patolojiAI
OrganizationComprehensive clinical pathology toolkit for Claude - skills for CAP/ICCR compliance, TNM staging, synoptic templates, SNOMED coding, tumor board summaries, scientific similarity checking, and reference verification.
Categories
Indexed Skills (15)
qupath-guide
Guides QuPath users in digital pathology with troubleshooting, interface navigation, image analysis workflows, and Groovy scripting. Use when the user mentions QuPath, or uses QuPath-specific signals such as .qpproj/.qpdata files, "Run for Project", "stain vectors", "TMA dearrayer", "detection objects", or "Brightfield (H-DAB)". Also use for QuPath cell detection, tissue/tumor annotation, IHC scoring (Ki-67, HER2, PD-L1), stain separation/deconvolution, pixel or object classification, TMA analysis, multiplex/mIF analysis, Groovy scripts for pathology slides, measurement export, batch processing, QuPath extensions, or QuPath errors. Provides menu paths, workflows, ready-to-run Groovy snippets, and fetches official QuPath docs for version-specific details. Do NOT use for general non-QuPath image processing, ImageJ/Fiji-only questions, or standalone deep-learning pipelines (e.g. StarDist/Cellpose in plain Python) outside QuPath.
breast-pathology-specialist
Comprehensive breast cancer pathology workflow combining CAP/ICCR compliance validation, synoptic template generation, TNM staging (AJCC 8th edition), biomarker reporting (ER/PR/HER2/Ki-67) per ASCO/CAP guidelines, tumor board summaries, and SNOMED coding for invasive breast carcinoma. Use when the user uploads or pastes a breast pathology report (mastectomy, lumpectomy, wide local excision, sentinel/axillary lymph node biopsy) and asks to "check breast report", "validate breast pathology", "stage this breast cancer", "interpret ER/PR/HER2", "generate breast template", or any breast-cancer-specific pathology task. Supports .pdf, .docx, .txt input in English and Turkish.
colorectal-pathology-specialist
Comprehensive colorectal cancer pathology workflow combining CAP/ICCR compliance validation, synoptic template generation, TNM staging (AJCC 8th edition), MSI/MMR testing interpretation, mesorectal excision quality (MERCURY) grading, tumor board summaries, and SNOMED coding. Use when the user uploads or pastes a colorectal pathology report (colectomy, low anterior resection, abdominoperineal resection, polypectomy) and asks to "check colorectal report", "validate CAP ColoRectal protocol", "stage this colorectal cancer", "interpret MSI/MMR", "assess TME quality", or any colorectal-cancer-specific pathology task. Supports .pdf, .docx, .txt input in English and Turkish.
gastric-pathology-specialist
Comprehensive gastric cancer pathology workflow combining CAP/ICCR compliance validation, synoptic template generation, TNM staging (AJCC 8th edition), Lauren classification (intestinal/diffuse/mixed), WHO histologic typing, HER2 testing interpretation per ASCO/CAP, MSI/MMR status, tumor board summaries, and SNOMED coding. Use when the user uploads or pastes a gastric pathology report (total/subtotal gastrectomy, esophagogastrectomy, endoscopic submucosal dissection) and asks to "check gastric report", "validate CAP Stomach protocol", "stage this gastric cancer", "interpret Lauren classification", "interpret HER2 IHC/FISH", or any gastric-cancer-specific pathology task. Supports .pdf, .docx, .txt input in English and Turkish.
pancreas-pathology-specialist
Comprehensive pancreatic cancer pathology workflow combining CAP/ICCR compliance validation, synoptic template generation, TNM staging (AJCC 8th edition for exocrine pancreas), Whipple/distal-pancreatectomy specimen dissection guidance, axial slicing and margin assessment (SMA, SMV, posterior, anterior, pancreatic neck, bile duct), tumor board summaries, and SNOMED coding. Use when the user uploads or pastes a pancreatic pathology report (Whipple, distal pancreatectomy, total pancreatectomy, pancreatic biopsy) and asks to "check pancreas report", "validate CAP Panc.Exo protocol", "stage this pancreatic cancer", "assess Whipple margins", or any pancreatic-cancer-specific pathology task. Supports .pdf, .docx, .txt input in English and Turkish.
pathology-compliance-checker
Validates surgical pathology cancer reports against CAP (College of American Pathologists) and ICCR (International Collaboration on Cancer Reporting) guidelines with severity-based compliance scoring (0-100) and automatic pT/pN/margin cross-validation. Use whenever the user pastes or uploads a pathology report (.pdf, .docx, .txt) and asks to "check compliance", "validate against CAP", "score this report", "audit this synoptic", "find missing elements", or "verify pT/pN consistency". Supports breast, colorectal, pancreas, and gastric carcinoma in English and Turkish.
pathology-template-generator
Generates blank or pre-filled CAP-compliant synoptic pathology report templates with every required data element listed. Use when the user asks to "generate a synoptic template", "create a CAP report skeleton", "give me a blank breast lumpectomy template", "Whipple specimen template", "pre-fill template with these findings", or any variant of synoptic template creation. Supports breast, colorectal, pancreas, and gastric carcinoma in English and Turkish (.txt, .md output).
