Welcome! Whether you are analyzing classic 2D slides or exploring full 3D volumes, you are in the right place.
Start here for a smooth, reliable 2D pipeline:
- Set up your input data: Preparing Your Data
- Run end-to-end matching: Workflow
- Review quality: Quality Control
Need segmentation help? Jump to Segmentation or Troubleshooting.
Great choice — the 3D path is designed to feel just as approachable as 2D, with a familiar workflow and clear checkpoints.
- Prepare volumes and metadata: 3D Data Preparation
- Run the full 3D pipeline: 3D Workflow
- Review quality: Quality Control
⚠️ Experimental note: Thenucleisky3dmodule is experimental. Please manually verify results before downstream analysis.
Everything you need to integrate, extend, and reason about both 2D and 3D behavior:
- Core APIs
- Matching internals
- Limits and failure modes
- Fastest way to try 2D: Workflow
- Fastest way to try 3D: 3D Workflow
- Prefer a GUI for 2D workflows: NucleiSkyApp