January 2023 - napari hub Newsletter #1020
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January 2023 - Q1 napari-hub newsletter
Greetings napari community!
Happy new year! We are delighted to share the first 2023 edition of our quarterly newsletter, in an effort to keep you informed about the latest developments and updates regarding plugins and the hub. We are excited to introduce a new section, Community Highlight, which will provide an opportunity for our community members to be recognized for their contributions. We encourage you to take a moment to read through the newsletter to stay informed about the latest happenings within our community.
Community Opportunities
Share your Favorite Plugins by Creating a Collection
We are excited to announce the launch of our Plugin Collections feature, designed to assist members of the napari community in sharing their most valuable, innovative, and intriguing plugins. We encourage everyone to curate and publish their own collections!
Here are some ideas for Collections:
To submit a Collection, you can follow the instructions here to submit a Collection directly to the Collections Github repo, or reach out to Dannielle McCarthy for help with the submission. We encourage everyone in our community to submit a Collection to help others find useful plugins to try.
What’s New on the Hub?
Launched Features
Enhancing User Experience: Introducing "Human-Readable" Plugin Naming Conventions
Are you a Plugin developer? You can now add “human-readable” display names to your metadata! This new feature allows for greater visibility and ease of discovery for your plugin by providing a more descriptive name. Additionally, the human-readable naming convention will provide users with a better understanding of the purpose and functionality of your plugin. See below for an example of the new feature.
Plugin Collections for Discovering and Sharing Plugins
We’ve streamlined Plugin discovery and sharing by adding community-curated Plugin Collections that group plugins together in ways not captured by the current categories or other plugin metadata. Check out below the Collection overview and Collection in-detail pages, and consider curating your own Plugin Collection.
Insightful Metrics on Plugin Usage in the Activity Tab
We’ve added a new Activity Tab to all plugin pages to showcase metrics around user installs of the plugin. We hope this feature will help developers understand how their user base changes over time and help users select new or established plugins to try out. Check out the example below.
napari hub Wiki
We just launched a wiki for the napari hub with guides for plugin developers and details about the hub architecture.
New Plugins to Check Out
We are pleased to announce that the napari hub is now growing with over 30 new plugins! While a select few have been highlighted, all of the new plugins can be easily accessed by utilizing the "Newest" button on the left sidebar sort.
napari-owncloud by Robert Hasse.
Browse folders and images in owncloud / nextcloud servers and open them using just a double-click!
Want to add a new feature or share a new analysis method with the community? Contribute a plugin to napari! Start with this presentation and tutorial. Check out the napari Plugin developer workshop series archive for even more info about creating high-quality plugins.
Community Highlight: Varun Kapoor
About Varun
What do you do for work?
I run a non-profit organization in Paris, France called KapoorLabs that does bio-image analysis based consulting work for biologist researchers using microscopy in their work. We create tailored workflows for them using Fiji and napari and provide them with super-computing accounts.
What motivated you to contribute to the napari hub?
Creating napari plugins and making them discoverable on the hub makes the workflow development and deployment fast and on the timescale that suits the PhD students, whose time on a project is limited, and researchers alike.
What’s something people wouldn’t guess about you?
I have been an inline speed skater since my school days. Whenever the weather permits I skate to my office and sometimes take a longer route on purpose to skate more before going to work.
Community Highlight
What plugins, Collections, or other work have you done in the napari community?
We’ve built 3 plugins and a plugin Collection.
What connects the plugins in your Collection?
Our first napari plugin, VollSeg is a denoising and segmentation plugin for cells or filaments in 2D, 3D, 2D+time, and 3D+time datasets. Our collection uses that as the base plugin to create analysis workflows. VollSeg-napari-mtrack plugin segments kymographs and does Ransac-based function fits on the segmented kymograph image. Vollseg-napari-trackmate performs track analysis from tracks computed using the TrackMate FIJI plugin.
What problem do your plugins solve?
Researchers use kymographs of filament structures for quantification of growth and shrink rates as well as catastrophe and rescue frequency. vollseg-napari-mtrack makes this process automated and interactive to do such a quantification in batch.
vollseg-napari-trackmate is a one-stop shop for analyzing tracks, doing statistical analysis of dividing and non-dividing trajectories separately, computing the distance of cells from tissue boundary, obtaining oscillation frequency of cell intensity, and classifying motion as brownian or non-brownian.
Connect with Varun!
Twitter | YouTube | Kapoor Labs | LinkedIn
Swag for Plugin Developers
We would like to extend our gratitude to all plugin developers within our napari community by offering a complimentary swag box as a token of appreciation for their contributions. If you have not yet received correspondence from us, we apologize for the oversight. Please contact Dannielle McCarthy at [email protected] to register for your swag box. We value your contributions and look forward to recognizing your efforts.
What's Upcoming on the Hub
Insightful Metrics on Plugin Maintenance in the Activity Tab
We’ve added a Plugin Maintenance section to the new Activity Tab on all plugin pages. This feature will provide a historical overview of commits to the plugin repo, enabling users to gain a better understanding of the ongoing maintenance and development of the plugin. Check out the design mockup of this new feature that we anticipate to launch in February!
We are so thrilled to share our updates, and we look forward to more progress in 2023. Please visit our roadmap for an overview of our work, and for more detailed information, look at our Github repository. If you have any questions or concerns, please do not hesitate to reach out.
Dannielle McCarthy
Application Scientist, CZI Imaging napari Hub Team
The napari hub is a service of the Chan Zuckerberg Initiative in collaboration with napari.
CZI Foundation | P.O. Box 8040, Redwood City, CA 94063
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