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 theImage
,Label
, andTables
objects. Moreover it can be used to derive a newNgff
images based on the current one.Image
andLabel
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 theImage
andLabel
objects.
Example Usage
Currently, the library is not yet stable. However, you can see some example usage in our demo notebooks.