Bio Image Processing Skills Index
DocumentsBio Image Processing Skills Index is an Agent Skill for documents published in the aristoteleo/PantheonOS repository on GitHub: a SKILL.md instruction file an AI agent can load to do this task.
Skills for biological image analysis: cell/nucleus segmentation, image restoration, and spatial data processing.
How to use this skill
Bring this guide into your coding agent with a prompt tailored to the tool you use.
- Open your project in Codex.
- Copy and paste the prompt below.
- Review files and risks before approving any action.
Inspect the Agent Skill at https://github.com/aristoteleo/PantheonOS/blob/HEAD/pantheon/factory/templates/skills/bio_image_processing/SKILL.md and all supporting files. Report provenance, permissions, scripts, dependencies, and security risks. Propose an exact installation into .agents/skills/bio-image-processing-skills-index, but wait for my approval before writing files or running scripts.
Copying this prompt does not install or run the skill. Review third-party files before use.
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