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 |
| 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 |
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