Installation

Napari is still considered alpha phase software and may not install correctly on the first attempt, if that happens please reach out to the napari developers directly here. If you’re having issues with empanada-napari, you can reach out to the developers here.

Important

empanada-napari version 1.2 is now available! This latest version has new models for nuclei and lipid doplets, new plugins and updated 2D and 3D inference modules.

Note

Python 3.10 to 3.13 and Napari 0.6.6 are preferred for new installation.

Please install git, gcc and g++ compilers before proceeding with installation.

1. Mac users please read this.

2. Windows users please read this.

Conda Installation

1. If not already installed, you can install miniconda here.

2. Download the correct installer for your OS (Mac, Linux, Windows).

3. After installing conda, open a new terminal or command/anaconda prompt window.

4. Verify conda installed correctly with:

   conda --version
   

Note

If you get a “conda not found error” the most likely cause is that the path wasn’t updated correctly. Try restarting the terminal or command prompt window. If that doesn’t work then see fixing conda path on Mac/Linux or fixing conda path on Windows.

New & Existing User Installation

Note

Users working with GPUs on Windows machines, please see our FAQ section regarding installation steps.

Note

Since the release of empanada-napari version 1.2.2, Python 3.9 and below are no longer supported. If you have an existing installation, we recommend creating a new environment with a supported Python version (3.10-3.13) to avoid conflicts.

Windows

1. Create a new virtual environment:

   conda create -y -n empanada -c conda-forge python=3.11
   

2. Activate the new environment:

   conda activate empanada
   

3. Install napari 0.6.6 with pip:

   pip install napari[all]==0.6.6
   

For alternative and more detailed installation instructions, see the official napari installation tutorial.

4. From here, install empanada-napari with pip:

   pip install empanada-napari
   

Linux

1. Create a new virtual environment:

   conda create -y -n empanada -c conda-forge python=3.11
   

2. Activate the new environment:

   conda activate empanada
   

3. Install napari 0.6.6 with pip:

   pip install napari[all]==0.6.6
   

For alternative and more detailed installation instructions, see the official napari installation tutorial.

4. From here, install empanada-napari with pip:

   pip install empanada-napari
   

MacOS (Apple Silicon)

1. Create a new virtual environment:

   conda create -y -n empanada -c conda-forge python=3.11
   

2. Activate the new environment:

   conda activate empanada
   

3. Install napari 0.6.6 and pyqt with conda:

   conda install -c conda-forge napari==0.6.6 pyqt
   

For alternative and more detailed installation instructions, see the official napari installation tutorial.

4. From here, install empanada-napari with pip:

   pip install empanada-napari
   

MacOS (Intel)

1. Create a new virtual environment:

   conda create -y -n empanada -c conda-forge python=3.11
   

2. Activate the new environment:

   conda activate empanada
   

3. Downgrade Numpy with pip:

   pip install --upgrade numpy==1.26.4
   

4. Install napari 0.6.6 and pyqt with conda:

   conda install -c conda-forge napari==0.6.6 pyqt
   

For alternative and more detailed installation instructions, see the official napari installation tutorial.

5. From here, install empanada-napari with pip:

   pip install empanada-napari
   

Note

Newer versions of dependencies such as PyTorch no longer support MacOS with Intel chips. If you are still having issues, we recommend creating an environment with python=3.9, then installing empanada-napari==1.2.1 and napari==0.4.18.

For step-by-step instructions, click here.

To verify installation, run:

napari &

If installation was successful you should see empanada-napari in the Plugins menu. If you don’t, restart napari. For further troubleshooting, please see the FAQ.