Bio Image Processing Skills Index

Documents

Skills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.

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How to use this skill

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I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/aristoteleo/PantheonOS/blob/HEAD/pantheon/factory/templates/skills/bio_image_processing/SKILL.md

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Copying this prompt does not install or run the skill. Review third-party files before use. Codex skill guide

Agent Skills for Biological Image Processing

Best practices and workflows for biological image analysis tasks including cell segmentation, image restoration, and spatial data processing. Load the relevant skill files when performing specific analysis tasks.

Cell & Nucleus Segmentation

Tools and workflows for instance segmentation of cells and nuclei in microscopy images. Covers deep-learning methods (Cellpose, SAM-based, StarDist) with guidance on model selection, GPU/CPU inference, fine-tuning, and 3D segmentation.

Skill index: segmentation/SKILL.md

Skills:

Cellpose: General-purpose cell/nucleus segmentation (Cellpose 3, Cellpose-SAM)
SAM-Based Methods: CellSAM, micro-sam, SAMCell for automatic and interactive segmentation

When to use:

Segmenting cells or nuclei in fluorescence, brightfield, or phase contrast images
Need instance masks from 2D or 3D microscopy data
Comparing or selecting between segmentation tools for your imaging modality
Fine-tuning a segmentation model on custom training data

Using Skills

Before analysis: Scan this index for relevant skills
Load skill file: Read the full skill document for detailed guidance
Follow best practices: Use the code snippets and workflows provided
Adapt as needed: Skills are templates; adjust for your specific data