Analyze whole-slide images with nucleus segmentation and stain normalization.
npx skills add https://github.com/Yezez9/Research-Agent --skill pathml-yezez9
Please help me install this Agent Skill. Skill: pathml Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/pathml Command: npx skills add https://github.com/Yezez9/Research-Agent --skill pathml-yezez9
This Skill provides a comprehensive toolkit for advanced whole-slide image analysis in computational pathology, enabling complex machine learning workflows and detailed spatial analysis.
Use the pathml skill to load a whole-slide image and perform nucleus segmentation.
High-intent search queries and answers about installing and using this skill.
Nucleus segmentation on whole-slide images is performed using integrated machine learning models like HoVer-Net. This computational pathology toolkit enables automatic detection and classification of nuclei within H&E stained tissue images.
Analyzing spatial relationships in multiplexed immunofluorescence images is done by constructing spatial graphs of cell-cell interactions. This allows quantification of marker expression and neighborhood analysis within the tumor microenvironment.
Yes, the computational pathology toolkit supports DICOM and OME-TIFF formats. It can load over 160 different whole-slide image formats, including Aperio, Hamamatsu, Leica, and Zeiss files.
Yes, you can use DeepCell Mesmer for cell segmentation on H&E stained tissue images. The toolkit integrates directly with DeepCell Mesmer to provide advanced cell segmentation capabilities.
Stain normalization is applied to whole-slide images during the preprocessing phase. This standardizes stain appearance before training machine learning models and includes artifact detection to clean the data.
Yes, the spatial omics analysis supports CODEX, Vectra, and MERFISH multiparametric imaging. It provides specialized preprocessing and graph construction for these specific multiplexed imaging platforms.
biomaps-infraAnalyze whole-slide images and multiplexed immunofluorescence data for computational pathology.
inflexa-aiQuantify immune cell composition and signature activity from expression data.
ovachieverExtract nuclei and cellular features from whole-slide pathology images.
robinbarvaagAnalyze whole-slide images and multiplexed data with Python.
