NGIO is a Python library to streamline OME-Zarr image analysis workflows.
Highlights:
- Abstract object base API for handling OME-Zarr files
- Validate OME-Zarr files
- Powefull iterators for reading and writing data using common access patterns
| Feature | Status | ETA | Description |
|---|---|---|---|
| Metadata Handling | ✅ Done | Read, Write, Validate OME-Zarr Metadata (0.4 supported, 0.5 ready) | |
| OME-Zarr Validation | ✅ Doneish | Validate OME-Zarr files for compliance with the OME-Zarr Specification + Compliance between Metadata and Data | |
| Base Image Handling | ✅ Doneish | Load data from OME-Zarr files, retrieve basic metadata, and write data | |
| ROI Handling | ✅ Doneish | Common ROI models | |
| Label Handling | Ongoing | Mid-September | Based on Image Handling |
| Table Validation | Ongoing | Mid-September | Validate Table fractal V1 + Compliance between Metadata and Data |
| Table Handling | Ongoing | Mid-September | Read, Write ROI, Features, and Masked Tables |
| Basic Iterators | Not started | End-September | Read and Write Iterators for common access patterns |
| Base Documentation | Not started | End-September | API Documentation and Examples |
| Beta Ready Testing | Not started | End-September | Beta Testing; Library is ready for testing, but the API is not stable |
| Mask Iterators | Not started | 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 |
Currently, the library is not available on PyPI. You can install it from the source code.
git clone https://github.com/lorenzocerrone/ngio.git
cd ngio
pip install .
pip install git+https://github.com/zarr-developers/zarr-python.gitZarrV3 stable is not yet released, ngio is using the latest version of zarr from the v3 branch.
from ngio import NGFFImage
path = "path/to/ome.zarr"
ngff = NGFFImage(path)
...TODO: Add valid examples