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name: model-inference description: "Plan and validate TIAToolbox model inference with PatchPredictor, DeepFeatureExtractor, semantic segmentation, nucleus detection, and multitask segmentation engines." disable-model-invocation: true metadata: disco-role: operating license: NOASSERTION

Model Inference

Use this sub-skill when a task needs TIAToolbox model engines, pretrained model selection, custom weights, device planning, IO config construction, output format decisions, or migration from deprecated nucleus instance segmentation APIs.

Start Here

• For engine/API signatures and run-parameter contracts, read references/api-reference.md.
• For pretrained model key selection without downloading weights, read references/model-registry.md and use scripts/model_registry_probe.py.
• For end-to-end planning patterns, read references/workflows.md.
• For common inference failures and safe mitigations, read references/troubleshooting.md.

Owned Capabilities

• Patch classification with PatchPredictor and deep embedding extraction with DeepFeatureExtractor.
• Semantic segmentation with SemanticSegmentor and nucleus detection with NucleusDetector.
• Multitask and nucleus instance segmentation with MultiTaskSegmentor, including migration away from deprecated NucleusInstanceSegmentor.
• Model zoo key validation, custom weight routing, CPU/GPU/MPS device choices, IO config validation, and output type planning.
• Inference CLI plan review for patch-predictor, deep-feature-extractor, semantic-segmentor, nucleus-detector, nucleus-instance-segment, and multitask-segmentor.

Boundaries

• For mask creation, tile selection, stain normalization, and patch extraction fundamentals, route to ../image-preprocessing/.
• For WSI reader metadata, resolution semantics, and WSIReader behavior, route to ../wsi-io/.
• For viewing or editing generated AnnotationStore outputs, route to ../annotation-visualization/.
• For an exhaustive CLI option catalog and project-level configuration conventions, route to ../cli-and-configuration/.

Safety Rules

• Do not imply pretrained weights are available locally; model-string construction may download weights unless weights points to local compatible weights.
• Prefer device="cpu" unless the user or environment explicitly confirms cuda or mps availability.
• Validate model keys with the bundled registry probe before constructing a pretrained engine.
• In WSI mode, require a save directory for file-backed outputs and verify output_type matches the engine capability.