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Welcome to NGIO

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.

🚧 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
Mask Iterators Ongoing October Iterators over Masked Tables
Advanced Iterators Not started October Iterators for advanced access patterns
Parallel Iterators Not started End of the Year Concurrent Iterators for parallel read and write
Full Documentation Not started End of the Year Complete Documentation
Release 1.0 (Commitment to API) Not started End of the Year API is stable; breaking changes will be avoided

Contributors

ngio is developed at the BioVisionCenter at the University of Zurich. The main contributors are: @lorenzocerrone, @jluethi.

License

ngio is released according to the BSD-3-Clause License. See LICENSE