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Contents

  • Overview
    • Motivation and problem statement
    • Design principles
      • Explicit axis semantics
      • OME aware, but not OME exclusive
      • Policy driven behavior
      • Memory aware by construction
      • Separation of concerns
    • Core functionality
      • Unified image reading
      • Metadata normalization and enforcement
      • Controlled merging along semantic axes
      • Folder based and BIDS like workflows
      • OME TIFF export
      • Napari integration
      • Creating metadata and image templates
    • Typical usage patterns
    • Scope and non-goals
    • License
    • Citation
  • Installation
    • Recommended installation method
    • For developers
    • Upgrading OMIO
  • Usage
    • Example data sets
      • Licensing and attribution
    • Core workflow: Read, inspect, view, write
      • Hello world
      • Single file reading and metadata inspection
      • Opening images in Napari and metadata modification
      • Ensured OME compliance upon reading
      • Ensured OME compliance upon writing
      • The imconvert convenience function
    • Supported file formats
      • Reading LSM files
      • Reading CZI files
      • Reading Thorlabs RAW files
    • TIFF container policies and special layouts
      • Reading multi-series TIFF stacks
      • Reading paginated TIFF stacks
      • Reading multi-file OME-TIFF stacks
    • Large file handling and out of core workflows
      • Read large files lazily with Zarr backend
      • Reuse an existing on-disk OMIO cache
      • Cleanup of temporary Zarr stores
      • Write Zarr-backed arrays as OME-TIFF without loading the full store
      • Efficiently view large images in Napari with OMIO’s DASK support
    • Folder reading and semantic merging
      • Imread’s folder reading and merging capability
      • Folder stacks reading and merging
    • Batch processing over a BIDS-like tree
      • OMIO’s flexible batch processing function
      • Discovery rules
      • File-type and exclude filtering
      • Basic batch processing
      • Folder-stack tags
      • Skip and error behavior
      • Persistent run and error reports
      • Creating Thorlabs RAW YAML sidecars from reports
      • Flexible batch processing with custom callables
    • Creating empty images and metadata
      • Creating empty, OME-compliant image arrays and metadata
      • Creating empty images as on-disk Zarr arrays
  • API reference
    • High level I/O
      • imread()
      • imwrite()
      • imconvert()
      • bids_batch_process()
      • discover_bids_like_batch_images()
      • batch_create_thorlabs_raw_yaml_templates()
    • Checks and utilities
      • hello_world()
      • OME_metadata_checkup()
      • cleanup_omio_cache()
      • open_in_napari()
    • Readers
      • read_tif()
      • read_czi()
      • read_thorlabs_raw()
    • Metadata and image helpers
      • create_empty_metadata()
      • create_empty_image()
      • update_metadata_from_image()
  • What’s new?
    • OMIO Changelog
      • 🚀 OMIO v0.3.0
        • 📃 Changes
          • ✨ Added
          • 🧩 Changed
          • 📚 Documentation
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.9
        • 📃 Changes
          • 🧩 Changed
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.8
        • 📃 Changes
          • 🧩 Changed
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.7
        • 📃 Changes
          • 🧩 Changed
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.6
        • 📃 Changes
          • 🧩 Changed
          • 📚 Documentation
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.5
        • 📃 Changes
          • ✨ Added
          • 🧩 Changed
          • 📚 Documentation
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.4
        • 📃 Changes
          • 🧩 Changed
          • 📚 Documentation
          • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.3
        • 📃 Changes
          • ✨ Added
          • 🧩 Changed
        • 📚 Documentation
        • 🧪 Testing and robustness
      • 🚀 OMIO v0.2.2
        • 📃 Changes
          • ✨ Added
          • 🧩 Changed
          • 🧪 Testing and robustness
          • 📚 Documentation and citation
      • 🚀 OMIO v0.2.1
        • 📃 Changes
          • 🧩 Fixed
          • 🧪 Testing and robustness
          • 🎨 Project identity
      • 🚀 OMIO v0.2.0
        • 📃 Changes
          • ✨ Highlights
          • ⚠️ Breaking changes
          • 🧬 TIFF and LSM reading improvements
          • 📁 Folder reading and OME-TIFF series detection
          • 🆕 New utility function
          • 👁️ Napari visualization updates
          • 🛠️ Utilities and tests
          • 📚 Documentation
          • 🧪 Example dataset
          • 📝 Notes for maintainers
      • 🚀 OMIO v0.1.4
        • 📃 Changes
          • 📚 Citation and Archiving
          • 📖 Documentation Updates
          • 🔎 Notes
      • 🚀 OMIO v0.1.3
      • 🚀 OMIO v0.1.2
        • 📃 Changes
          • 🧩 Fixed
          • 🧪 Quality
      • 🚀 OMIO v0.1.1
        • 📃 Changes
          • ✨ Highlights
          • 🧠 Core Functionality
          • 🔬 Thorlabs RAW Support
          • 📦 Zarr Integration
          • 👁️ Napari Integration
          • 🔗 Merging and Utilities
          • 🧪 Testing and Robustness
          • 📦 Packaging
          • 🔭 Scope and Outlook
  • Contributing and community guidelines
    • How to contribute
    • Contribution guidelines
    • Requests for new file formats and reader extensions
    • Code of conduct
    • Where to start
OMIO
  • Overview: module code

All modules for which code is available

  • omio.batch
  • omio.cache
  • omio.convert
  • omio.core
  • omio.read
  • omio.readers.czi
  • omio.readers.thorlabs_raw
  • omio.readers.tif
  • omio.templates
  • omio.viewer
  • omio.writers.ome_tiff

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