Skills

A skill is a package of structured files that teaches an AI coding agent how to work with a specific tool or framework. The skill below was generated by Great Docs from this project’s documentation. Install it in your agent and it will be able to run commands, edit configuration, write content, and troubleshoot problems without step-by-step guidance from you.

Any agent — install with npx:

npx skills add https://hocheggerlab.github.io/omero-screen/

Codex / OpenCode

Tell the agent:
Fetch the skill file at https://hocheggerlab.github.io/omero-screen/skill.md and follow the instructions.

Manual — download the skill file:

curl -O https://hocheggerlab.github.io/omero-screen/skill.md

Or browse the SKILL.md file.

SKILL.md

---
name: omero-screen
description: >
  High-content image analysis pipeline for data stored in OMERO. Use when writing Python code that uses the omero_screen package.
compatibility: Requires Python >=3.12,<3.15.
---

# OMERO-Screen

High-content image analysis pipeline for data stored in OMERO

## Installation

```bash
pip install omero-screen
```

## API overview

### Pipeline

Running a plate through the analysis pipeline.

- `loops.plate_loop`
- `plate_dataset.PlateDataset`

### Metadata

Plate layout, channel names and channel roles.

- `metadata_parser.MetadataParser`
- `metadata_parser.resolve_channel_roles`

### Configuration

Environment files and logging setup.

- `config.set_env_vars`
- `config.configure_logging`

## Resources

- [Full documentation](https://hocheggerlab.github.io/omero-screen/)
- [llms.txt](llms.txt) — Indexed API reference for LLMs
- [llms-full.txt](llms-full.txt) — Comprehensive documentation for LLMs