https://github.com/hereariim/napari-pixel-correction
This directory contains the files that make up the napari-pixel-correction module. This module is used to annotate the segmentation masks.
https://github.com/hereariim/napari-pixel-correction
napari-plugin python tensorflow
Last synced: about 2 months ago
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This directory contains the files that make up the napari-pixel-correction module. This module is used to annotate the segmentation masks.
- Host: GitHub
- URL: https://github.com/hereariim/napari-pixel-correction
- Owner: hereariim
- License: bsd-3-clause
- Created: 2022-09-05T13:46:12.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2023-10-22T16:55:20.000Z (over 2 years ago)
- Last Synced: 2025-09-28T17:44:11.063Z (9 months ago)
- Topics: napari-plugin, python, tensorflow
- Language: Python
- Homepage:
- Size: 5.11 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# napari-pixel-correction
[](https://github.com/hereariim/napari-pixel-correction/raw/main/LICENSE)
[](https://pypi.org/project/napari-pixel-correction)
[](https://python.org)
[](https://github.com/hereariim/napari-pixel-correction/actions)
[](https://codecov.io/gh/hereariim/napari-pixel-correction)
[](https://napari-hub.org/plugins/napari-pixel-correction)
Plugin to correct manually pixel wrongly predicted on image by annotation
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
This plugin allows you to manually correct the images of the apple tree flowers by annotation. Below, a piece of an image shows the predicted pixels (in brown). A pixel in brown is assigned to the flower class. We can see that the brown colour does not necessarily cover a flower in this image.
## Installation
You can install `napari-pixel-correction` via [pip]:
pip install napari-pixel-correction
To install latest development version :
pip install git+https://github.com/hereariim/napari-pixel-correction.git
## How does it work
First, you need a compressed file (in .zip format) were you have all your images. For a compressed file named as `input.zip`, the compressed file should be built like :
```
.
└── input.zip
└── repository
├── image
│ ├── im_1.JPG
│ ├── im_2.JPG
│ ├── im_3.JPG
│ ...
│ └── im_n.JPG
│
└── mask
├── im_1_mask.JPG
├── im_2_mask.JPG
├── im_3_mask.JPG
...
└── im_n_mask.JPG
```
In repository, each image folder should have two elements : image in RGB and the segmented mask in binary image (where no-flower class is 0 and flower class is 255)
## 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.
## License
Distributed under the terms of the [BSD-3] license,
"napari-pixel-correction" 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/hereariim/napari-pixel-correction/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/