getting started with napari
Welcome to the getting started with napari tutorial!
This tutorial assumes you have already installed napari. For help with installation see our installation tutorial.
This tutorial will teach you all the different ways to launch napari. At the end of the tutorial you should be able to launch napari and see the viewer your favorite way.
There are four ways to launch the napari viewer:
- command line
- python script
- IPython console
- jupyter notebook
All four of these methods will launch the same napari viewer but depending on your use-case different ones may be preferable.
command line usage
To launch napari from the command line simply run
This command will launch an empty viewer:
Once you have the viewer open you can add images through the
File/Open dropdown menu
or by dragging and dropping images directly on the viewer.
We currently only support files that can be read with
We plan on adding support for more exotic file types shortly - see issue #379 for discussion.
You can also create new empty
labels layers using the new layer buttons in the bottom right of the viewer.
You can also directly load an image into the viewer from the command line by passing the path to the image as an argument as follows
If the image is
RGBA use the
Launching napari directly from the command line is the simplest and fastest way to open the viewer, but it doesn’t allow you to preprocess your images before opening them. It is also currently not possible to save images or other layer types directly from the viewer, but we’ll be adding support for this functionality soon as discussed in #379.
python script usage
To launch napari from a python script, inside your script you should import
create a Qt GUI context, and then create the
Viewer by adding some data.
For example, to add an image and some points inside your script you should include:
import napari # create Qt GUI context with napari.gui_qt(): # create a Viewer and add an image here viewer = napari.view_image(my_image_data) # custom code to add data here viewer.add_points(my_points_data)
then run your script from the command line to launch the viewer with your data:
See the scripts inside the
examples in the main repository for examples of using napari this way.
An advantage of launching napari from a python script is that you can preprocess your images and add multiple layers before displaying the viewer.
IPython console usage
To launch napari from an IPython console,
first instantiate a Qt GUI and then import
napari and create a
It is best to launch the viewer with the GUI already set to be Qt by
Then inside IPython
# instantiate Qt GUI import napari from skimage.data import astronaut # create the viewer and display the image viewer = napari.view_image(astronaut(), rgb=True)
If you did not launch IPython with the GUI already then you can set it from within IPython using
but be warned that the Qt GUI can take a few seconds to be created and if you create the
Viewer before it is finished,
the kernel will die, and the viewer will not launch.
An advantage of launching napari from an IPython console is that the you can continue to programmatically interact with the viewer from the IPython console, including bidirectional communication, where code run in the console will update the current viewer and where data changed in the GUI will be accessible in the console.
jupyter notebook usage
You can also launch napari from a jupyter notebook,
As in the case of the IPython console though you must wait for the Qt GUI to instantiate following the
%gui qt magic command.
Instantiating the Qt GUI can take a few seconds and if you create the
Viewer before it is finished,
the kernel will die and the viewer will not launch.
For this reason, the
%gui qt magic command should always be run in a separate cell from creating the viewer.
Similar to launching from the IPython console, an advantage of launching napari from a jupyter notebook is that you can continue to programmatically interact with the viewer from jupyter notebook, including bidirectional communication, where code run in the notebook will update the current viewer and where data changed in the GUI will be accessible in the notebook.
To learn more about how to use the napari viewer with different types of napari layers checkout the viewer tutorial and more of our tutorials listed below.
- installing napari
- getting started tutorial
- viewer tutorial
- image layer tutorial
- labels layer tutorial
- points layer tutorial
- shapes layer tutorial
- surface layer tutorial
- vectors layer tutorial