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pathml

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About pathml

P

pathml

Supports local computational pathology research

pathml is an agent skill for local computational pathology research with PathML. It covers loading and tiling slides, preprocessing and quality control, storage in h5path files, multiplex quantification and spatial analysis. The skill is clear about its boundaries. PathML is beta research software. It is not a validated medical device, diagnostic system or clinical decision support tool, and it is not a substitute for a pathologist, so the outputs must not be used to diagnose, grade, stage or treat a patient. Pathology files can contain identifying information, such as faces, labels, accession numbers, patient identifiers, DICOM tags, file names and linked clinical data. The skill asks you to confirm authorisation, consent or waiver, data-use terms and institutional policy before you process anything. It asks you to de-identify the pixels and the metadata, keep the re-identification key outside the analysis workspace, and use pseudonymous identifiers for patients, slides and specimens. Inputs, intermediate files and outputs should stay on approved, encrypted local storage, and you should split the data by patient, then by slide, before tiling or fitting any preprocessing step.

View pathmlAll AI Skills apps
Price
Free
Made by
k-dense-ai
Category
AI Skills
Website
github.com/k-dense-ai/scientific-agent-skills/pathml