3.3. Using the napari plugin - HenriquesLab/NanoPyx GitHub Wiki

Using NanoPyx through napari

Installation

As usual it is recommend that you use a virtual environment for this installation. You can install the napari plugin of NanoPyx via [pip]:

pip install napari-nanopyx

It should install the plugin as well as the NanoPyx library together with napari. It is recommended that you perform this installation in a clean environment, using either python venv or conda.

Notes for Mac M1/2 users

You might need to install pyqt separately as it is not currently distributed together with the installation of napari-nanopyx. The recommended way of installing should be by using conda and running:

conda install pyqt

Afterwards, you should be able to just run "napari" in your terminal and napari's interface should load.

Opening napari

  1. Start by opening a terminal and activating the virtual environment in which you installed napari-nanopyx.
  1. Then simply type napari and press Enter in the terminal and it should open napari GUI.

Using napari-NanoPyx

  1. Navigate to the Plugins tab and a dropdown menu will appear with all the plugins that are currently installed.
  2. Hover the cursor on top of napari-nanopyx and a menu will appear with all methods currently implemented in napari-NanoPyx.
  1. Click on the method that you want to use and a new panel will appear on the right side, allowing you to select which image to use, as well as defining the required parameters for the selected method.