Napari installation guide

3 minute read

In this tutorial, we will install Napariꜛ and all necessary Python packages on your computer. We will use conda to create a new Python environment and install all necessary packages. Conda is a package manager that allows you to install and manage multiple Python environments on your computer. This is very useful if you want to work with different versions of Python or different versions of Python packages.

1. Install Conda

You have conda already installed and it is working? Skip this step and proceed with Step 2.

Visit Anaconda.comꜛ or conda.ioꜛ and download either the Anaconda or the miniconda installer, respectively, for your operating system. Execute the installer and follow the instructions.

Miniconda installation dialog under macOS.

Info: Windows-users who installed miniconda may receive an error message like conda is not recognized as an internal or external command while trying to use conda in the later steps of this installation guide. In such a case, please perform the steps described in this this blog post. You can find solutions for other common conda related errors on Windows there as well.

2. Download the course material

Please, download or clone this GitHub repositoryꜛ. If you are not familiar with GitHub: You can download the repository as a .zip file by clicking on the green Code button and then on Download ZIP.
Unzip the downloaded file and move the folder to a location of your choice. We will refer to this location as the course folder.
Please, also download the data from this Google Drive folderꜛ and merge it with the course folder.

3. Create the Python environment

Open a new terminal (macOS/Linux) or PowerShell/Anaconda Prompt (Windows).
If you haven’t performed this on your system already, please add the conda-forge channel to your conda configuration by executing the following command in the terminal/PowerShell/Anaconda Prompt:
```
  conda config --add channels conda-forge
```
Create a new Python environment named napari_bioimage_analysis by executing the following command:
```
  conda create -n napari_bioimage_analysis -y python=3.9
```
This command creates a new Python environment and installs Python version 3.9. When this is done, activate the environment by executing the following command:
```
  conda activate napari_bioimage_analysis
```

The PowerShell in Windows.

4. Install the required Python packages

Next, we need to install all required Python packages. Depending on your system, please execute one of the following commands.

Mac-users

Mac-users please continue with the following commands:

conda install -y mamba

and then:

mamba install -y napari napari-assistant napari-brightness-contrast napari-bleach-correct napari-skimage-regionprops napari-crop napari-pystackreg napari-filament-annotator napari-simpleitk-image-processing napari-PICASSO napari-accelerated-pixel-and-object-classification napari-clusters-plotter napari-feature-classifier napari-laptrack napari-layer-details-display stardist-napari cellpose-napari ocl_icd_wrapper_apple ipykernel

Wait until all packages are installed. This can take a few minutes.

PC-users

PC-users please continue with the following commands

pip install napari[all] ipykernel napari-simpleitk-image-processing stardist-napari napari-crop napari-pystackreg napari-brightness-contrast cellpose-napari napari-skimage-regionprops napari-assistant napari-annotator napari-PICASSO napari-accelerated-pixel-and-object-classification napari-clusters-plotter napari-feature-classifier napari-layer-details-display napari-laptrack napari-bleach-correct napari-filament-annotator

Wait until all packages are installed. This can take a few minutes.

Troubleshooting

If you receive an error message regarding a specific package, please exclude it from the commands above. For example, if you receive an error message regarding the package laptrack, e.g. due to conflicting packages versions, remove it from the commands above and re-execute it. After the installation of the remaining packages is finished, you can try to install the missing package by executing one of the following commands:

Mac-users:

pip install <MISSING_PACKAGE>

PC-users:

conda install -y <MISSING_PACKAGE>

If this does not work and you still receive an error message regarding conflicting package versions, we can create a separate Python environment for this package (or all missing packages). To do so, follow the procedure described in step 3 and 4, but reduce the installation commands (mamba install -y .../pip install) to the missing packages. Choose a different name for you separate Python environment, e.g. napari_bioimage_analysis_2 or napari_bioimage_analysis_<MISSING_PACKAGES>.

Removing a Python environment
In case you want to remove the conda environment, e.g., to perform a fresh reinstallation, you can do so by executing the following commands.

First, deactivate the environment if it is currently active:

conda deactivate

Then, remove the environment:

conda env remove -n napari_bioimage_analysis

4. Starting Napari

After the successful installation, you can verify that Napari is working by executing the following commands:

napari

After executing the last command, Napari will open. If you close Napari and want to start it again, simply re-execute the last command, you don’t need to activate the environment again.

Starting Napari in the Windows PowerShell.

Napari main window.