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https://github.com/insightsoftwareconsortium/napari-itk-io
File IO with itk for napari.
https://github.com/insightsoftwareconsortium/napari-itk-io
hacktoberfest io itk medical-imaging napari napari-plugin open-source python scientific-computing
Last synced: about 2 months ago
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File IO with itk for napari.
- Host: GitHub
- URL: https://github.com/insightsoftwareconsortium/napari-itk-io
- Owner: InsightSoftwareConsortium
- License: apache-2.0
- Created: 2021-04-28T21:41:45.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-06-21T02:11:34.000Z (8 months ago)
- Last Synced: 2024-10-29T17:34:34.640Z (3 months ago)
- Topics: hacktoberfest, io, itk, medical-imaging, napari, napari-plugin, open-source, python, scientific-computing
- Language: Python
- Homepage:
- Size: 44.9 KB
- Stars: 7
- Watchers: 16
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# napari-itk-io
[](https://github.com/InsightSoftwareConsortium/napari-itk-io/raw/master/LICENSE)
[](https://pypi.org/project/napari-itk-io)
[](https://python.org)
[](https://github.com/InsightSoftwareConsortium/napari-itk-io/actions)
[](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/