ngio

NGIO - Next Generation file format IO

NGIO is a Python library to streamline OME-Zarr image analysis workflows.

Main Goals:

• Abstract object base API for handling OME-Zarr files
• Powefull iterators for processing data using common access patterns
• Tight integration with Fractal's Table Fractal
• Validate OME-Zarr files

To get started, check out the Getting Started guide. Or checkout our Documentation

🚧 Ngio is Under active Development 🚧

Roadmap

Feature	Status	ETA	Description
Metadata Handling	✅		Read, Write, Validate OME-Zarr Metadata (0.4 supported, 0.5 ready)
OME-Zarr Validation	✅		Validate OME-Zarr files for compliance with the OME-Zarr Specification + Compliance between Metadata and Data
Base Image Handling	✅		Load data from OME-Zarr files, retrieve basic metadata, and write data
ROI Handling	✅		Common ROI models
Label Handling	✅	Mid-September	Based on Image Handling
Table Validation	✅	Mid-September	Validate Table fractal V1 + Compliance between Metadata and Data
Table Handling	✅	Mid-September	Read, Write ROI, Features, and Masked Tables
Basic Iterators	Ongoing	End-September	Read and Write Iterators for common access patterns
Base Documentation	✅	End-September	API Documentation and Examples
Beta Ready Testing	✅	End-September	Beta Testing; Library is ready for testing, but the API is not stable
Streaming from Fractal	Ongoing	December	Ngio can stream ome-zarr from fractal
Mask Iterators	Ongoing	Early 2025	Iterators over Masked Tables
Advanced Iterators	Not started	mid-2025	Iterators for advanced access patterns
Parallel Iterators	Not started	mid-2025	Concurrent Iterators for parallel read and write
Full Documentation	Not started	2025	Complete Documentation
Release 1.0 (Commitment to API)	Not started	2025	API is stable; breaking changes will be avoided