Pancreas Morphology

Umbrella page for pancreatic morphology studies across PDAC, adenosquamous, solid-pseudopapillary, ampullary, and more

What this project is

The group runs a family of pancreatic morphology studies that share cohorts, stains, and analytic infrastructure. This page is the index: each sub-study is a dedicated repo; this page documents the common methods, the shared data dictionary, and which repo you should open for what question.

Shared infrastructure

Case selection schema: organ = pancreas, with subclassifications in a common YAML.
De-identified image cohort held on the Memorial share (not in git).
Analysis done via ClinicoPathJamoviModule (descriptives, survival, agreement).

Sub-studies

PDAC (ductal adenocarcinoma)

PDAC-adrenal-invasion — adrenal-gland invasion patterns and prognostic impact.
PDAC-benign-vs-malignant — distinguishing PDAC from benign mimics on limited material.
PDAC-cytology — cytologic features in FNAs.
PDAC_LN_shell — lymph-node shell involvement patterns.
pdac-large-duct — large-duct PDAC variant morphology.

Variant and uncommon tumors

Ampulla / duodenum / ectopia

Interface / methods

morphology-research-pancreas-interface — shared data-entry and review interface used across the studies above.

Status snapshot

Study	Status
Adrenal invasion	Analysis complete; manuscript in revision
Benign vs malignant	Cohort frozen; analysis in progress
LN shell	Annotation phase
Large-duct PDAC	Pilot
Adenosquamous	Manuscript drafted
Solid-pseudopapillary	Manuscript submitted
Ampullary	Active enrollment

How to contribute

Ask which sub-study needs a second reviewer.
Clone that repo and read its protocol.md (every sub-study has one).
Review the pilot batch of cases and record your findings in the shared sheet.

Pitfalls

Don’t re-run IHC interpretations across sub-studies independently; the shared IHC database is the single source of truth.
When a case spans two sub-studies, it’s tagged in both, but analyzed once in its primary study to avoid double-counting.

In the research wiki

Pancreas Cohorts — the shared case-selection schema and IHC database that make these sub-studies one family rather than ten projects.
Descriptive Tables — the table that opens each of these papers, done once and reproducibly.
Survival Analysis Workflow — the route from cohort table to a defensible prognostic result.
Competing Risks — pancreatic cohorts carry enough non-cancer death that naive survival estimates overstate risk.
Interobserver Agreement — the second-reviewer step in the contribution flow is an agreement study already; measuring it costs almost nothing extra.
Pancreas Morphology — this project’s own pointer page, alongside the cohort and method pages it draws on.