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Matt McCormick

# napari-itk-io

[![License](https://img.shields.io/pypi/l/napari-itk-io.svg?color=green)](https://github.com/InsightSoftwareConsortium/napari-itk-io/raw/master/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-itk-io.svg?color=green)](https://pypi.org/project/napari-itk-io)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-itk-io.svg?color=green)](https://python.org)
[![tests](https://github.com/InsightSoftwareConsortium/napari-itk-io/workflows/tests/badge.svg)](https://github.com/InsightSoftwareConsortium/napari-itk-io/actions)
[![codecov](https://codecov.io/gh/InsightSoftwareConsortium/napari-itk-io/branch/master/graph/badge.svg)](https://codecov.io/gh/InsightSoftwareConsortium/napari-itk-io)

File IO with [itk](https://itk.org) for [napari](https://napari.org).

Image metadata, e.g. the pixel spacing, origin, and metadata tags, are preserved and passed into napari.

Supported image file formats:

- [BioRad](http://www.bio-rad.com/)
- [BMP](https://en.wikipedia.org/wiki/BMP_file_format)
- [DICOM](http://dicom.nema.org/)
- [DICOM Series](http://dicom.nema.org/)
- [ITK HDF5](https://support.hdfgroup.org/HDF5/)
- [JPEG](https://en.wikipedia.org/wiki/JPEG_File_Interchange_Format)
- [GE4,GE5,GEAdw](http://www3.gehealthcare.com)
- [Gipl (Guys Image Processing Lab)](https://www.ncbi.nlm.nih.gov/pubmed/12956259)
- [LSM](http://www.openwetware.org/wiki/Dissecting_LSM_files)
- [MetaImage](https://itk.org/Wiki/ITK/MetaIO/Documentation)
- [MINC 2.0](https://en.wikibooks.org/wiki/MINC/SoftwareDevelopment/MINC2.0_File_Format_Reference)
- [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat)
- [MRC](http://www.ccpem.ac.uk/mrc_format/mrc_format.php)
- [NifTi](https://nifti.nimh.nih.gov/nifti-1)
- [NRRD](http://teem.sourceforge.net/nrrd/format.html)
- [Portable Network Graphics (PNG)](https://en.wikipedia.org/wiki/Portable_Network_Graphics)
- [Tagged Image File Format (TIFF)](https://en.wikipedia.org/wiki/TIFF)
- [VTK legacy file format for images](http://www.vtk.org/VTK/img/file-formats.pdf)

For DICOM Series, select the folder containing the series with *File -> Open
Folder...*. The first series will be selected and sorted spatially.

## Installation

You can install `napari-itk-io` via [pip]:

    pip install napari-itk-io

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

Follow the [itk contributing
guidelines](https://github.com/InsightSoftwareConsortium/ITK/blob/master/CONTRIBUTING.md)
and the [itk code of
conduct](https://github.com/InsightSoftwareConsortium/ITK/blob/master/CODE_OF_CONDUCT.md).

## License

Distributed under the terms of the [Apache Software License 2.0] license,
"napari-itk-io" is free and open source software.

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/InsightSoftwareConsortium/napari-itk-io/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/


napari-itk-io





File IO with itk for napari.
Image metadata, e.g. the pixel spacing, origin, and metadata tags, are preserved and passed into napari.
Supported image file formats:

BioRad
BMP
DICOM
DICOM Series
ITK HDF5
JPEG
GE4,GE5,GEAdw
Gipl (Guys Image Processing Lab)
LSM
MetaImage
MINC 2.0
MGH
MRC
NifTi
NRRD
Portable Network Graphics (PNG)
Tagged Image File Format (TIFF)
VTK legacy file format for images

For DICOM Series, select the folder containing the series with File -> Open
Folder.... The first series will be selected and sorted spatially.
Installation
You can install napari-itk-io via pip:
pip install napari-itk-io

Contributing
Contributions are very welcome. Tests can be run with tox, please ensure
the coverage at least stays the same before you submit a pull request.
Follow the itk contributing
guidelines
and the itk code of
conduct.
License
Distributed under the terms of the Apache Software License 2.0 license,
"napari-itk-io" is free and open source software.
Issues
If you encounter any problems, please file an issue along with a detailed description.

napari-itk-io

napari-itk-io

File IO with itk for napari

Installation¶

Contributing¶

License¶

Issues¶