{"name":"napari-moltrack","display_name":"MolTrack","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-moltrack.make_qwidget","title":"Make moltrack QWidget","python_name":"moltrack:QWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-moltrack.make_qwidget","display_name":"MolTrack","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-moltrack","version":"0.1.9","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"A user-friendly SMLM analysis platfrom for napari, which includes single molecule localisation, tracking, and analysis features.","description":"# napari-moltrack\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-moltrack.svg?color=green)](https://github.com/piedrro/napari-moltrack/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-moltrack.svg?color=green)](https://pypi.org/project/napari-moltrack)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-moltrack.svg?color=green)](https://python.org)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-moltrack)](https://napari-hub.org/plugins/napari-moltrack)\n\nA user-friendly SMLM analysis platfrom for napari, which includes single molecule localisation, tracking, and analysis features. \nBased on established python packages such as **Picasso**, **GPUfit** and **Trackpy**.\nThis plugin was designed to detect/track single molecules inside cells, but can be used for any other SMLM/tracking application.\n\nAll functions are parallelised/GPU accelerated where possible to increase performance.\nMultiple datasets can be loaded and processed in parallel.\n\nSingle molecule localisations can be filtered by their properties (e.g. photons, width, etc.) and can be rendered as a super resolution image.\n\nNapari-moltrack is also compatible with **FRET** and **ALEX FRET** image data, can be used to calculate FRET efficiencies of single molecules/tracks.\n\nSegmentations can be used to exclude regions from single molecule localisation and tracking.\nSegmentations can be added automatically using Cellpose or can be added manually. Includes tools for editing/modifying segmentations at a sub-pixel resolution.\n\nCompatible with both single and multi-channel .tif and .fits files.\n\nnapari-moltrack was written by Piers Turner, Kapanidis Group, University of Oxford.\n\nhttps://www.physics.ox.ac.uk/research/group/gene-machines\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n\n\n## Installation\n\nYou can install `napari-moltrack` via [pip]:\n\n pip install napari-moltrack\n\nTo update `napari-moltrack` to the latest version, use:\n\n pip install napari-moltrack --upgrade\n\nTo install latest development version :\n\n pip install git+https://github.com/piedrro/napari-moltrack.git\n\n\n## BactFit\n\nnapari-moltrack integrates BactFit, a package for fitting the shape of rod shaped bacterial cells to an ideal cell model.\nBactFit allows cell renders and heatmaps to be generated through the transformation of SMLM localisations to an ideal cell model.\n\n### BactFit Heatmap\n\n![Feature Image](resources/heatmap.png)\n\n### BactFit Cell Render\n\n![Feature Image](resources/render.png)\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-moltrack\" 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-moltrack/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":"Copyright (c) 2024, Piers Turner\nAll rights reserved.\n\nRedistribution and use in source and binary forms, with or without\nmodification, are permitted provided that the following conditions are met:\n\n* Redistributions of source code must retain the above copyright notice, this\n list of conditions and the following disclaimer.\n\n* Redistributions in binary form must reproduce the above copyright notice,\n this list of conditions and the following disclaimer in the documentation\n and/or other materials provided with the distribution.\n\n* Neither the name of copyright holder nor the names of its\n contributors may be used to endorse or promote products derived from\n this software without specific prior written permission.\n\nTHIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS \"AS IS\"\nAND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE\nIMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE\nDISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE\nFOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL\nDAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR\nSERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER\nCAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,\nOR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE\nOF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.\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","bactfit>=0.1.6","numpy","magicgui","qtpy","scipy","pyqtgraph","picassosr==0.8.0","pandas","matplotlib>=3.7.0","scipy","opencv-python","tqdm","originpro","pyqt5-tools","torch","torchvision","cellpose==3.0.1","omnipose","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-moltrack/issues","Documentation, https://github.com/piedrro/napari-moltrack#README.md","Source Code, https://github.com/piedrro/napari-moltrack","User Support, https://github.com/piedrro/napari-moltrack/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}