Data formats & features

• Mosaic Grid Format (OME-Zarr)
  • Overview
  • File Structure
  • Array Dimensions
  • Metadata
  • Reading OME-Zarr Files
  • Writing OME-Zarr Files
  • Chunking and Sharding
  • Data Types
  • Naming Convention
  • Viewing OME-Zarr Files
  • Compression
  • Troubleshooting
  • Related Tools
• XY Shifts File Format
  • Overview
  • File Format
  • Shift Direction
  • Generation
  • Usage in Reconstruction
  • Handling Missing or Skipped Slices
  • Validation
  • Correcting Erroneous Shifts
  • Troubleshooting
  • Related Files
  • Example
• Slice Configuration Feature
  • Overview
  • Problem Statement
  • Solution
  • Quality Assessment
  • Galvo Shift Detection Algorithm
  • Implementation
  • Cumulative Shift Handling
  • Usage Workflow
  • Backward Compatibility
  • Validation
  • Python API: linumpy.io.slice_config
  • Pipeline flow: slice_config.csv as a flowing artifact
  • Concurrency
  • Files Changed
  • Testing
  • Troubleshooting Galvo Detection
• Slice Interpolation Feature
  • Overview
  • Background
  • Methods
  • Pipeline integration and per-slice trace
  • Per-slice diagnostics JSON
  • Configuration
  • Outputs
  • Validation and quality checks
  • Limitations
  • References
  • Files
• GPU Acceleration
  • Overview
  • Quick Start
  • Installation
  • BaSiCPy (fix_illumination)
  • GPU-Accelerated Scripts
  • GPU-Accelerated Operations
  • Multi-GPU Systems
  • Memory Management
  • Troubleshooting
  • Reference Benchmarks
  • Module Reference
• N4 Bias-Field Correction — GPU Backend
  • 1. Reference
  • 2. Mathematical model
  • 3. Implementation
  • 4. Equivalency tests
  • 5. Performance
  • 6. Reproducing the numbers
  • 7. Pipeline integration