reference-verifier
Comprehensive academic reference auditor that performs four levels of verification on citations in uploaded manuscripts (.pdf, .docx). Level 1 checks if references actually exist. Level 2 verifies metadata accuracy (authors, year, journal, volume, pages). Level 3 checks whether the cited paper actually covers the topic it is cited for. Level 4 analyzes whether each citation is used correctly in context — confirming if the cited source truly supports, contradicts, or is neutral toward the claim being made. Saves a BibTeX file (.bib) and a markdown audit report (HTML optional) in the current working directory. Use whenever the user uploads a manuscript and asks to check, verify, validate, or audit references, citations, or bibliography, generate a .bib file, detect fake or hallucinated references, check citation accuracy, verify citation context, or audit a reference list. Especially tuned for biomedical/PubMed-indexed literature but works for any discipline.
report-converter
Converts free-text narrative pathology reports into structured CAP synoptic format and generates amendments/addenda/corrections for previously-issued reports. Use when the user uploads or pastes a narrative pathology report (.pdf, .docx, .txt) and asks to "convert to synoptic", "convert to CAP format", "structure this report", "make this synoptic", "generate an amendment", "add an addendum", or "issue a corrected report". Extracts diagnostic elements (tumor type, grade, size, stage, margins, nodes, biomarkers) and maps them to CAP data elements.
scientific-similarity-checker
Analyze a scientific article (.pdf, .docx, image, or text) to find similar work across PubMed, OpenAlex, Semantic Scholar, IEEE, arXiv, Crossref, and the web. Detects similarity by abstract content, topic, authors, and journal. Issues tiered warnings (red/amber/green) when similarity levels suggest self-plagiarism, duplicate publication, salami slicing, or research misconduct. Saves a structured report as markdown (and optionally HTML) in the current working directory. Use whenever a user uploads or pastes a scientific article, manuscript, preprint, or abstract and asks to "check this paper", "find similar studies", "is this published elsewhere", "duplicate publication check", "misconduct screening", "novelty check", "plagiarism screen", or "find the authors' other work" — including when academic integrity checking is implied.
statistical-methods-reviewer
Critically review the statistical methods used in a research article (.pdf, .docx, .pptx, .html, .txt). Extract every test and model the authors used, judge whether each is appropriate for the study design and data, and evaluate assumption checks, multiplicity control, sample-size justification, effect-size reporting, model specification, missing-data handling, validation/calibration, and reproducibility. Produces a scored rubric (0-2 across 9 aspects, total 0-18), a red-flag list, and concrete recommendations for better statistical tests where appropriate. Saves the review as a markdown file (and optionally HTML) in the current working directory. Use when the user supplies a research article and asks to "review the stats", "check the statistical methods", "audit the analysis", "are these tests correct", "score this paper's statistics", or any variant of statistical critique.
tnm-stage-calculator
Fast TNM stage group calculation from pT, pN, pM categories using AJCC 8th edition criteria, with automatic consistency validation. Use when the user asks "what stage is pT2 N1 M0", "calculate TNM stage", "stage group for pT3 N1b breast", "is pT2 N0 M0 stage I or II", "stage this pancreatic cancer", or any pT/pN/pM to stage-group conversion. Supports breast, colorectal, pancreas, and gastric carcinoma. Flags inconsistencies like tumor-size-vs-pT mismatches and node-count-vs-pN mismatches.
pathology-report-checker
Analyzes surgical pathology cancer reports for compliance with CAP (College of American Pathologists) and ICCR (International Collaboration on Cancer Reporting) guidelines. Validates pTNM staging (AJCC 8th edition), checks required element completeness with severity-based scoring, generates blank or pre-filled CAP synoptic templates, creates 3-5 line tumor board summaries, suggests SNOMED CT and ICD-O-3 codes, converts free-text narratives to structured synoptic format, and drafts amendments/addenda. Use when the user pastes or uploads a pathology report (txt, pdf, docx, image, xlsx) and asks to "check CAP compliance", "verify staging", "generate synoptic template", "tumor board summary", "convert to synoptic", "calculate TNM stage", or "code with SNOMED" for breast invasive carcinoma, colorectal resection, exocrine pancreas carcinoma, or gastric carcinoma. Supports English and Turkish. Do NOT use for non-cancer pathology (inflammatory, infectious), cytology, or unsupported tumor types.
pathology-coder
Suggests SNOMED CT and ICD-O-3 morphology/topography codes for pathology diagnoses, procedures, and biomarkers, with hierarchical parent/child relationships and synonyms. Use when the user asks "SNOMED code for [diagnosis]", "ICD-O-3 code for [tumor type]", "what's the code for invasive ductal carcinoma", "code this diagnosis", "morphology code for", or any pathology-coding lookup. Supports common cancer diagnoses (breast, colorectal, pancreas, gastric, prostate, lung, lymphoma, GIST) and standard pathology procedures.
pathology-tumor-board-summary
Generates concise 3-5 line tumor board summaries from full pathology reports, extracting the diagnosis, TNM stage, margins, lymph node status, key biomarkers, and risk factors that drive MDT decisions. Use when the user pastes or uploads a pathology report (.pdf, .docx, .txt) and asks to "create a tumor board summary", "MDT summary", "oncology consult summary", "3-line summary for the MDT", or "summarize for tumor board".
Bio shown is the top-scored skill's repo description as a fallback — real GitHub bios land in a future update.