{"name":"napari-molseeq","display_name":"molSEEQ","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-molseeq.make_qwidget","title":"Make a QWidget","python_name":"molseeq:QWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-molseeq.make_qwidget","display_name":"napari-molseeq","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-molseeq","version":"1.0.8","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A Napari plugin for extracting single molecule sequences from single/multi-channel SMLM microscopy data.","description":"# napari-molSEEQ\n\n[![License MIT](https://img.shields.io/pypi/l/napari-GapSeq2.svg?color=green)](https://github.com/piedrro/napari-molseeq/blob/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-GapSeq2.svg?color=green)](https://pypi.org/project/napari-molseeq/)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-GapSeq2.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-GapSeq2)](https://napari-hub.org/plugins/napari-molseeq)\n\nA **Napari** plugin for extracting single molecule sequences from single/multi-channel SMLM microscopy data. \n\nCompatible with both ALEX and FRET data. All functions are parallelised/GPU accelerated where possible to increase performance.\nMultiple datasets can be loaded and processed in parallel.\n\nnapari-molseeq uses **Picasso** (picassosr) as a backend and includes features for **aligning** image channels/datasets, **undrifting** images, **detecting/fitting** localisations and extracting **traces**, and supports both **ALEX** and **FRET** data. Traces can be exported in different formats for downstream analysis.\n\nnapari-molseeq traces can be analysed with TraceAnalyser: https://github.com/piedrro/TraceAnalyser\n\nThis is still undergoing development, so some features may not work as expected.\n\nThis was built by Dr Piers Turner from the Kapanidis Lab, University of Oxford.\n\n----------------------------------\n\n## Installation\n\nYou can install `napari-molseeq` via [pip]:\n\n    pip install napari-molseeq\n\nYou can install `napari-molseeq` via [GitHub]:\n\n    conda create –-name napari-molseeq python==3.9\n    conda activate napari-molseeq\n    conda install -c anaconda git\n    conda update --all\n\n    pip install git+https://github.com/piedrro/napari-molseeq.git\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 [MIT] license,\n\"napari-molseeq\" 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/piedrro/napari-GapSeq2/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":"Piers Turner","author_email":"piers.turner@physics.ox.ac.uk","maintainer":null,"maintainer_email":null,"license":"The MIT License (MIT)\n\nCopyright (c) 2023 Piers Turner\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 :: 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 :: 3.9","Programming Language :: Python :: 3.10","Programming Language :: Python :: 3.11","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["napari[all]==0.5.0","numpy","magicgui","qtpy","scipy","pyqtgraph","picassosr==0.7.3","pandas","matplotlib>=3.7.0","scipy","opencv-python","tqdm","originpro","pyqt5-tools","trackpy","shapely","astropy","mat4py","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/piedrro/napari-molseeq/issues","Documentation, https://github.com/piedrro/napari-molseeq#README.md","Source Code, https://github.com/piedrro/napari-molseeq","User Support, https://github.com/piedrro/napari-molseeq/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}