Mission and Values

This document is meant to help guide decisions about the future of AICSImageIO, be it in terms of whether to accept new functionality, changes to existing functionality, changes to package administrative tasks, etc. It serves as a reference for core developers in guiding their work, and, as an introduction for newcomers who want to learn where the project is headed and what the team’s values are. You can also learn how the project is managed by looking at our governance model.

Mission

AICSImageIO aims to provide a consistent intuitive API for reading in or out-of-memory image pixel data and metadata for the many existing proprietary microscopy file formats, and, an easy-to-use API for converting from proprietary file formats to an open, common, standard – all using either language agnostic or pure Python tooling.

In short:

AICSImageIO provides a method to fully read and convert from an existing proprietary microscopy file format to, or emulate, a Python representation of the community standard metadata model regardless of image size, format, or location.

(The current community standard for microscopy images is the Open Microscopy Environment)

We hope to accomplish this by:

  • being easy to use and install. We will take extra care to ensure that this library is easy to use and fully installable on Windows, Mac-OS, and Ubuntu.

  • being well-documented with our entire API having up-to-date, useful docstrings and additionally providing examples of more complex use-cases when possible.

  • providing a consistent and stable API to users by following semantic versioning and limiting the amount of breaking changes introduced unless necessary for the future robustness or scalability of the library.

  • sustaining comparable or better performance when compared to more tailored file format reading libraries. We will regularly run benchmarks utilizing a set of varied size images from all the file formats the library is capable of reading.

  • working closely with the microscopy community while deciding on standards and best practices for open, accessible, file formats and imaging and in deciding which proprietary file formats and metadata selection are in need of support.

Values

  • We are inclusive. We welcome and mentor newcomers who are making their first contribution and strive to grow our most dedicated contributors into core developers. We have a Code of Conduct to ensure that the AICSImageIO remains a welcoming place for all.

  • We are community-driven. We respond to feature requests and proposals on our issue tracker and make decisions that are driven by our user’s requirements.

  • We focus on file IO and metadata conversion, leaving image analysis functionality and visualization to other libraries.

  • We aim to develop new methods of metadata extraction and conversion, instead of duplicating existing, or porting, from other libraries primarily by creating language agnostic methods for metadata manipulation.

  • We value simple, readable implementations. Readable code that is easy to understand, for newcomers and maintainers alike, makes it easier to contribute new code as well as prevent bugs.

  • We value education and documentation. All functions should have docstrings, preferably with examples, and major functionality should be explained in our tutorials. Core developers can take an active role in finishing documentation examples.

  • We minimize `magic <https://en.wikipedia.org/wiki/Magic_(programming>`_) and always provide a way for users to opt out of magical behaviour and guessing by providing explicit ways to control functionality.

Acknowledgments

We share a lot of our mission and values with the napari project, and acknowledge the influence of their mission and values statement on this document.

Additionally, much of the work produced for this library is built on the shoulders of giants. Notably:

  • Christoph Gohlke – maintainer of tifffile, czifile, and the imagecodecs libraries

  • Paul Watkins – original creator of pylibczi

  • OME and Bio-Formats Team – proprietary microscopy file format conversion and standards development

  • Python-Bio-Formats Team – Python Java Bridge for Bio-Formats and original implementations of OME Python representation

  • imageio Team – robust, expansive, cross platform image reading

  • Dask Team – delayed and out-of-memory parallel array manipulation

  • xarray Team – coordinate and metadata attached array handling and manipulation