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Getting Started

Warning

The library is still in development and is not yet stable. The API is subject to change, bugs and breaking changes are expected.

Warning

The documentation is still under development. It is not yet complete and may contain errors and inaccuracies.

Installation

Currently, ngio is not available on PyPI. You can install it from the source code.

pip install "ngio[v2]"

The v2 extra installs the latest version of zarr-python from the v2 branch. ngio is currently not completely compatible with the v3 release of zarr-python.

ngio API Overview

ngio implements an abstract object base API for handling OME-Zarr files. The three main objects are NgffImage, Image (Label), and ROITables.

  • NgffImage is the main entry point to the library. It is used to open an OME-Zarr Image and manage its metadata. This object can not be used to access the data directly. but it can be used to access and create the Image, Label, and Tables objects. Moreover it can be used to derive a new Ngff images based on the current one.
  • Image and Label are used to access "ImageLike" objects. They are the main objects to access the data in the OME-Zarr file, manage the metadata, and write data.
  • ROITables can be used to access specific region of interest in the image. They are tightly integrated with the Image and Label objects.

Example Usage

Currently, the library is not yet stable. However, you can see some example usage in our demo notebooks.