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Contributing to the napari community:

widgets, plugins, napari core, documentation—oh my!

Peter Sobolewski (he/him)

Systems Analyst
Imaging Applications
Research IT
The Jackson Laboratory

Member, napari core developer team

What is napari?

a Python library for n-dimensional image visualisation, annotation, and analysis.

What can napari be used for?

• view & explore 2D, 3D, and higher-dimensional arrays
• overlay derived data such as points, polygons, labels, and more
• seamlessly weave exploration, computation, and annotation together in imaging data analysis
• leverage scientific Python ecosystem

napari is an open-source, community developed project—anyone can contribute!

What is the napari community?

• napari users: local and global
• napari plugin developers
• napari core developers
• broader scientific Python community

Ask and answer questions!

• image.sc forum: https://forum.image.sc/tag/napari

• napari Zulip chat: https://napari.zulipchat.com

• napari community meetings: https://napari.org/stable/community/meeting_schedule.html

domain specific knowledge is valuable too! feedback, Q&A, share use cases

No accounts are needed to lurk…

Report bugs—or test existing ones

• GitHub Issues: https://github.com/napari/napari/issues

• Reporting bugs/problems/inconstencies/confusion is extremely valuable!

• When in doubt, report—we prefer duplicates than crickets!

reporting problems is very valuable!

This does require an account (free), but you can use that account to login at image.sc and zulipchat.com!

Discuss features and use-cases

• napari roadmap: https://github.com/orgs/napari/projects/24/views/1
• GitHub Issues: https://github.com/napari/napari/issues

Please check existing issues and/or join a Community meeting!

Headless napari is just Python!

– Juan Nunez-Iglesias (@jni)

Share Python scripts & notebooks!

expand for full code

from skimage import data
from scipy import ndimage as ndi

import napari

blobs = data.binary_blobs(length=128, volume_fraction=0.1, n_dim=3)
labeled = ndi.label(blobs)[0]
viewer, image_layer = napari.imshow(blobs, name='blobs')
viewer.add_labels(labeled, name='blob ID')
viewer.dims.ndisplay = 3
viewer.camera.zoom = 3
viewer.camera.angles = (3, 38, 53)

if __name__ == '__main__':
    napari.run()

Python scripts can handle keyboard and mouse events!

• Customize napari functionality:
  • keyboard and mouse events: https://napari.org/stable/howtos/connecting_events.html

@viewer.bind_key('a')
def accept_image(viewer):
    msg = 'this is a good image'
    viewer.status = msg
    print(msg)

• Example: https://napari.org/stable/gallery/custom_mouse_functions.html

events how-to

Python scripts can contribute widgets!

Example: https://napari.org/stable/gallery/magic_parameter_sweep.html

Python scripts can contribute widgets!

• magicgui makes this quite easy, see https://napari.org/stable/guides/magicgui.html
• …but you can also use Qt for maximal control by subclassing QWidget

How to share Python scripts & notebooks

• email/fileshare with colleagues, collaborators, etc.
• use GitHub:
  • use GitHub Gists: https://gist.github.com
  • make a repository of scripts
• with publication (Zenodo, etc.)

Develop a napari plugin

napari plugins are Python packages that can:

• add file-type readers & writers
• customize functionality (events)
• extend the GUI (widgets, menus)
• provide demo/sample data

Plugin developer guide: https://napari.org/dev/plugins/index.html

over 350, you can also choose to contribute to existing plugins

Plugins can be installed from within napari

• plugins can be publically discoverable and have global reach via PyPI and napari-hub.org

Contribute to documentation

napari documentation repository: https://github.com/napari/docs

Contribution guide: https://napari.org/dev/developers/documentation/index.html

• write a how-to, guide, or tutorial
• share a workshop
• help document features/use cases
• copy edit & review

plugin docs

Don’t forget you can contribute to the documentation of your favorite plugin too!

Contribute code

napari repository: https://github.com/napari/napari Contribution guide: https://napari.org/dev/developers/contributing.html

• fix a bug (close an issue)
• write an example for the Gallery
• implement a feature
• review code

other napari repos npe2 napari ecosystem

Don’t forget about plugins! You can contribute code to them too!

Hope to see you soon!
Thank you!