https://github.com/insightsoftwareconsortium/itkioomezarrngff
ITK IO for images stored in OME-Zarr format.
https://github.com/insightsoftwareconsortium/itkioomezarrngff
imaging insight-toolkit itk ome-zarr ome-zarr-converter
Last synced: 7 months ago
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ITK IO for images stored in OME-Zarr format.
- Host: GitHub
- URL: https://github.com/insightsoftwareconsortium/itkioomezarrngff
- Owner: InsightSoftwareConsortium
- License: apache-2.0
- Created: 2019-07-08T04:12:29.000Z (over 6 years ago)
- Default Branch: main
- Last Pushed: 2024-10-21T13:32:02.000Z (over 1 year ago)
- Last Synced: 2025-06-30T15:21:20.500Z (7 months ago)
- Topics: imaging, insight-toolkit, itk, ome-zarr, ome-zarr-converter
- Language: C++
- Homepage:
- Size: 151 KB
- Stars: 10
- Watchers: 4
- Forks: 5
- Open Issues: 18
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ITKIOOMEZarrNGFF
[](https://pypi.python.org/pypi/itk-ioomezarrngff)
[](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF/blob/main/LICENSE)
## Overview
This is an [ITK](https://itk.org/) external module for IO of images stored in [Zarr](https://zarr.dev/)-backed
[OME-NGFF](https://ngff.openmicroscopy.org/0.4/) file format.
## Installation
The `itk-ioomezarrngff` Python package is available on the Python Package Index.
```sh
> python -m pip install itk-ioomezarrngff
```
## Example Usage
### C++
Usage from C++ should not require any special action. In special situations, you might need to invoke:
```C++
itk::OMEZarrNGFFImageIOFactory::RegisterOneFactory();
```
### Python
In Python, we need to explicitly specify the IO, otherwise DICOM IO will be invoked because it is the built-in default for directories. Example:
```python
import sys
import itk
imageio = itk.OMEZarrNGFFImageIO.New()
image = itk.imread(sys.argv[1], imageio=imageio)
itk.imwrite(image, sys.argv[2], imageio=imageio, compression=False)
```
## Build Instructions
ITKIOOMEZarrNGFF is an ITK C++ external module. It may be built with `CMake` and build tools such as
Ninja, gcc, or MSVC.
In the future ITKIOOMEZarrNGFF may be made available as an ITK remote module for direct
inclusion in the ITK build process.
### Prerequisites
- [CMake](https://cmake.org/)
- [Perl](https://www.perl.org/)
- [NASM](https://www.nasm.us/)
- An existing C++ build of [ITK](https://itk.org/)
### Building
ITKIOOMEZarrNGFF uses CMake for its build process.
```sh
# Create the build directory
> mkdir path/to/ITKIOOMEZarrNGFF-build
> cd path/to/ITKIOOMEZarrNGFF-build
# Configure the project
path/to/ITKIOOMEZarrNGFF-build > cmake -DITK_DIR:PATH="path/to/ITK-build" "path/to/ITKIOOMEZarrNGFF"
# Build the project
path/to/ITKIOOMEZarrNGFF-build > cmake --build . --config "Release"
```
### Testing
ITKIOOMEZarrNGFF tests may be run with [CTest](https://cmake.org/cmake/help/latest/manual/ctest.1.html):
```sh
path/to/ITKIOOMEZarrNGFF-build > ctest -C "Release"
```
### Wrapping
See the [ITK Software Guide](https://itk.org/ItkSoftwareGuide.pdf) for information on wrapping ITK external modules for Python.
### Additional Notes
ITKIOOMEZarrNGFF depends on a fork of Google's [Tensorstore](https://github.com/google/tensorstore)
library for Zarr interoperation. The [InsightSoftwareConsortium/Tensorstore](https://github.com/InsightSoftwareConsortium/tensorstore)
fork implements additional zip support, both for filesystem and in memory zip reading and writing.
----------------
## Acknowledgements
ITKIOOMEZarrNGFF was developed in part with support from:
- [NIH NIMH BRAIN Initiative](https://braininitiative.nih.gov/) under award 1RF1MH126732.
- The [Allen Institute for Neural Dynamics (AIND)](https://alleninstitute.org/division/neural-dynamics/).