Pathml Skill for Codex

Histolab

by christophacham

×3

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.

Omero Integration

by christophacham

×3

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

Transformers

by christophacham

×3

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 K-Dense-AI

×1

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

×1

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

×1

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.

Config Evals

by n8n-io

vendor

>- Builds and maintains configuration-based evaluations on a workflow with the eval-config tool. Use when the user asks to set up, add, view, change, or remove an evaluation, score, grade, or judge a workflow's output, or measure answer quality against a test dataset. This is the only eval form Instance AI handles — it does not touch on-canvas evaluation nodes.

Fal Train

by nexu-io

| Train custom AI models (LoRA) on fal.ai for personalized image generation tailored to a brand, character, or style.