Version Compatibility

Reference examples tested with: Cellpose 3.0+, anndata 0.10+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scanpy 1.10+, steinbock 0.16+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Cell Segmentation for IMC

"Segment cells from my IMC images" → Identify individual cell boundaries in multiplexed imaging data using deep learning (Cellpose) or watershed-based approaches for single-cell extraction.

• Python: cellpose.models.Cellpose() for deep learning segmentation
• CLI: steinbock segment for pipeline-based segmentation

Cellpose Segmentation