Pathology Annotation

Annotate whole-slide images with deep zoom, tissue and cellular labels, pathology ontologies, AI assistance, and expert review.

Unitlab supports whole-slide pathology workflows from tissue overview to cellular detail. Teams can label regions of interest, tissue compartments, tumor margins, cells, nuclei, biomarkers, and slide-level properties without losing the spatial context of the original slide.

Use this guide when: you are building computational pathology, histopathology, tissue segmentation, cell or nuclei detection, tumor modeling, or biomarker datasets.

See pathology annotation in action

The demo shows current whole-slide navigation and annotation behavior for pathology data.

Open the demo in a new tab.

Before you begin

1. Create or select a project whose data and ontology match this modality.

2. Confirm the project instructions define the unit of annotation, boundary or timing policy, required properties, and review route.

3. Open the project and enter the assigned item from the project data view or queue. The Workbench loads the modality-native editor inside the shared Unitlab shell.

See Annotation Workbench for navigation, saving, item state, comments, issues, and workflow actions.

Understand the pathology work surface

The pathology experience applies Unitlab’s image annotation and ontology model to very large whole-slide imagery. Deep zoom keeps the slide continuous while the Workbench provides geometry, properties, relations, item context, comments, history, and workflow actions.

Whole-slide pathology view with a focused region and cellular-detail inset

One continuous slide supports overview inspection, region selection, and cellular annotation.

Supported annotation model

Annotation type	Use it for
Bounding box or ROI	Tissue, tumor, lesion, cell cluster, or review regions.
Tissue segmentation mask	Pixel-level tissue, tumor, necrosis, lesion, or biomarker areas.
Polygon or tissue region	Irregular tissue compartments, glands, margins, and other editable regions.
Cell or nuclei instance	Distinct cellular objects for detection, counting, and morphology analysis.
Polyline or tissue boundary	Margins, vessels, and elongated structures.
Point or cell marker	Cell centers, nuclei, glands, or microscopic landmarks.
Classification or finding	Tissue type, grade, stain, biomarker status, or another project-defined label.
Slide Item Property	Source, cohort, quality, stain, acquisition, or another whole-slide value.
Relation	A contextual connection between findings, cells, and tissue regions.

Define minimum object size, edge handling, touching-instance policy, magnification requirements, and whether findings are exhaustive or sampled before annotators begin.

Deep zoom and multi-resolution review

Start at the whole-slide overview to understand tissue distribution, then move through region and cellular detail without creating disconnected crops. Record which magnification level is required for each decision. Reviewers should return to the broader tissue context before approving high-magnification labels.

One pathology specimen shown at overview, region, and cellular resolutions

Multi-resolution viewing preserves the relationship between a cell-level label and its tissue context.

Pathology ontologies

Define tissue regions, findings, cell types, class properties, relations, and slide Item Properties in one reusable ontology. Required values make incomplete findings visible; relations can connect a cellular observation to the relevant tissue region or project-defined context.

Pathology ontology for tissue regions, findings, attributes, relations, and slide properties

Ontology structure keeps microscopic geometry and slide-level clinical context distinct but connected.

AI-assisted repetitive labeling

Use Magic Touch to create an editable mask and Find Similar to propose matching structures on the current image. For dense cells or nuclei, calibrate on representative fields before expanding volume. Check merge and split errors, boundary leakage, false positives in background tissue, and missed morphology variants.

Pathology cells with matching masks and Find Similar assistance

AI assistance can accelerate repetitive structures, but expert review remains responsible for morphology and label meaning.

Annotate one production item

1

1. Survey the whole slide

Inspect tissue coverage, artifacts, empty regions, stain variation, orientation, and the project’s required review areas.

2

2. Navigate to the correct resolution

Zoom from overview to region and cellular detail. Confirm the required magnification for the target label.

3

3. Choose class and geometry

Select the tissue, finding, cell, or nuclei class and use the required ROI, mask, polygon, line, or point tool.

4

4. Create and refine the annotation

Trace the intended boundary or instance, correct holes and touching objects, and keep enough surrounding tissue visible to interpret the structure.

5

5. Add pathology structure

Complete class properties, slide Item Properties, findings, relations, and uncertainty or quality values exactly as the ontology requires.

6

6. Review across scales and route

Inspect dense regions, edge cases, and broader tissue context; resolve validation, save, and submit to the configured expert review stage.

Quality review

Review focus	What to check
Magnification	Use the required resolution for each label and review the result at both detail and context levels.
Instance separation	Check touching cells, merged nuclei, fragments, and duplicate instances.
Tissue boundary	Review holes, folds, tears, staining artifacts, necrosis, and uncertain margins.
Slide context	Validate stain, cohort, source, quality, and whole-slide properties.
Expert calibration	Measure agreement on representative fields before scaling annotation volume.

A saved annotation is not automatically a production-ready annotation. Required values, boundary or timing policy, cross-item consistency, and the configured review stage still apply.

Move from labels to governed data

Pathology outputs should preserve slide identity, coordinate system, magnification context, region or instance geometry, class and slide properties, relations, ontology version, and reviewer provenance. Promote approved cohorts through dataset versions and releases so training and evaluation remain reproducible.

Integrated Unitlab workflow connecting model assistance, annotation, review, and quality assurance

Use workflows to keep model output, human correction, review, and approval in one traceable operating path.

Next steps

• Use Detect Anything (SAM 1–SAM 3) to calibrate interactive and batch assistance.

• Use Multimodal overview when related files or views must stay in one task.

• Curate difficult cases and review cohorts in Data curation.

• Read the current pathology annotation product overview for the feature overview and current media.