{"name":"napari-noise2vst","display_name":"Noise2VST","visibility":"public","icon":"","categories":[],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-noise2vst.make_noise2vst_widget","title":"Noise2VST Denoising Widget","python_name":"napari_noise2vst:Noise2VSTWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-noise2vst.make_noise2vst_widget","display_name":"Denoising","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-noise2vst","version":"0.1.1","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A plugin for denoising microscopy images using Noise2VST","description":"# napari-noise2vst\n\n[![License MIT](https://img.shields.io/pypi/l/napari-noise2vst.svg?color=green)](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-noise2vst.svg?color=green)](https://pypi.org/project/napari-noise2vst)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-noise2vst.svg?color=green)](https://python.org)\n[![tests](https://github.com/IbrahimaAlain/napari-noise2vst/workflows/tests/badge.svg)](https://github.com/IbrahimaAlain/napari-noise2vst/actions)\n[![codecov](https://codecov.io/gh/IbrahimaAlain/napari-noise2vst/branch/main/graph/badge.svg)](https://codecov.io/gh/IbrahimaAlain/napari-noise2vst)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-noise2vst)](https://napari-hub.org/plugins/napari-noise2vst)\n[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)\n[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)\n\n> A plugin for denoising microscopy images using Noise2VST  \n> Developed by **Ibrahima Alain GUEYE**\n\n----------------------------------\n\nThis [napari] plugin was generated with [copier] using the [napari-plugin-template].\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/napari-plugin-template#gett\nDependenciesing-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\n\n## Dependencies\n\nThis plugin relies on the Noise2VST framework [S. Herbreteau and M. Unser, ICCV'25].\nThe source code is available at:\nhttps://github.com/sherbret/Noise2VST\n- ✅ No manual installation is required — this version is installed automatically when you install the plugin.\n\n## Installation\n\nTo install in an environment using conda:\n\n```\nconda create --name napari-env\nconda activate napari-env\nconda install pip\n```\n\nYou can install `napari-noise2vst` via [pip]:\n\n```\npip install napari-noise2vst\n```\n\nIf napari is not already installed, you can install `napari-noise2vst` with napari and Qt via:\n\n```\npip install \"napari-noise2vst[all]\"\n```\n\nIf you prefer installing napari separately:\n\n```\npip install \"napari[all]\"\n```\n\nTo install latest development version:\n\n```\npip install git+https://github.com/IbrahimaAlain/napari-noise2vst.git\n```\n\n## Usage\n\nAfter installation, you can launch the **Noise2VST Denoising** plugin directly from the napari interface.\nIn the napari top menu, go to:\n\n**`Plugins > Noise2VST Denoising (Denoising Noise2VST)`**\n\n![image_0.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_0.png)\n\nOpen your image by clicking:\n**`File → Open File(s)...`**\nSelect the noisy image (e.g., .tif, .png, etc.) that you want to denoise. The image will appear in the napari viewer.\n\n![image_1.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_1.png)\n\nOnce the image is loaded, scroll to the plugin panel on the right.\nSet the number of training iterations using the slider (e.g., 2000).\nThen click the Fit button to train the denoising model on the image.\n\nThe region shown here highlights the relevant settings and the training button.\n\n![image_2.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_2.png)\n![image_3.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_3.png)\n\nA progress bar appears, indicating the training status in real time.\nYou can follow the advancement of model fitting visually.\n\n![image_4.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_4.png)\n\nOnce training is complete, the plugin automatically stores the model weights.\nClick the Run Denoising button to generate the denoised version of the input image.\n\n![image_5.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_5.png)\n\nThe denoised image appears as a new layer in the napari viewer, alongside the original one.\nYou can toggle visibility, adjust contrast, and compare both layers interactively.\n\n![image_6.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_6.png)\n\nClick the Visualize VST button to display the spline transformation (VST) learned during training.\nA matplotlib window pops up with a plot showing the input-output relationship.\n\n![image_7.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_7.png)\n\nTo save the spline transformation values, click the Save Spline Knots button.\nA dialog window opens to let you choose where to store the CSV file containing the knots.\n\n![image_8.png](https://github.com/IbrahimaAlain/napari-noise2vst/raw/main/docs/images/image_8.png)\n\n\n## Citation\n\n```BibTex\n@article{herbreteau2024noise2vst,\n  title={Self-Calibrated Variance-Stabilizing Transformations for Real-World Image Denoising},\n  author={Herbreteau, S{\\'e}bastien and Unser, Michael},\n  journal={arXiv preprint arXiv:2407.17399},\n  year={2024}\n}\n```\n\n## Issues\n\nIf you encounter any problems, please [file an issue] along with a detailed description.\n\n[napari]: https://github.com/napari/napari\n[copier]: https://copier.readthedocs.io/en/stable/\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[napari-plugin-template]: https://github.com/napari/napari-plugin-template\n\n[file an issue]: https://github.com/IbrahimaAlain/napari-noise2vst/issues\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":null,"author_email":"Ibrahima Alain Gueye <gueyeibrahimaalain@gmail.com>","maintainer":null,"maintainer_email":null,"license":"The MIT License (MIT)\n\nCopyright (c) 2025 Ibrahima Alain Gueye\n\nPermission is hereby granted, free of charge, to any person obtaining a copy\nof this software and associated documentation files (the \"Software\"), to deal\nin the Software without restriction, including without limitation the rights\nto use, copy, modify, merge, publish, distribute, sublicense, and/or sell\ncopies of the Software, and to permit persons to whom the Software is\nfurnished to do so, subject to the following conditions:\n\nThe above copyright notice and this permission notice shall be included in\nall copies or substantial portions of the Software.\n\nTHE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\nIMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\nFITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE\nAUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\nLIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,\nOUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN\nTHE SOFTWARE.\n","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: MIT License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Programming Language :: Python :: 3.12","Programming Language :: Python :: 3.13","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","matplotlib","torch","magicgui","qtpy","scikit-image","napari","torchvision","Noise2VST","napari[all]; extra == \"all\"","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari[qt]; extra == \"testing\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/IbrahimaAlain/napari-noise2vst/issues","Documentation, https://github.com/IbrahimaAlain/napari-noise2vst","Source Code, https://github.com/IbrahimaAlain/napari-noise2vst","User Support, https://github.com/IbrahimaAlain/napari-noise2vst/issues"],"provides_extra":["all","testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}