Results for “histopathology”

Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Digital pathology image processing toolkit for whole slide images (WSI). Use this skill when working with histopathology slides, processing H&E or IHC stained tissue images, extracting tiles from gigapixel pathology images, detecting tissue regions, segmenting tissue masks, or preparing datasets for computational pathology deep learning pipelines. Applies to WSI formats (SVS, TIFF, NDPI), tile-based analysis, and histological image preprocessing workflows.

Process whole slide images for digital pathology: detect tissue, extract tiles, and prepare datasets for deep learning pipelines.

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preprocessing — building tile datasets for ML training, tissue segmentation, or quick tile-based inspection of histopathology slides. For end-to-end computational-pathology, deep-learning model training, nucleus segmentation, or multiplexed/spatial-proteomics (CODEX, Vectra) pipelines prefer alterlab-pathml instead. Part of the AlterLab Academic Skills suite.

Full-featured computational pathology toolkit. Use for advanced WSI analysis including multiplexed immunofluorescence (CODEX, Vectra), nucleus segmentation, tissue graph construction, and ML model training on pathology data. Supports 160+ slide formats. For simple tile extraction from H&E slides, histolab may be simpler.

Lightweight WSI tile extraction and preprocessing. Use for basic slide processing tissue detection, tile extraction, stain normalization for H&E images. Best for simple pipelines, dataset preparation, quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.

Loads and processes whole-slide pathology images, builds spatial graphs, trains deep learning models, and analyzes multiplexed immunofluorescence data across 160+ slide formats.

Analyzes biochemical processes, including enzyme kinetics, metabolic pathways, and biomolecule characterization, with practical techniques and examples.

Kit de ferramentas de patologia computacional para análise de imagens de lâminas inteiras (WSI) e dados de imagem multiparamétrica. Use esta habilidade ao trabalhar com lâminas de histopatologia, imagens coradas com H&E, imunofluorescência multiplex (CODEX, Vectra), proteômica espacial, detecção/segmentação de núcleos, construção de gráficos de tecido ou treinamento de modelos ML em dados de patologia. Suporta 160+ formatos de lâmina incluindo Aperio SVS, NDPI, DICOM, OME-TIFF para fluxos de trabalho de patologia digital.

Analyze whole-slide pathology images with Python: load 160+ slide formats, preprocess H&E stains, segment nuclei, construct spatial graphs, train ML models, and process multiplex immunofluorescence data (CODEX, Vectra).

Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.

Explains biomedical concepts, vital signs, biological signals, medical device classifications, and healthcare data standards for technical teams.

Run full computational-pathology workflows with PathML — whole-slide-image (WSI) analysis across 160+ slide formats, multiplexed immunofluorescence (CODEX, Vectra, MERFISH), nucleus segmentation/classification (HoVer-Net, HACTNet), tissue- and cell-graph construction, HDF5 dataset management, and deep-learning model training on pathology data. Use when the user builds end-to-end deep-learning pathology pipelines, analyzes multiplexed or spatial-proteomics slides, or segments nuclei. For lightweight H&E slide preprocessing, tissue masking, or plain Random/Grid/Score tile extraction prefer alterlab-histolab instead. Part of the AlterLab Academic Skills suite.

Runs NV-Segment-CTMR segmentation on CT or MRI NIfTI volumes and records label-map evidence.

Holarchic reasoning framework implementing λ-calculus over simplicial complexes. Entities (ο) transform through operations (λ) toward terminals (τ) via the universal form λο.τ. Persistent homology captures multi-scale structure; sheaf theory ensures local-to-global consistency. Use when knowledge requires: (1) homoiconic self-reference where structure mirrors content, (2) scale-invariant holonic decomposition, (3) topological invariants preserved across transformations, or (4) formal Lex-style axiom systems over property graphs.

Karpathy's LLM Wiki: build/query interlinked markdown KB.

Expert HIPAA compliance assistant for healthcare and software contexts. Use this skill whenever the user mentions HIPAA, PHI (Protected Health Information), ePHI, covered entities, business associates, healthcare data privacy, medical records, health information security, BAA (Business Associate Agreements), or any compliance review involving patient data. Also trigger for requests to draft privacy notices, HIPAA policies, consent forms, security risk assessments, or breach notification letters. Use for developers building healthcare software who need technical safeguard guidance (encryption, access controls, audit logs), compliance officers reviewing documents or procedures, and anyone asking "is this HIPAA compliant?" or "what does HIPAA require for X?". When in doubt about whether a healthcare or data privacy question falls under this skill — use it.

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

Detect and analyze heap spray attacks in memory dumps using Volatility3 plugins to identify NOP sled patterns, shellcode landing zones, and suspicious large allocations in process virtual address space.

Use when studying cell biology.

Generates professor-style chapter lectures and interactive HTML quizzes from course materials like PPT, PDF, and Word files.

Expert en biotechnologies avancées (bioinformatics, genomics, CRISPR, drug discovery, DZ research)

Karpathy's LLM Wiki: build/query interlinked markdown KB.

Generate professional clinical decision support documents for pharmaceutical and clinical research, including biomarker-stratified cohort analyses and evidence-based treatment recommendation reports with GRADE grading, statistical analysis, and publication-ready LaTeX/PDF output.

Build and maintain a persistent, interlinked markdown knowledge base that compiles knowledge once and keeps it current, with cross-references and contradiction flags.

Detect process hollowing (T1055.012) by analyzing memory-mapped sections, hollowed process indicators, and parent-child process anomalies in EDR telemetry.

Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries.

Karpathy's LLM Wiki: build/query interlinked markdown KB.

Guides HIPAA-specific healthcare privacy and security work, routing to implementation and review skills with decision gates and guardrails.

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

Curating cross-agent knowledge and institutional memory: extracts patterns from agent journals into METAPATTERNS.md, detects knowledge decay, propagates best practices. Use for memory curation.

Use when the user asks to run a full empirical / causal analysis in Python — by default in the style of an applied economics paper (AER / QJE / JPE / ReStud / AEJ) with DID / RD / IV / SCM / DML / matching, written-out estimating equation + identifying assumption, Table 1 / Table 2 / event-study figure / robustness gauntlet — OR in epidemiology / public health style (target-trial emulation, IPTW + g-formula + TMLE triplet, Mendelian randomization, KM/AFT survival, E-value sensitivity, STROBE/TRIPOD reporting) — OR in ML causal inference style (DML, S/T/X/R/DR meta-learners, causal forest, Dragonnet/TARNet/CEVAE, BCF, CATE distribution, policy learning, conformal causal, fairness audit, causal discovery) — OR in distributional / gap-decomposition style (Oaxaca–Blinder `sp.oaxaca`, Kitagawa `sp.kitagawa_decompose`, DiNardo–Fortin–Lemieux `sp.dfl_decompose`, Gelbach `sp.gelbach`, Fairlie `sp.fairlie`, RIF / FFL `sp.rif_decomposition`, all reachable through the `sp.decompose` dispatcher). Also covers exporting mu