ngio

Ngio - Next Generation file format IO

ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.

What is Ngio?

Ngio is built for the OME-Zarr file format, a modern, cloud-optimized format for biological imaging data. OME-Zarr stores large, multi-dimensional microscopy images and metadata in an efficient and scalable way.

Ngio's mission is to streamline working with OME-Zarr files by providing a simple, object-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates. It also offers comprehensive support for labels, tables and regions of interest (ROIs), making it easy to extract and analyze specific regions in your data.

Key Features

📊 Simple Object-Based API

• Easily open, explore, and manipulate OME-Zarr images and HCS plates
• Create and derive new images and labels with minimal boilerplate code

🔍 Rich Tables and Regions of Interest (ROI) Support

• Extract and analyze specific regions of interest
• Tight integration with Tabular Data

🔄 Scalable Data Processing (Coming Soon)

• Powerful iterators for processing data at scale
• Efficient memory management for large datasets

Installation

You can install ngio via pip:

pip install ngio

To get started check out the Quickstart Guide.

Supported OME-Zarr versions

Currently, ngio only supports OME-Zarr v0.4. Support for version 0.5 and higher is planned for future releases.

Development Status

!!! warning Ngio is under active development and is not yet stable. The API is subject to change, and bugs and breaking changes are expected. We follow Semantic Versioning. Which means for 0.x releases potentially breaking changes can be introduced in minor releases.

Available Features

• ✅ OME-Zarr metadata handling and validation
• ✅ Image and label access across pyramid levels
• ✅ ROI and table support
• ✅ Streaming from remote sources
• ✅ Documentation and examples

Upcoming Features

• Advanced image processing iterators
• Parallel processing capabilities
• Support for OME-Zarr v0.5 and Zarr v3

Contributors

Ngio is developed at the BioVisionCenter, University of Zurich, by @lorenzocerrone and @jluethi.

License

Ngio is released under the BSD-3-Clause License. See LICENSE for details.