OmicVerse Data I/O

OmicVerse provides its own data readers under ov.io. These replace scanpy's IO functions with better format handling, spatial geometry support, and Rust backend options. When working in an OmicVerse project, always use ov.io.* for data loading — never fall back to sc.read_* or scanpy.read_*.

Why this matters

OmicVerse's readers are not thin wrappers — they are independent implementations that handle edge cases scanpy misses:

• 10x H5/MTX: Proper v2/v3 format detection, flexible prefix/compression options
• Visium: Auto-resolves tissue positions (parquet > csv > legacy csv), loads images + scale factors
• Visium HD: Cell segmentation with GeoJSON→WKT polygon conversion (not available in scanpy at all)
• Nanostring SMI: Auto-detects column names across CosMx format variants (not in scanpy)

Migration table: scanpy → OmicVerse