HistAI Skillsets

A skills repository providing clean and secure integration between AI coding agents (Claude Code, OpenAI Codex, Gemini CLI) and the HistAI computational pathology platform — covering the Whole Slide Image Data Hub, the CellDX AI Autopilot model trainer, training job monitoring, and slide-level AI analysis.

Overview

This repository bundles four complementary skills:

• 🔬 Cohort Builder (Data Hub) — search pathology cases by diagnosis, organ, age, stains, and clinical criteria; build research cohorts; export whole slide images (WSI) with comprehensive metadata; manage costs with volume-based pricing and selective slide downloads.
• 🤖 CellDX AI Autopilot (Model Trainer) — submit slide classification training jobs on Azure GPU compute, with a full pipeline (parameter tuning → multi-strategy comparison → best model → deployment) and a quick mode for fast single-model iteration.
• 📈 Training Monitor — monitor running training jobs with real-time epoch-by-epoch metrics, stop/adjust/resume training, compare strategy results, and deploy trained models as widgets.
• 🧪 Slide Analyzer — upload your own WSIs to "My Cases", install AI widgets (public store or custom-trained), run them on slides, and retrieve results including segmentation masks.

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/skillsets
   

2. Install all skills at once:

   /plugin install histai-skillsets
   

   This is the preferred way — the skills are designed to work together (e.g. build a cohort → train a model → monitor training). Installing individually is possible but not recommended.

3. Configure your API key:

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

     export CELLDX_API_KEY="your-api-key"
     

4. Start using:

   • Example: "Search for breast cancer cases with HER2 IHC staining"
   • Example: "Train a classifier on my breast cancer cohort"
   • Example: "How is my training job going?"
   • Example: "Upload this slide and run the melanocytic widget on it"
   • Example: "List my cases and show which widgets are installed"

Manual Installation (Alternative)

If you prefer local installation:

1. Clone this repository:

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

2. Register as a local plugin:

   /plugin add-local
   

   Point to the repository root directory.

OpenAI Codex

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

1. Clone the repository:

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

2. Verify skills are loaded:

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

3. Configure API key:

   export CELLDX_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/skillsets.git --consent
   

   Or install locally:

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

2. Configure API key:

   export CELLDX_API_KEY="your-api-key"
   

3. Start using:

   • The Gemini CLI will automatically load all four skills
   • 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

🤖 CellDX AI Autopilot (Model Trainer)

Submit slide classification training jobs on Azure GPU compute. Supports a full pipeline (parameter tuning → multi-strategy comparison → best model → deployment) and quick mode for fast single-model iteration.

Full documentation: skills/ai_model_trainer/SKILL.md

📈 Training Monitor

Monitor running training jobs with epoch-by-epoch metrics, stop/adjust/resume training, compare strategy results, and deploy trained models as widgets.

Full documentation: skills/training_monitor/SKILL.md

🧪 Slide Analyzer

Upload your own WSIs to "My Cases", install AI widgets (public store or custom-trained), run them on uploaded slides, and retrieve the result — including segmentation masks — via a single poll endpoint. Also covers case/slide browsing and deletion.

Full documentation: skills/slide_analyzer/SKILL.md

Repository Structure

skillsets/
├── .claude-plugin/
│   ├── plugin.json                # Claude Code plugin configuration
│   └── marketplace.json           # Claude Code marketplace configuration
├── agents/
│   └── AGENTS.md                  # OpenAI Codex skill definitions
├── skills/
│   ├── cohort_builder/
│   │   └── SKILL.md               # Cohort building and data export
│   ├── ai_model_trainer/
│   │   └── SKILL.md               # ML training job submission
│   ├── training_monitor/
│   │   └── SKILL.md               # Training monitoring and deployment
│   └── slide_analyzer/
│       └── SKILL.md               # Upload WSIs to My Cases and run AI widgets
├── 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
• Environment variable: CELLDX_API_KEY
• Documentation: See individual skill files for detailed API reference

Support

For issues, custom data requests, or enterprise inquiries:

• 📧 Sales: sales@hist.ai
• 📚 Documentation: See skill files in skills/ directory
• 🌐 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).