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docs: improve README.md for clarity and add tutorials section
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README.md

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@@ -155,8 +155,7 @@ Axis squeezing and cache generation are performed explicitly and transparently.
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OMIO provides utility functions to create empty metadata and image templates that can be populated programmatically or used as blueprints for new datasets.
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## Expected project structure (BIDS-like)
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OMIO supports batch processing of projects organized in a BIDS-like manner.
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An abstract example is shown below:
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OMIO supports batch processing of projects organized in a BIDS-like manner. An abstract example is shown below:
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```bash
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project_name/
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```
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### Batch processing over a BIDS-like project
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`bids_batch_process()` supports
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explicit subject IDs or subject-prefix discovery, arbitrary folder-token levels,
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file-pattern filtering, name-based exclusion, skip-if-already-converted behavior, and
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persistent run/error reports in the project root.
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Use `output_folder_name` for relative or absolute output locations; `save_options`
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is reserved for writer settings such as `overwrite` or `compression_level`.
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OME-TIFF multi-file series are collapsed during discovery by default, and optional
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`folder_stacks` tags can be used to merge tagged stack folders before processing.
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`bids_batch_process()` supports explicit subject IDs or subject-prefix discovery, arbitrary folder-token levels, file-pattern filtering, name-based exclusion, skip-if-already-converted behavior, and persistent run/error reports in the project root. Use `output_folder_name` for relative or absolute output locations; `save_options` is reserved for writer settings such as `overwrite` or `compression_level`. OME-TIFF multi-file series are collapsed during discovery by default, and optional `folder_stacks` tags can be used to merge tagged stack folders before processing.
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```python
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result = omio.bids_batch_process(
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* `tifffile`, `czifile`, `numpy`, `zarr`, `dask`, `napari`, `tqdm`, `pyyaml`, `imagecodecs`, `numcodecs`
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## Tutorials and documentation
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A comprehensive documentation website is available at: <https://omio.readthedocs.io>
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The repository folder `additional_scripts` contains example scripts and Jupyter notebooks that demonstrate typical usage patterns, including:
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* `usage_example_interactive.py`
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* `usage_example_interactive.ipynb`
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Both scripts demonstrate interactive usage of OMIO in a Python script, including reading, merging, writing, and visualization in napari. Also included: Zarr-backed caching, BIDS-like batch processing, and Thorlabs RAW YAML sidecar generation, empty metadata and image templates, and OME-compliance checks upon writing.
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## Requests for new file formats and reader extensions
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OMIO is designed to grow and evolve based on user needs and real-world microscopy data. By intention, we will add support for additional file formats or format variants over time, bases on user requests and contributions.
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