QuPath Repositories

The group’s QuPath-adjacent repos — extensions, scripts, annotation tooling, and PACS integration

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What this is

A curated index of every Memorial repo that touches QuPath. Use this to find the right extension or script before starting a new one.

PACS and scanner integration

• sectra-qupath-extension — Groovy extension connecting QuPath to Sectra PACS.
• sectra-python-qupath-extension — Python-scripted variant for automation.

Annotation & curation

• QuickAnnotator — browser-based rapid-annotation interface feeding GeoJSON into QuPath.
• HistomicsML — interactive region labeling used alongside QuPath.
• CohortFinder — batch-level QuPath project curation.
• TissueSelector — tissue-region filtering before annotation.

QC pipelines

• HistoQC — slide-level QC, outputs used as QuPath-project filters.
• grandQC_quality_study — internal QC-reproducibility study.
• PathProfiler — whole-cohort profiling.

WSI viewers and I/O

• DIYWSI — DIY viewer playground.
• simple_wsi_viewer, slide_viewer_47, video-wsi, imageTypes.

Downstream DL toolchains

• pathml, pathml-tutorial — Dana-Farber / Weill Cornell WSI framework.
• tiatoolbox — Warwick toolbox.
• pathology-hooknet — HookNet segmentation pipeline.
• DL4MicEverywhere — DL-for-microscopy ported workflows.

Conventions

• GeoJSON is the interchange format between QuPath and every downstream tool. Name annotations as {organ}__{class}__{reviewer}.geojson.
• Scripts live in the project repo where they are used. Only truly generic scripts belong in the extension repos.
• Don’t commit .qpproj project files for cohorts containing patient identifiers — keep them on the Memorial share.

How to contribute

1. Pick the repo matching your task (PACS, annotation, QC, viewer, DL).
2. Read its README; run the bundled example.
3. Open an issue before building a new script that overlaps with an existing one.