they are. Use this during on-boarding to strengthen non-repudiation and data integrity.
How CERF Compares
Most histopathology labs manage data in tools that were never designed for their workflows. Here is how CERF compares to the most common alternatives.
| Capability | CERF 6 | Shared Drives / SharePoint | Generic ELN (Benchling, etc.) | Pathology Viewer (Aperio, QuPath) |
|---|---|---|---|---|
| 21 CFR Part 11 Compliant | ✓ Full | ✗ | ~ Partial | ✗ |
| PKI Digital Signatures | ✓ DSA (federal standard) | ✗ | ✗ | ✗ |
| Immutable Audit Trail | ✓ Computer-generated | ✗ | ~ Limited | ✗ |
| Histology-Specific Metadata | ✓ Tissue Sample type (CERF 6) | ✗ | ✗ | ~ Image metadata only |
| WSI / Large Image File Management | ✓ JP2, SVS, NDPI, CZI, TIFF, PSD | ~ Storage only, no metadata | ✗ | ✓ Analysis focused |
| Formal Peer Review Workflow | ✓ PKI-signed, auditable | ✗ | ~ Limited | ✗ |
| SOP / Controlled Document Management | ✓ Full version control + approval | ~ Basic version history | ~ Limited | ✗ |
| Semantic Full-Text Search | ✓ Across all data and metadata | ✗ | ✓ | ✗ |
| Perpetual Archiving | ✓ No record ever deleted | ✗ | ~ Vendor-dependent | ✗ |
| Deployment: On-Premise / Sealed LAN | ✓ | ~ Varies | ✗ Cloud only (most) | ~ Varies |
| Integrates with specialized local applications | ✓ Round-trip to any app | ✗ | ✗ | ✗ |
Common Questions
Answers to the questions histopathologists and lab managers ask most frequently about CERF.
Lab-Ally will be exhibiting at the 12th Annual Digital Pathology & AI Congress USA — May 7–8, 2026, Hilton Columbus Downtown. Visit our booth for a live demonstration of CERF 6, or request a demo at a time that suits you.
Lab-Ally LLC · Columbus, Ohio · +1 (614) 407-4547 · cerf-notebook.com