Inspected packages/nanovirdx dataclasses, inference base, Histo preprocessing adapter, and DiffSim consumer without editing the monorepo.
Inspected Histo v2’s public domain_representation API, typed settings, scan input, output-store names, and Hydra config packaging.
Identified the thin adapter boundary: compose settings, load models once, translate each WSIBatch entry into ScanInput, call process_scan, and translate the five persisted Zarr outputs into DomainRepresentationBatch.
Reported that the current batch omits the required nuclei segmentation path and that from_vxdata likewise omits the required vxData nuclei_segmentation reference.
Reported that Histo’s repository-root Hydra config is not included by its current wheel packaging, so NanoVirDx needs an explicit config/settings input unless Histo ships package data or NanoVirDx intentionally owns a copy.
Lessons Learned: Pitfalls
The installed Histo environment under the older inference checkout did not contain the current v2 pipeline. The active Histo source checkout was required to inspect the actual API.
A broad file listing under NanoVirDx included its .pixi environment and produced large irrelevant output. Restrict future inspection to src/, tests/, and project metadata.
The Histo workstream index documents operational history but not the v2 adapter boundary or its five-output artifact contract.
Lessons Learned: Improvements
Document Histo v2’s stable integration boundary and fixed five-artifact output names in the Histo workstream SOPs.
Document whether Hydra defaults are a supported installed-package resource. This would prevent downstream adapters from assuming a source checkout.
Keep NanoVirDx’s domain batch schema synchronized with the vxData HistoDomainRep required fields, especially nuclei_segmentation.
