A simple plugin to use AFMSlicer with napari
This napari plugin was generated with copier using the napari-plugin-template.
You can install napari-afmslicer via pip:
pip install napari-afmslicerIf napari is not already installed, you can install napari-afmslicer with napari and Qt via:
pip install "napari-afmslicer[all]"To install latest development version :
pip install git+https://github.com/AFM-SPM/napari-afmslicer.gitOnce installed you can launch napari from the command line.
napariThe resulting widgets implemented in this package can be found under the Plugins > AFMSlicer menu. Selecting each brings up a "widget" on the right hand side of the window (by default). There are the following widgets.
- AFMSlicer 3D Viewer
- AFMSlicer Filtering
- AFMSlicer Slicing (WIP)
From each of the widgets configuration options can be toggled that change the settings for running/processing the image. Clicking on the Run button at the bottom of any of these should result in a new Layer being displayed in Napari that show the effects of processing the selected image.
Because AFMSlicer uses some of the functionality of TopoStats the napari-TopoStats is included as a dependency and installed when napari-AFMSlicer is installed. Further the napari-skimage package is also included as a dependency and will be available.
Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.
Distributed under the terms of the GNU GPL v3.0 license, "napari-afmslicer" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.