Introduction¶

The Aignostics Platform runs computational pathology applications — such as Atlas H&E-TME, which analyzes the tumor microenvironment in H&E-stained tissue — on your whole slide images. The Aignostics Python SDK is how you work with it, through the interfaces below.

Choose your interface¶

Choose your preferred interface for working with the Aignostics Platform. Each interface is designed for different user roles and use cases:

🖥️ Launchpad (Desktop Application)¶


What it is	Graphical application for analyzing slides and viewing results in QuPath or Python notebooks
Best for	Pathologists and researchers who want to analyze slides without writing code
Use when	Running analyses on individual cases or small cohorts (1-20 slides) and exploring results interactively
Get started	Get started with Launchpad

⌨️ CLI (Command-Line Interface)¶


What it is	Terminal tool for scripting and automation
Best for	Bioinformaticians and technical researchers who work with terminal-based workflows
Use when	Processing large cohorts (10s-100s of slides), automating repetitive analyses, or integrating with computational pipelines
Get started	Get started with the CLI

📚 Python Library¶


What it is	Python library for programmatic access in scripts, notebooks, and applications
Best for	Data scientists and developers who want to integrate the platform into Python-based workflows
Use when	Building custom analysis pipeline in Python for repeated usage and processing large datasets (10s-1000s of slides)
Get started	Get started with the Python Library

🤖 MCP Server (AI Agent Integration)¶


What it is	Model Context Protocol server that exposes SDK functionality to AI agents like Claude
Best for	Users who want AI assistants to help with platform operations
Use when	Working with Claude Desktop or other MCP-compatible AI tools to manage datasets, submit runs, or query results
Get started	Get started with the MCP Server

💡 Each interface has its own step-by-step guide (linked above) that includes installation. Launchpad and the CLI handle authentication for you; the Python Library guide covers credential setup.

Next Steps¶

The best next step is to run your first analysis end to end.

New here? Start with the Get started with Launchpad guide — it walks you through signing up, installing, and running Atlas H&E-TME on a public example slide, then viewing the results in QuPath, with no coding required. Prefer the terminal or Python? Use the Get started with the CLI or Get started with the Python Library guide instead.

Once you’ve run your first analysis:

Understand the platform: Read the Aignostics Platform Overview for architecture and core concepts.
Go deeper: See the CLI reference and Python Library reference.
Get support: Contact support@aignostics.com or browse the full documentation.

We take quality and security seriously¶

We know you take quality and security as seriously as we do. That’s why the Aignostics Python SDK is built following best practices and with full transparency. This includes (1) making the complete source code of the SDK available on GitHub, maintaining a (2) A-grade code quality with high test coverage in all releases, (3) achieving A-grade security with active scanning of dependencies, and (4) providing extensive documentation. Read more about how we achieve operational excellence and security.