{"name":"napari-superres","display_name":"superres","visibility":"public","icon":"","categories":[],"schema_version":"0.2.0","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-superres.get_reader","title":"Open data with superres","python_name":"napari_superres._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.write_multiple","title":"Save multi-layer data with superres","python_name":"napari_superres._writer:write_multiple","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.write_single_image","title":"Save image data with superres","python_name":"napari_superres._writer:write_single_image","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.make_mssr_caller","title":"Make MSSR plugin GUI","python_name":"napari_superres._gui_creator:mssr_caller","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.make_esi_caller","title":"Make ESI plugin GUI","python_name":"napari_superres._gui_creator:esi_caller","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.make_sofi_caller","title":"Make SOFI plugin GUI","python_name":"napari_superres._gui_creator:sofi_caller","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.make_srrf_caller","title":"Make SRRF plugin GUI","python_name":"napari_superres._gui_creator:srrf_caller","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.make_musical_caller","title":"Make MUSICAL plugin GUI","python_name":"napari_superres._gui_creator:musical_caller","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-superres.make_SplitChannel","title":"Make Split Channel plugin","python_name":"napari_superres._gui_creator:SplitChannelsWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-superres.get_reader","filename_patterns":["*.npy"],"accepts_directories":false}],"writers":[{"command":"napari-superres.write_multiple","layer_types":["image*","labels*"],"filename_extensions":[],"display_name":""},{"command":"napari-superres.write_single_image","layer_types":["image"],"filename_extensions":[".npy"],"display_name":""}],"widgets":[{"command":"napari-superres.make_mssr_caller","display_name":"MSSR","autogenerate":false},{"command":"napari-superres.make_esi_caller","display_name":"ESI","autogenerate":false},{"command":"napari-superres.make_sofi_caller","display_name":"SOFI","autogenerate":false},{"command":"napari-superres.make_srrf_caller","display_name":"SRRF","autogenerate":false},{"command":"napari-superres.make_musical_caller","display_name":"MUSICAL","autogenerate":false},{"command":"napari-superres.make_SplitChannel","display_name":"Split Channels","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-superres","version":"0.1.1","dynamic":null,"platform":null,"supported_platform":null,"summary":"Fluorescence Fluctuation-based Super Resolution (FF-SRM) Methods","description":"# napari-superres\n\n[](https://github.com/RoccoDAnt/napari-superres/blob/main/LICENSE)\n[](https://pypi.org/project/napari-superres)\n[](https://python.org)\n[](https://github.com/RoccoDAnt/napari-superres/actions)\n[](https://codecov.io/gh/RoccoDAnt/napari-superres)\n[](https://napari-hub.org/plugins/napari-superres)\n\n\nA collection of super-resolution microscopy FF-SRM methods.\n\nOpen-source implementation of methods for Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM):\n\nReview: [Alva et al., 2022. “Fluorescence Fluctuation-Based Super-Resolution Microscopy: Basic Concepts for an Easy Start.” Journal of Microscopy, August.](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135)\n\nMSSR article: [Torres-García, E., Pinto-Cámara, R., Linares, A. et al. Extending resolution within a single imaging frame. Nat Commun 13, 7452 (2022).](https://doi.org/10.1038/s41467-022-34693-9)\n\nESI article: [Idir Yahiatene, Simon Hennig, Marcel Müller, Thomas Huser (2015/2016). \"Entropy-based Super-resolution Imaging (ESI): From Disorder to Fine Detail\" ACS Photonics 8, 2 (2015)](https://doi.org/10.1021/acsphotonics.5b00307)\n\nSOFI article: [T. Dertinger, R. Colyer, G. Iyer, and J. Enderlein. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). PNAS 52, 106 (2009) ](https://doi.org/10.1073/pnas.0907866106)\n\nSRRF article: [Gustafsson, N., Culley, S., Ashdown, G., D. M. Owen, P. Matos Pereira, and R. Henriques. Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations. Nat Commun 7, 12471 (2016)](https://www.nature.com/articles/ncomms12471)\n\nMUSICAL article: [K. Agarwal and R. Machan, Multiple Signal Classification Algorithm for super-resolution fluorescence microscopy, Nature Communications, vol. 7, article id. 13752, (2016)](https://www.nature.com/articles/ncomms13752)\n\n\n\nMethods implemented:\n- MSSR\n- ESI\n- SOFI\n- SRRF\n- MUSICAL\n- Split channels\n\n\n| **Super Resolution Radial Fluctuations (SRRF)** | **Mean-Shift Super Resolution (MSSR)** | **Entropy-based Super-resolution Imaging (ESI)** |\n| --- | --- | --- |\n|  |  |  |\nfrom Fig. 7 of [Alva et al., 2022](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135) | from Fig. 2 of [García et al., 2021](https://www.biorxiv.org/content/10.1101/2021.10.17.464398v2.full)| from Fig. 6 of [Alva et al., 2022](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135)|\n\n\nRepositories available:\n- [ESI](https://github.com/biophotonics-bielefeld/ESI) GitHub repository\n- [PySOFI](https://github.com/xiyuyi-at-LLNL/pysofi) GitHub repository\n- [MUSICAL](https://sites.google.com/site/uthkrishth/musical) Google site\n\n----------------------------------\n\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n\n\n## Installation\nFirst install napari viewer (if you haven't):\n\n conda create -y -n napari-env -c conda-forge python=3.9\n conda activate napari-env\n pip install \"napari[all]\"\n\nFor details check: https://napari.org/stable/\n\n\n\n\nYou can install the plugin [graphically](https://github.com/LIBREhub/napari-LatAm-Workshop-2023/blob/napari-superres/docs/day3/napari-superres/napari-superres_installation_guide.pdf).\n\nor install latest development version :\n\n pip install git+https://github.com/RoccoDAnt/napari-superres.git\n\nYou might need to install [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) first.\n\n----------------------------------\nExamples of use:\n\n| **Original** | **tMSSR** |\n| --- | --- |\n| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/single-frame-good-exposure.png\")
| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/tmssr-mean-mag2.png\")
|\n| Parameters: | Amplification: 2, Order: 0, PSF FWHM: 6,
Interpolation: Bicubic, Statistical integration: CV*sigma |\n\n| **Original** | **ESI** |\n| --- | --- |\n| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/synt.png\")
| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/ESI.png\")
|\n| Parameters: | image in output: 2, bins: 2, Order: 2 |\n\n| **Original** | **SOFI** |\n| --- | --- |\n| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/noSOFI.png\")
| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/SOFI.png\")
|\n| Parameters: | Amplification factor: 2, Moment Order: 4, lambda parameter: 1.5, No. Iterations: 20, Window size: 100|\n\n| **Original** | **SRRF** |\n| --- | --- |\n|
| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/SRRF.png\")
|\n| Parameters: | Amplification: 2, Spatial radius: 5, Symmetry Axis: 6, Start frame: 0, End frame: 48|\n\n| **Original** | **MUSICAL** |\n| --- | --- |\n| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/musical_mean.png\")
| ![](\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/MUSICAL-CardioMyoblast_Mitochondria.png\")
|\n| Parameters: | Emission [nm]: 510 NA: 1.4, Mag: 100, Pizel size: 8000, Threshold: -0.5, Alpha: 4, Subpixels per pixel: 20|\n----------------------------------\n\n\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-superres\" is free and open source software\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[Cookiecutter]: https://github.com/audreyr/cookiecutter\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[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[file an issue]: https://github.com/RoccoDAnt/napari-superres/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":"https://github.com/RoccoDAnt/napari-superres","download_url":null,"author":"\"Rocco D'Antuono, Adán Guerrero, Raúl Pinto Cámara, Paúl Hernández Herrera, Esley Torres Garcia, Haydee Hernández, Julián Mejía\"","author_email":"rocco.dantuono@hotmail.it","maintainer":null,"maintainer_email":null,"license":"BSD-3-Clause","classifier":["Development Status :: 2 - Pre-Alpha","Framework :: napari","Intended Audience :: Developers","License :: OSI Approved :: BSD License","Operating System :: OS Independent","Programming Language :: Python","Programming Language :: Python :: 3","Programming Language :: Python :: 3 :: Only","Programming Language :: Python :: 3.8","Programming Language :: Python :: 3.9","Programming Language :: Python :: 3.10","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["matplotlib","magicgui","qtpy","tox ; extra == 'testing'","pytest ; extra == 'testing'","pytest-cov ; extra == 'testing'","pytest-qt ; extra == 'testing'","napari ; extra == 'testing'","pyqt5 ; extra == 'testing'"],"requires_python":">=3.8","requires_external":null,"project_url":["Bug Tracker, https://github.com/RoccoDAnt/napari-superres/issues","Documentation, https://github.com/RoccoDAnt/napari-superres#README.md","Source Code, https://github.com/RoccoDAnt/napari-superres","User Support, https://github.com/RoccoDAnt/napari-superres/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}