Results for “histopathology”

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.

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.

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.

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

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

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.

从 claim graph 编译论文大纲：编译 evidence map → 叙事结构 → 章节计划 + figure plan + citation plan，Review LLM review 必选

Build clinical deep-learning pipelines with PyHealth: load EHR, signal, and imaging datasets, define prediction tasks, instantiate models, train with the PyHealth Trainer, and compute clinical metrics.

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).

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

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

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

Karpathy's LLM Wiki — build and maintain a persistent, interlinked markdown knowledge base. Ingest sources, query compiled knowledge, and lint for consistency.