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# ngio | ||
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[![License](https://img.shields.io/pypi/l/ngio.svg?color=green)](https://github.com/lorenzocerrone/ngio/raw/main/LICENSE) | ||
[![PyPI](https://img.shields.io/pypi/v/ngio.svg?color=green)](https://pypi.org/project/ngio) | ||
[![Python Version](https://img.shields.io/pypi/pyversions/ngio.svg?color=green)](https://python.org) | ||
[![CI](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml/badge.svg)](https://github.com/lorenzocerrone/ngio/actions/workflows/ci.yml) | ||
[![codecov](https://codecov.io/gh/lorenzocerrone/ngio/branch/main/graph/badge.svg?token=ELJ6CFL0K4)](https://codecov.io/gh/lorenzocerrone/ngio) | ||
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Next Generation file format IO | ||
# NGIO - Next Generation file format IO | ||
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NGIO is a Python library to streamline OME-Zarr image analysis workflows. | ||
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**Highlights:** | ||
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- Abstract object base API for handling OME-Zarr files | ||
- Validate OME-Zarr files | ||
- Powefull iterators for reading and writing data using common access patterns | ||
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## 🚧 Ngio is Under active Development 🚧 | ||
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### Roadmap | ||
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Here’s the table with grammar corrections: | ||
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| Feature | Status | ETA | Description | | ||
|---------|--------|-----|-------------| | ||
| Metadata Handling | ✅ Done | | Read, Write, Validate OME-Zarr Metadata (0.4 supported, 0.5 ready) | | ||
| OME-Zarr Validation | ✅ Done | | Validate OME-Zarr files for compliance with the OME-Zarr Specification + Compliance between Metadata and Data | | ||
| Base Image Handling | ✅ Done | | Load data from OME-Zarr files, retrieve basic metadata, and write data | | ||
| ROI Handling | ✅ Done | | 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 | | ||
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## Installation | ||
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Currently, the library is not available on PyPI. You can install it from the source code. | ||
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```bash | ||
git clone https://github.com/lorenzocerrone/ngio.git | ||
cd ngio | ||
pip install . | ||
pip install git+https://github.com/zarr-developers/zarr-python.git | ||
``` | ||
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ZarrV3 stable is not yet released, `ngio` is using the latest version of `zarr` from the `v3` branch. | ||
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## Examples | ||
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## NGFFImage | ||
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```python | ||
from ngio import NGFFImage | ||
path = "path/to/ome.zarr" | ||
ngff = NGFFImage(path) | ||
... | ||
``` | ||
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TODO: Add valid examples |