Usage

In this section, we provide detailed usage examples and explanations of the core functions and features of OMIO. Each subsection focuses on a specific aspect of the library, guiding users through common workflows and use cases.

You can use the code examples provided here as a starting point for your own projects. All code snippets are also available in the example script usage_example_interactive.py``located in the ``additional_scripts folder of the OMIO repository. That script is meant to be run interactively, e.g., using VS Code’s interactive window features.

• 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
  • 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 Conversion over a BIDS-like Tree
  • OMIO’s Batch Conversion Function
• Creating Empty Images and Metadata
  • Creating Empty, OME-Compliant Image Arrays and Metadata