Omero Integration Agent Skill

Transformers

by ComeOnOliver

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This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.

Histolab

by ComeOnOliver

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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.

Omero Integration

by ComeOnOliver

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Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.

Pathml

by ComeOnOliver

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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.

Histolab

by K-Dense-AI

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

Cellpose Cell Segmentation

by BioTender-max

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DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.

Nnunet Segmentation

by BioTender-max

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Medical image segmentation with nnU-Net's self-configuring framework — auto-selects architecture, preprocessing, training for any modality. CT, MRI, microscopy, ultrasound in 2D, 3D full-res, 3D low-res, cascade. Pipeline: convert → plan/preprocess → train (5-fold CV) → best config → predict → ensemble. Use when classical segmentation fails and annotated data exists.

Inference Sh

by ComeOnOliver

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| Run 150+ AI apps via inference.sh CLI - image generation, video creation, LLMs, search, 3D, Twitter automation. Use when running AI apps, generating images/videos, calling LLMs, web search, or automating Twitter. image generation, video generation, openrouter, tavily, exa search, twitter api, grok