Getting Started#

Install#

Install iohub from PyPI:

pip install iohub

Command-line interface#

To check if iohub works for a dataset:

iohub info /path/to/data/

The CLI can show a summary of the dataset, point to relevant Python calls, and convert other data formats to the latest OME-Zarr. See the full CLI help message by typing iohub or iohub [command] --help in the terminal.

Why iohub?#

This project is inspired by the existing Python libraries for bioimaging data I/O, including ome-zarr-py, tifffile and aicsimageio. They support some of the most widely adopted and/or promising formats in microscopy, such as OME-Zarr and OME-Tiff.

iohub bridges the gaps among them with the following features:

  • Efficient reading of data in various TIFF-based formats produced by the Micro-Manager/Pycro-Manager acquisition stack.

  • Efficient and customizable conversion of data and metadata from Tiff to OME-Zarr.

  • Pythonic and atomic access of OME-Zarr data with parallelized analysis in mind.

  • OME-Zarr metadata is automatically constructed and updated for writing, and verified against the specification when reading.

  • Adherence to the latest OME-NGFF specification (v0.4) whenever possible.

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