HistAI Pathology Datahub

A skills repository providing clean and secure integration between AI coding agents (Claude Code, OpenAI Codex, Gemini CLI) and the HistAI Whole Slide Image Data Hub.

Overview

This repository provides:

• 🔍 Search pathology cases by diagnosis, organ, age, stains, and clinical criteria
• 📊 Build research cohorts for machine learning and clinical studies
• 💾 Export whole slide images (WSI) with comprehensive metadata
• 💰 Manage costs with volume-based pricing and selective slide downloads

Security & Access Requirements

To use these skills, you must:

1. Have an active subscription on our CellDX platform
2. Have 2FA authentication enabled on your CellDX account
3. Generate an API Key from Profile Settings → API Keys

Integration

This repository is compatible with Claude Code, OpenAI Codex, and Gemini CLI. Choose your preferred agent below:

Claude Code

Quick Install (Recommended)

1. Register this repository as a plugin marketplace:

   /plugin marketplace add histai/datahub
   

2. Install the Cohort Builder skill:

   /plugin install cohort-builder@histai-datahub
   

3. Configure your API key:

   • Generate an API key from CellDX Platform → Profile Settings → API Keys
   • Set it as an environment variable:

     export HISTAI_API_KEY="your-api-key"

4. Start using:

   • Example: "Search for breast cancer cases with HER2 IHC staining"

Manual Installation (Alternative)

If you prefer local installation:

1. Clone this repository:

   git clone https://github.com/histai/datahub.git
   cd datahub

2. Register as a local skill:

   /plugin add-local
   

   Point to the skills/cohort_builder/SKILL.md file.

OpenAI Codex

Codex automatically detects skills via the agents/AGENTS.md file.

1. Clone the repository:

   git clone https://github.com/histai/datahub.git
   cd datahub

2. Verify skills are loaded:

   codex --ask-for-approval never "Summarize the current instructions."

3. Configure API key:

   export HISTAI_API_KEY="your-api-key"

For more details, see the Codex AGENTS guide.

Gemini CLI

This repository includes gemini-extension.json for Gemini CLI integration.

1. Install from GitHub:

   gemini extensions install https://github.com/histai/datahub.git --consent

   Or install locally:

   git clone https://github.com/histai/datahub.git
   cd datahub
   gemini extensions install . --consent

2. Configure API key:

   export HISTAI_API_KEY="your-api-key"

3. Start using:

   • The Gemini CLI will automatically load the cohort_builder skill
   • Interact with the HistAI Datahub through natural language

See Gemini CLI extensions docs for more help.

Available Skills

🔬 Cohort Builder

Search pathology cases by diagnosis, organ, age, and stains. Filter datasets (benign/malignant, cancer types), build research cohorts, and export whole slide images with clinical and technical metadata.

Full documentation: skills/cohort_builder/SKILL.md

Repository Structure

datahub/
├── .claude-plugin/
│   └── marketplace.json          # Claude Code marketplace configuration
├── agents/
│   └── AGENTS.md                 # OpenAI Codex skill definitions
├── skills/
│   └── cohort_builder/
│       └── SKILL.md              # Main skill documentation
├── gemini-extension.json         # Gemini CLI extension configuration
└── README.md                     # This file

API Access

• Base URL: https://prod.celldx.net
• Authentication: API Key via X-API-KEY header
• Documentation: See individual skill files for detailed API reference

Support

For issues, custom data requests, or enterprise inquiries:

• 📧 Sales: sales@hist.ai
• 📚 Documentation: skills/cohort_builder/SKILL.md
• 🌐 Platform: https://celldx.hist.ai

Data Licensing

All Whole Slide Images (WSI) accessed through this API are distributed under the HistAI Commercial License.

• 📄 License: HistAI Commercial License (DLA)
• 🔒 Terms: Review the Data Licensing Agreement before purchasing cohorts
• ⚖️ Usage Rights: Commercial and research use as specified in the DLA

License

This repository and its code are provided under the LICENSE file. Note that the WSI data accessed through the API has separate licensing terms (see Data Licensing above).