histo | VIRDX

Histopathology imaging, whole-slide-image tiling/serving, tissue segmentation, and vxAnnotate-produced pathology assessments.

Goal: produce and serve histopathology ground truth (whole-slide images, tissue/anatomy segmentation, PIRADS/ISUP/PIQUAL pathology assessments) that grounds the diffsim biophysical tissue model and provides labels/eval data for ve2e.

No dedicated monthly report has ever been filed for histo (not even an explicit gap stub beyond January) — treat month-by-month status as largely undocumented here; the June 2026 engineering report notes histo ran a large-scale formal evaluation of vxAnnotate outputs (243 files / 57k lines) that same month.

What’s documented so far

WSI tile serving: dashboard-api serves histo WSI tiles directly (no separate tile server) via large_image TIFF tiling + OME-Zarr streaming, behind the @virdx/ui-components TileViewer. See Dashboard histo tile serving.
Preprocessing performance: the histo-preprocessing inference service (mono apps/inference) is libvips/pyvips-based; libvips is not cgroup-aware and will oversubscribe threads unless VIPS_CONCURRENCY is pinned. See Histo preprocessing libvips container performance.
viseg segmentation inference: resolve model weights via ClearML and run VisegInferenceModel. See Viseg segmentation inference; for the data-access half use vxData SDK + schema model (the old vxp_client API died with the archived data-platform repo).
New schemas paired with histo output: HistoScan (zarr-backed tissue scan), HistoMap (zarr-backed parameter/segmentation map over a HistoScan), DiffSimOutput (diffusion-sim .nii referencing a HistoScan+HistoMap) landed in vxData May 2026 — see vxData SDK + schema model for the current payload-type list.
vxAnnotate integration bugs: the ISUP/PIRADS mask silent-drop bug (VBC-1250, pl.col(...).first() in a group_by) and the empty-mask RLE bug (native-res masks truncated because the frontend picked the wrong reference series) are both fixed; the traps they came from are written up in vxData jobs ingestion patterns and workstreams/infrastructure/sops/vxannotate-vxdata-sync.md.

SOPs

See sops/. No projects/ subdirectory exists yet — add one as time-bound histo projects get synthesized from inbox/.