Installation instructions

Option 1 (simple): Using standalone napari app

Note

The only disadvantage of this option is inability to install GPU-accelerated version of torch

1. Download and install napari as standalone app using installation instructions

2. Search, download and install napari-nuclephaser plugin by opening the app, navigating to Plugins window and choosing Install/Uninstall plugins.

Option 2 (recommended): Using Anaconda

We recommend installation using Anaconda Distribution

1. Install Anaconda with Installation instructions

2. Open Anaconda Prompt using Search Bar or Anaconda Navigator

3. Create new environment with default anaconda packages using command

conda create --name napari-env python=3.10

4. Activate new environment using command

conda activate napari-env

5. Install Napari using command

pip install napari[all]

6. Verify napari installation using following command. It should open napari GUI.

napari

7. Install napari-nuclephaser plugin using command

pip install napari-nuclephaser

8. Plugin is ready to be used! Start napari by typing

napari

Initialize plugin’s widgets by opening Plugins window and choosing NuclePhaser.

Option 2 advanced: installation with GPU

If you have NVIDIA GPU with CUDA, you can significantly increase plugin’s speed.

To install GPU-powered version of the plugin, you first need to do all the steps for the installation using Anaconda (above). Then you need to:

1. Install CUDA using official instructions

Tip

Check which versions of CUDA are supported by current torch installation and consider installing earlier ones

2. Check CUDA installation with nvidia-smi command in the command line.

nvidia-smi

3. In the environment with napari and napari-nuclephaser installed, install CUDA-supported torch by typing specific command for your system, which can be found at torch installation page. For example, if you have Windows-based system and CUDA 12.6, your line should look like

pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126

Warning

During our tests, torchvision wasn’t installed using this line. To avoid that, add -U after install:

pip3 install -U torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu126