alterlab-pathml
De la autor
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.
Instalare
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-pathml -a claude-code
Se instalează în .claude/skills/alterlab-pathml/ · Fiecare comandă descarcă skill-ul direct de pe GitHub cu utilitarul open source skills.
Fără descărcare: licența acestui skill (GPL-2.0) nu ne permite să-i redistribuim fișierele. Comenzile de instalare le iau direct de pe GitHub.
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Skill-uri similare
Cele mai apropiate de acesta prin ce fac și când sunt folosite.
- pathmlforyourhealth111-pixel/Vibe-SkillsComputational 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.Documente★ 3.8K
- alterlab-histolabAlterLab-IEU/AlterLab-Academic-SkillsExtract 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.Documente★ 78
- histolabK-Dense-AI/scientific-agent-skillsExtracts and preprocesses whole-slide histology image tiles with Histolab. Use for WSI inspection, tissue masks, random/grid/score-based tile extraction, H&E stain normalization, and tile dataset preparation. For multiplexed imaging or deep learning inference pipelines, use pathml.Documente★ 54.9K
- histolab-wsi-processingjaechang-hits/SciAgent-SkillsWSI processing for digital pathology. Tissue detection, tile extraction (random, grid, score-based), filter pipelines for H&E/IHC. For dataset prep, tile-based DL, slide QC. Use pathml for multiplexed imaging.Documente★ 383
- digital-pathologyawslabs/hcls-agent-skillsGenerate correct code for whole-slide image (WSI) analysis using TIAToolbox and foundation models (H-optimus-0, UNI, Prov-GigaPath). Triggers on requests involving whole-slide images, WSI, digital pathology, histopathology, SVS/NDPI/pyramidal TIFF, tissue segmentation, patch extraction, stain normalization, H-optimus-0, TIAToolbox, CAMELYON16/17, SlideGraph, MIL aggregation, HoVer-Net, PanNuke, or SageMaker deployment of pathology models. Produces deterministic commands and Python snippets for slide-info inspection, tissue masking, tile extraction at specified mpp, foundation-model feature embedding, slide-level aggregation, and regulated cloud inference.DevOps★ 67
- alterlab-pyopenmsAlterLab-IEU/AlterLab-Academic-SkillsBuild complete mass-spectrometry workflows with pyOpenMS — feature detection, peptide identification, protein quantification, and full LC-MS/MS pipelines across many MS file formats (mzML, mzXML) and algorithms. Use for comprehensive proteomics and MS data processing — for simple spectral comparison and metabolite identification use matchms. Part of the AlterLab Academic Skills suite.Știință★ 78
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