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Using Napari

Napari is a multi-dimensional image viewer for Python.

Setting up Napari

Automatic install

We have written a script that sets up Napari with a single command. In a terminal run

napari_setup.sh

If the command is successful you can go to Running Napari.

In case of problems you can look at the step-by-step install instructions below.

Note

If you already have a napari environment the script will ask you if you want to update or reset the environment:

Napari virtual environment already exists
Do you want to (U)pdate/(R)eset/(Q)uit? (default: Q)

If you want to update the environment type U. This will update the packages in your environment to the latest recommended version.

If you want to reset the environment type R. This will delete the environment and create a new fresh one.

If you want to quit type Q. This will exit the script without doing anything.

Step-by-step install

The following command creates a Python virtual environment

mkenv napari --python /soft/conda/envs/napari/bin/python

An additional fix needed is to run the following command:

echo "unset LD_LIBRARY_PATH" >> $HOME/Python/napari/bin/activate

Activate the environment with

workon napari

And install napari

pip install napari[pyside2]==0.4.17 pyside2==5.13.2

If you want to create a Desktop entry for Napari follow the instructions below.

cat > ~/bin/run_napari.sh <<<EOF
#!/bin/bash

source ~/Python/napari/bin/activate
napari $@
EOF
cat > ~/Desktop/Napari.desktop<<EOF
[Desktop Entry]
Version=0.4.17
Type=Application
Name=Napari
Comment=
Exec=/home/user/bin/run_napari.sh
Icon=/soft/conda/envs/napari/lib/python3.9/site-packages/napari/resources/logo.png
Path=
Terminal=false
StartupNotify=true
EOF

And make it executable

chmod +x ~/Desktop/Napari.desktop

Running Napari

As part of the automatic install and setup described above there is a script installed in $HOME/bin/run_napari.sh that launches napari. To use it, in a terminal:

$HOME/bin/run_napari.sh
Note

This script makes sure to activate the napari environment and run napari with the correct command taking into account the availability of a GPU.

If you want to launch napari without using the script above open a terminal and make sure you are in the napari virtual environment (run workon napari if unsure).

napari

If you hace access to a GPU and want to use GPU acceleration in Napari

vglrun napari

Alternatively you can use the File Manager, navigate to a file or a directory and use the right click menu to open it with Napari:

If Open with Napari does not appear, use Open with other application and select Napari.

Napari Plugins

Note

The plugins described below are installed by default in the napari virtual environment by the automatic setup script described above.

Multiscale plugin

The Napari multiscale plugin allows to visualize STPT and AxioScan data cubes in 2D and 3D. To install it first activate the napari virtual environment

workon napari

and use pip

pip install imaxt-multiscale-plugin

If you want to be able to create animations install as well the napari-animation plugin

pip install napari-animation

The plugin integrates into Napari adding support for IMAXT multiscale data. In order to open a dataset start napari with the location of the dataset, e.g.

$HOME/bin/run_napari.sh /storage/imaxt.processed/stpt/20230418_MPR_Balbc_lung_infl_dapi_100x20um

or navigate the the sample with the File Manager and open the sample with Napari as explained in Running Napari.

Napari can also perform 3D visualization of the cube. It is recommended however in this case to use GPU accelleration. Note that multiscale rendering is only supported in 2D. In 3D, only the lowest resolution scale is displayed.

STPT 3D viewer

In order to install the napari-stpt plugin activate the napari environment

workon napari

and use pip

pip install napari-stpt

Then start it with

napari-stpt

or if there is GPU available

vglrun napari-stpt

and select the dataset to load from the dropdown menu.

Opening Napari from the browser

This is in preview – not yet rolled out.

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