{"name":"napari-intensity-plotter","display_name":"Intensity Plotter","visibility":"public","icon":"","categories":["Annotation","Segmentation","Acquisition"],"schema_version":"0.2.1","on_activate":null,"on_deactivate":null,"contributions":{"commands":[{"id":"napari-intensity-plotter.IntensityPlotWidget","title":"Intensity Plot","python_name":"napari_intensity_plotter._widget:IntensityPlotWidget","short_title":null,"category":null,"icon":null,"enablement":null},{"id":"napari-intensity-plotter.IntensityPlotControlWidget","title":"Intensity Plot Control","python_name":"napari_intensity_plotter._widget:IntensityPlotControlWidget","short_title":null,"category":null,"icon":null,"enablement":null}],"readers":null,"writers":null,"widgets":[{"command":"napari-intensity-plotter.IntensityPlotWidget","display_name":"Intensity Plot","autogenerate":false},{"command":"napari-intensity-plotter.IntensityPlotControlWidget","display_name":"Intensity Plot Control","autogenerate":false}],"sample_data":null,"themes":null,"menus":{},"submenus":null,"keybindings":null,"configuration":[]},"package_metadata":{"metadata_version":"2.1","name":"napari-intensity-plotter","version":"0.1.6","dynamic":null,"platform":null,"supported_platform":null,"summary":"A plugin for plotting intensity profiles with control features in napari.","description":"# napari-intensity-plotter\n\n[![License BSD-3](https://img.shields.io/pypi/l/napari-intensity-plotter.svg?color=green)](https://github.com/Tbrn1103/napari-intensity-plotter/raw/main/LICENSE)\n[![PyPI](https://img.shields.io/pypi/v/napari-intensity-plotter.svg?color=green)](https://pypi.org/project/napari-intensity-plotter)\n[![Python Version](https://img.shields.io/pypi/pyversions/napari-intensity-plotter.svg?color=green)](https://python.org)\n[![tests](https://github.com/Tbrn1103/napari-intensity-plotter/workflows/tests/badge.svg)](https://github.com/Tbrn1103/napari-intensity-plotter/actions)\n[![codecov](https://codecov.io/gh/Tbrn1103/napari-intensity-plotter/branch/main/graph/badge.svg)](https://codecov.io/gh/Tbrn1103/napari-intensity-plotter)\n[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-intensity-plotter)](https://napari-hub.org/plugins/napari-intensity-plotter)\n\n# napari-intensity-plotter\n\n**napari-intensity-plotter** is a plugin for **[napari](https://napari.org)** that provides tools to measure and plot intensity profiles in 2D time-series images.\n\n![Intensity Plot Widget](images/intensity_plot_widget_example.png)\n\n*Screenshot: Intensity profile of a region of interest in a 2D time-series image.*\n\n## Features\n\n- **Intensity Plot Widget**: Allows you to select a region of interest in a 2D time-series image and plot the intensity profile over time.\n- **Intensity Plot Control Widget**: Lets you fine-tune plot parameters and save the results as CSV or PNG files.\n\n## Installation\n\nYou can install `napari-intensity-plotter` via pip:\n\n```bash\npip install napari-intensity-plotter\n```\n\nAlternatively, you can install it directly from the napari plugin interface.\n\n### Usage\n\n1. **Load a 2D Time-Series Image**  \n   Load a 2D time-series image (e.g., fluorescence microscopy data) in napari.\n\n2. **Activate the Widgets**  \n   Open the `Intensity Plot Widget` and `Intensity Plot Control Widget` from the `Plugins` menu in napari.\n\n3. **Intensity Plot Widget**  \n   - Move your mouse over the image, or click on a specific location to plot the intensity profile of the selected region across slices (e.g., time).\n   - The region of interest (ROI) size can be adjusted using the square size setting in the control widget.\n\n4. **Intensity Plot Control Widget**  \n   - Configure the square size for the ROI (ensures that the region size remains odd).\n   - Set the directory to save plots and intensity data.\n   - Save the intensity profile as a `.csv` or `.png` file by clicking the corresponding buttons or using keyboard shortcuts (`Ctrl+S`).\n\n5. **Additional Controls**  \n   - Hide all layers using the `Hide All Layers` button or `Ctrl+D`.\n   - Use the rectangle to visualize the selected ROI.\n\n### Example Workflow\n\n**Step 1**: Load a 2D time-series image (e.g., `tif` or `nd2`) into napari. Ensure the layer is visible.\n\n**Step 2**: Open the `Intensity Plot Widget` to visualize intensity changes over time or slices for a specific ROI.\n\n**Step 3**: Use the `Intensity Plot Control Widget` to:\n- Adjust the square size for the ROI.\n- Specify a directory to save intensity data.\n- Enable saving in CSV or PNG formats.\n  \n**Step 4**: Save the plotted intensity data by clicking `Save to CSV/PNG` or pressing `Ctrl+S`.\n\n**Step 5**: Hide all layers if necessary using `Hide All Layers` or `Ctrl+D`.\n\n## Contributing\n\nContributions are welcome! If you encounter issues or have ideas for new features, please submit them via the [GitHub Issues](https://github.com/Tbrn1103/napari-intensity-plotter/issues).\n\n## Acknowledgements\n\nThis plugin was developed using the **napari plugin cookiecutter template**, which greatly streamlined the creation of this tool. See the [cookiecutter-napari-plugin](https://github.com/napari/cookiecutter-napari-plugin) for more details.\n\nSpecial thanks to the napari community for their continuous support and resources.\n\n## License\n\nThis project is licensed under the BSD 3-Clause License. See the [LICENSE](LICENSE) file for details.\n","description_content_type":"text/markdown","keywords":null,"home_page":null,"download_url":null,"author":"Toranosuke Takagi","author_email":"toranporin_1224@yahoo.co.jp","maintainer":null,"maintainer_email":null,"license":"Copyright (c) 2024, Toranosuke Takagi\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","Programming Language :: Python :: 3.12","Topic :: Scientific/Engineering :: Image Processing"],"requires_dist":["numpy","magicgui","qtpy","scikit-image","tox; extra == \"testing\"","pytest; extra == \"testing\"","pytest-cov; extra == \"testing\"","pytest-qt; extra == \"testing\"","napari; extra == \"testing\"","pyqt5; extra == \"testing\"","pyqtgraph; extra == \"testing\""],"requires_python":">=3.9","requires_external":null,"project_url":["Bug Tracker, https://github.com/Tbrn1103/napari-intensity-plotter/issues","Documentation, https://github.com/Tbrn1103/napari-intensity-plotter#README.md","Source Code, https://github.com/Tbrn1103/napari-intensity-plotter","User Support, https://github.com/Tbrn1103/napari-intensity-plotter/issues"],"provides_extra":["testing"],"provides_dist":null,"obsoletes_dist":null},"npe1_shim":false}