{"name":"napari-afmreader","display_name":"AFMReader","visibility":"public","icon":"","categories":["Utilities"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-afmreader.get_reader","title":"Open AFM data with AFMReader","python_name":"napari_afmreader._reader:napari_get_reader","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":[{"command":"napari-afmreader.get_reader","filename_patterns":["*.asd","*.gwy","*.ibw","*.jpk","*.spm","*.stp","*.top","*.topostats"],"accepts_directories":false}],"writers":null,"widgets":null,"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.4","name":"napari-afmreader","version":"0.0.2","dynamic":["license-file"],"platform":null,"supported_platform":null,"summary":"Napari plugin using AFMReader to load various Atomic Force Microscopy Images.","description":"# napari-AFMReader\n\n\n\n[](https://badge.fury.io/py/napari-afmreader)\n\n[](https://github.com/astral-sh/ruff)\n[](https://github.com/psf/black)\n[](https://github.com/psf/flake8)\n[](https://codecov.io/gh/AFM-SPM/napari-afmreader)\n[](https://results.pre-commit.ci/latest/github/AFM-SPM/napari-afmreader/main)\n[](https://figshare.shef.ac.uk/articles/software/napar-AFMReader/)\n[](https://fair-software.eu)\n\n
\n\n\n[](https://pepy.tech/project/napari-afmreader)\n[](https://pepy.tech/project/napari-afmreader)\n[](https://pepy.tech/project/napari-afmreader)\n\n
\n\n\n| [Installation](#installation) | [Usage](#usage) | [Licence](#licence) | [Citation](#citation) |\n\n
\n\nA [Napari](https://napari.org/) plugin to read in Atomic Force Microscopy (AFM) files using\n[AFMReader](https://github.com/AFM-SPM/AFMReader.git).\n\nYou can drag and drop your favourite AFM image files directly into the Napari viewer to use the awesome tools the image\nanalysis community have developed over at the [Napari Hub](https://www.napari-hub.org/) to analyse your images using\nopen-source software and a GUI!\n\n\n\n\n\n| File Extension | Supported by AFMReader | Description |\n| -------------- | ---------------------- | ------------------------ |\n| `.asd` | ✅ | High-speed AFM format. |\n| `.gwy` | ✅ | Gwyddion saved format. |\n| `.ibw` | ✅ | Igor binary-wave format. |\n| `.jpk` | ✅ | JPK instruments format. |\n| `.spm` | ✅ | Bruker spm format. |\n| `.stp` | ✅ | Homemade stp format. |\n| `.top` | ✅ | Homemade top format. |\n| `.topostats` | ✅ | topostats output format. |\n\n\n\n## Installation\n\n### Via Napari-Hub\n\nThis software should be installable directly from Napari!\n\nAll you need to do is:\n\n1. [Install Napari](https://napari.org/stable/tutorials/fundamentals/installation.html) into an environment.\n2. Open Napari by typing `napari` into your command line with your Napari environment activated.\n\n ```bash\n napari\n ```\n\n3. Go to `Plugins` > `Install/Uninstall Plugins`, and search for `napari-afmreader`.\n\n### Via Git\n\nOccasionally the Napari-Hub version of `napari-AFMReader` may not be the most up-to-date. This is when you might want\nto install both the most up-to-date `AFMReader` and `napari-AFMReader` versions via Git.\n\n`napari-AFMReader` has been designed to need minimal maintenance, with most of the new file type additions being solely\nadded to AFMReader.\n\n1. With [Git installed](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) on your machine, clone both the\n `AFMReader` and `napari-AFMReader` repositories:\n\n ```bash\n git clone https://github.com/AFM-SPM/AFMReader.git\n ```\n\n ```bash\n git clone https://github.com/AFM-SPM/napari-AFMReader.git\n ```\n\n2. Activate your Python environment (e.g. Conda) and install the dependencies for each - make sure that the `AFMReader`\n dependency is installed second to overwrite the possibly outdated `afmreader` package!\n\n ```bash\n cd napari-AFMReader\n pip install .\n cd ..\n ```\n\n ```bash\n cd AFMReader\n pip install .\n ```\n\n3. Now when you open Napari via the `napari` command, it should use the latest version of `AFMReader`, and\n `napari-AFMReader`.\n\n ```bash\n napari\n ```\n\n## Usage\n\nThis package should be fairly straight-forward and intuitive to use, requiring you to:\n\n1. Drag and drop your supported AFM file into the Napari Viewer.\n\n2. Type in the name of the channel you would like to use. You may not need to specify a channel for e.g. `.stp`, or the\n channel may refer to image key in the `.napari-afmreader` file.\\*.\n\n \\*_Possible channel names will not appear at first due to the order in which AFMReader processes an image. Thus,\n when provided with an non-existent channel name, the dialogue box will then return a list of possible channels to\n choose from._\n\n## Licence\n\n**This software is licensed as specified by the [GPL License](COPYING) and [LGPL License](COPYING.LESSER).**\n\n## Citation\n\nPlease use the [Citation File Format](https://citation-file-format.github.io/) which is available in this repository.\n","description_content_type":"text/markdown","keywords":"afm,image processing,napari","home_page":null,"download_url":null,"author":null,"author_email":"TopoStats Team , Max Gamill ","maintainer":null,"maintainer_email":null,"license":"GNU GPLv3 only","classifier":["Development Status :: 4 - Beta","Framework :: napari","Intended Audience :: End Users/Desktop","License :: OSI Approved :: GNU General Public License v3 (GPLv3)","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","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["afmreader","magicgui","napari[all]","qtpy","tox","pytest; extra == \"tests\"","pytest-cov; extra == \"tests\"","pytest-qt; extra == \"tests\"","qtpy; extra == \"tests\"","black; extra == \"dev\"","codespell; extra == \"dev\"","pre-commit; extra == \"dev\"","pylint; extra == \"dev\"","ruff; extra == \"dev\"","pytest-testmon; extra == \"dev\"","build; extra == \"pypi\"","setuptools_scm[toml]; extra == \"pypi\"","wheel; extra == \"pypi\""],"requires_python":">=3.10","requires_external":null,"project_url":["Bug Tracker, https://github.com/AFM-SPM/napari-afmreader/issues","Documentation, https://github.com/AFM-SPM/napari-afmreader#README.md","Source Code, https://github.com/AFM-SPM/napari-afmreader","User Support, https://github.com/AFM-SPM/napari-afmreader/issues"],"provides_extra":["tests","dev","pypi"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}