OMIO Example Datasets: Dummy Microscopy Files Plus Curated Third-Party Samples for I/O Testing

This Zenodo record provides a compact set of example microscopy datasets for testing and demonstrating OMIO (Open Microscopy Image I/O). The record contains two categories of data:

1. OMIO generated dummy datasets. Small, deterministic toy datasets generated specifically for OMIO tests and tutorials. They cover typical axis layouts (YX, TYX, ZTYX, CZTYX, TZCYX), ImageJ style metadata variants (including sample axis S), OME TIFF metadata examples, and multi series or paginated TIFF edge cases. These files are designed to be small enough for fast CI style tests while still exposing common pitfalls in axis handling, metadata parsing, and series interpretation.
2. Curated third party sample files. A small selection of real world microscopy files from public repositories, included to test OMIO against formats and metadata variants that occur in practice (for example CZI, LSM, and representative multi channel TIFF stacks). Each third party file is stored in its own folder together with a dedicated README that documents the original source, DOI, and license.

Intended use

The datasets are intended for:

• OMIO unit and integration tests
• documentation examples and tutorials
• user validation of OMIO on representative file formats
• regression tests for metadata parsing and axis normalization to canonical OME order (TZCYX)

Not intended for scientific analysis

The OMIO generated datasets contain artificial toy image data only. They are not microscopy measurements and must not be used for scientific interpretation. Third party files are real data, but are included here solely for file format testing and demonstration of OMIO I/O behavior.

Repository structure (high level)

• tif_dummy_data/
  • Dummy TIFF, ImageJ TIFF, OME TIFF, paginated and multi series examples, plus batch and folder structure examples.
• thorlabs_dummy_data/
  • Dummy Thorlabs RAW plus minimal XML metadata cases for read_thorlabs_raw testing.
• third party data
  • One folder per third party example file, each with a README describing provenance, citation, and license:
    • czi_test_file/
    • lsm_test_file/
    • tif_cell_single_tif/
    • tif_files_from_3P_paper/
    • tif_large_Ca_imaging_large/

Licensing and third party material

This Zenodo record is a collection. Individual files and subfolders may be licensed differently.

• OMIO generated dummy datasets and the accompanying generation scripts are released under the license selected for this Zenodo record.
• Third party files are redistributed under their original licenses, which are documented in the corresponding per folder README files and in THIRD_PARTY_NOTICES.md.

Where third party licenses require attribution (for example CC BY 4.0 or CC BY 2.0), the required attribution is provided in the per folder README files.

Third party sources included (summary)

• CZI example file from Zenodo record 10.5281/zenodo.8305531, CC BY 4.0. (unmodified)
• LSM example file originating from Dryad DOI 10.5061/dryad.68864, CC0 1.0 as shown in the Zenodo mirrored record, CC0. (unmodified)
• Calcium imaging TIFF from Zenodo record 10.5281/zenodo.7779164, CC BY 4.0. (unmodified)
• Structural imaging dataset originating from Dryad DOI 10.5061/dryad.tqjq2bw90
• DeepCAD dataset example originates from Zenodo record 10.5281/zenodo.8079113, CC BY 4.0. (unmodified)
• Additional TIFF example(s) from the Cell Image Library are included under the license stated on the corresponding CIL record page (documented in the local README). (unmodified)

How to cite

If you use this record in OMIO related work, cite this Zenodo record DOI. If you use any third party file beyond simple OMIO I/O testing, additionally cite the original source listed in the corresponding per folder README.

Maintainer

Fabrizio Musacchio