{"name":"napari-file2folder","display_name":"Save multidimensional file as folder of tifs","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-file2folder.make_qwidget","title":"Save multidimensional file as folder of tifs","python_name":"napari_file2folder:File2FolderWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-file2folder.make_qwidget","display_name":"Save multidimensional file as folder of tifs","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-file2folder","version":"0.0.4","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Save multidimensional file as folder of tifs","description":"# napari-file2folder\n\n[![License MIT](https://img.shields.io/pypi/l/napari-file2folder.svg?color=green)](https://github.com/GuignardLab/napari-file2folder/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-file2folder.svg?color=green)](https://pypi.org/project/napari-file2folder)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-file2folder.svg?color=green)](https://python.org)\n[![tests](https://github.com/jules-vanaret/napari-file2folder/workflows/tests/badge.svg)](https://github.com/jules-vanaret/napari-file2folder/actions)\n[![codecov](https://codecov.io/gh/jules-vanaret/napari-file2folder/branch/main/graph/badge.svg)](https://codecov.io/gh/jules-vanaret/napari-file2folder)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-file2folder)](https://napari-hub.org/plugins/napari-file2folder)\n\n<img src=\"https://github.com/GuignardLab/tapenade/blob/main/imgs/tapenade3.png\" width=\"100\">\n\nA plugin to inspect bioimages (e.g. .tif, .czi, .nd2, .lsm...) and save them as individual .tif files in a folder.\n\n`napari-file2folder` is a [napari] plugin that is part of the [Tapenade](https://github.com/GuignardLab/tapenade) project. Tapenade is a tool for the analysis of dense 3D tissues acquired with deep imaging microscopy. It is designed to be user-friendly and to provide a comprehensive analysis of the data.\n\nIf you use this plugin for your research, please [cite us](https://github.com/GuignardLab/tapenade/blob/main/README.md#how-to-cite).\n\n## Overview\n\n<img src=\"imgs/napari-file2folder-demo.gif\"/>\n\nThis plugin allows you to inspect (possibly large) bioimages by displaying their shape (number of elements in each dimension), and allowing you to save each element along a chosen dimension as a separate .tif file in a folder. This is useful when you have a large movie or stack of images and you want to save each frame or slice as a separate file. Optionally, the plugin allows the user to visualize the middle element of a given dimension to help the user decide which dimension to save as separate files.\n\nThe plugin currently supports the following file formats:\n- .tif\n- .ome.tiff\n- .zarr\n- .ome.zarr\n- .nd2\n- .lsm\n- .czi\n\nThis plugin leverages [tifffile], [bioio], and [zarr] to circumvent loading the entire images in memory, which allows inspection of very large images.\n\n> [!CAUTION]\n> When inspecting the middle element of a dimension, or when saving one element of a dimension as a separate file, the plugin loads the element in memory, which means that at least this lone element must fit in memory.\n\n## Installation\n\nThe plugin obviously requires [napari] to run. If you don't have it yet, follow the instructions [here](https://napari.org/stable/tutorials/fundamentals/installation.html).\n\nThe simplest way to install `napari-file2folder` is via the [napari] plugin manager. Open Napari, go to `Plugins > Install/Uninstall Packages...` and search for `napari-file2folder`. Click on the install button and you are ready to go!\n\nYou can install `napari-file2folder` via [pip]:\n\n    pip install napari-file2folder\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 [MIT] license,\n\"napari-file2folder\" 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----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/stable/plugins/index.html\n-->\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[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[tifffile]: https://github.com/cgohlke/tifffile\n[bioio]: https://github.com/bioio-devs/bioio\n[zarr]: https://github.com/zarr-developers/zarr-python\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Jules Vanaret","author_email":"jules.vanaret@univ-amu.fr","maintainer":null,"maintainer_email":null,"license":"The MIT License (MIT)\n\nCopyright (c) 2024 Jules Vanaret\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 :: MIT 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","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","qtpy","magicgui","tifffile","bioio","bioio-ome-tiff","bioio-ome-zarr","bioio-nd2","bioio-czi","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":null,"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}