Pathology Report Extractor

Extract the accession number, specimen, gross and microscopic findings, diagnosis, and stains from a pathology report PDF. Extraction only, no interpretation.

The full guide: Specimen, ICD-O diagnosis, and IHC on a pathology report

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Upload a file or pick a sample, and see the fields come back.

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Questions about Pathology Report Extractor.

How is a pathology report different from a radiology report or a lab result?

A pathology report is the diagnosis of a tissue or fluid specimen examined under the microscope, not an imaging read or an analyzer result. The extractor reads the accession or case number, the report status (preliminary, final, amended), the specimen type, collection date, anatomic location, and laterality, and the ordering provider and pathologist names — the specimen-centered structure a radiology or lab document does not have.

Which examination sections come out?

The clinical history, the gross (macroscopic) description, the microscopic findings, the final diagnosis, the special stains performed, the immunohistochemistry markers and results, the molecular or genetic studies, and the concluding summary each come back as their own field, preserving the report's section structure.

Does it structure specimens, diagnoses, and studies into tables?

Yes. A specimens table returns each specimen's ID, type, collection date, anatomic location, and laterality; a diagnoses table returns each diagnosis with its ICD code as printed; and a special studies table returns each study's type, name, and result. The tool transcribes codes present on the page — it does not assign or interpret them.

Does the tool diagnose or interpret the findings?

No. It is extraction-only: it captures the text and values already on the report — including the pathologist's stated diagnosis — into structured fields. It does not make a diagnosis, interpret findings, or provide medical advice. The report contains PHI and is handled accordingly.

What are the upload limits and is the report retained?

One PDF up to 10MB and 100 pages. The report is processed via the Talonic API for extraction only, is not retained for training, and is not shared. Export as CSV, XLSX, or JSON.

Doing this to one file, or to ten thousand?

The tool reads a single document. The platform reads the whole estate once and keeps it queryable — the same engine, with a memory.

See document data extraction if you run this for clinical and billing teams, or the extraction API if you are building it in.

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