Reposted by napari
Do you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!
December 23, 2025 at 7:52 PM
Do you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!
Reposted by napari
OCTRON stands on the shoulders of giants. We make use of #SAM2 (meta), #YOLO11 (ultralytics) and some of THE best multi-object trackers out there #BoxMOT. For rapid data access we use python-zarr (>3.1).
We couldn’t have done it without the super supportive community surrounding @napari.org.
We couldn’t have done it without the super supportive community surrounding @napari.org.
December 23, 2025 at 7:57 PM
OCTRON stands on the shoulders of giants. We make use of #SAM2 (meta), #YOLO11 (ultralytics) and some of THE best multi-object trackers out there #BoxMOT. For rapid data access we use python-zarr (>3.1).
We couldn’t have done it without the super supportive community surrounding @napari.org.
We couldn’t have done it without the super supportive community surrounding @napari.org.
Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate
December 24, 2025 at 2:59 AM
Has napari helped your research this year? Why not say thank you to free and open source software by making a small donation? Every bit helps your friendly core team fix bugs and bring new features to life! CZI will match up to $75K in donations! opencollective.com/napari/donate
Reposted by napari
New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...
Using Appose with Pixi and Napari for reproducible deep learning segmentation workflows.
YouTube video by Brian Northan
www.youtube.com
December 19, 2025 at 1:43 PM
New video: more examples showing deep learning segmentation failure modes—and how to detect them with Napari. I show how Napari’s layer system compares images, ground truth, and results, and how Appose enables comparison across incompatible DL packages. www.youtube.com/watch?v=c369...
Reposted by napari
Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff:
Paper: doi.org/10.1242/jcs....
Code: github.com/pertzlab/arc...
Plugin: github.com/pertzlab/arc...
Paper: doi.org/10.1242/jcs....
Code: github.com/pertzlab/arc...
Plugin: github.com/pertzlab/arc...
December 18, 2025 at 4:16 PM
Tracking coordinated cellular dynamics directly from images -- New method paper by labmates @bgraedel.bsky.social & @macdobry.bsky.social ! Python package & @napari.org plugin, all the good stuff:
Paper: doi.org/10.1242/jcs....
Code: github.com/pertzlab/arc...
Plugin: github.com/pertzlab/arc...
Paper: doi.org/10.1242/jcs....
Code: github.com/pertzlab/arc...
Plugin: github.com/pertzlab/arc...
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
opencollective.com/napari/donate
December 18, 2025 at 12:03 PM
We're a bit late in ringing in the giving season, but it is indeed upon us. Enjoy our special edition holiday logo ☃️ and, if you can spare a bit and appreciate napari, please donate to our development efforts! 🙏 CZI will match donations up to $75K.
opencollective.com/napari/donate
opencollective.com/napari/donate
Reposted by napari
🦠🔬🤖🧑💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
October 27, 2025 at 12:08 PM
🦠🔬🤖🧑💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
Reposted by napari
And that’s a wrap for the @cbias.bsky.social napari workshop as well. Two days of learning, working collaboratively and finished off with a presentation from each of five project groups detailing the progress they made. Organised by Rocco D’Antuono, @giuliapaci.bsky.social and yours truly
November 27, 2025 at 7:24 PM
And that’s a wrap for the @cbias.bsky.social napari workshop as well. Two days of learning, working collaboratively and finished off with a presentation from each of five project groups detailing the progress they made. Organised by Rocco D’Antuono, @giuliapaci.bsky.social and yours truly
Reposted by napari
I wrote my first proper post on LinkedIn today. It was cheesy, bit of a weird thing to do.
Bottom line is I'm still buzzing from spending two days playing with napari sourounded by kind microscopy nerds at the #CBIAS2025 Napari Workshop.
Bottom line is I'm still buzzing from spending two days playing with napari sourounded by kind microscopy nerds at the #CBIAS2025 Napari Workshop.
December 5, 2025 at 12:39 AM
I wrote my first proper post on LinkedIn today. It was cheesy, bit of a weird thing to do.
Bottom line is I'm still buzzing from spending two days playing with napari sourounded by kind microscopy nerds at the #CBIAS2025 Napari Workshop.
Bottom line is I'm still buzzing from spending two days playing with napari sourounded by kind microscopy nerds at the #CBIAS2025 Napari Workshop.
Reposted by napari
Happy to finally share micromorph with everyone!
If you are interested in performing morphological measurements of bacteria, and like using Python and Napari then this is for you!
You can read about it in our preprint, and find the code on our Github repo, PyPi or directly from the napari hub!
If you are interested in performing morphological measurements of bacteria, and like using Python and Napari then this is for you!
You can read about it in our preprint, and find the code on our Github repo, PyPi or directly from the napari hub!
micromorph: a Python toolkit for measurement of microbial morphology
Detection of morphological phenotypes from light microscopy is a key part of microbiology. Despite advances in automated morphological analysis, accurate measurements still often require significant u...
www.biorxiv.org
December 11, 2025 at 8:53 AM
Happy to finally share micromorph with everyone!
If you are interested in performing morphological measurements of bacteria, and like using Python and Napari then this is for you!
You can read about it in our preprint, and find the code on our Github repo, PyPi or directly from the napari hub!
If you are interested in performing morphological measurements of bacteria, and like using Python and Napari then this is for you!
You can read about it in our preprint, and find the code on our Github repo, PyPi or directly from the napari hub!
Reposted by napari
Applications for the next @royalmicrosoc.bsky.social “Introduction to image analysis” workshop are now open!
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Introduction to Image Analysis 2026
www.rms.org.uk
December 1, 2025 at 10:09 AM
Applications for the next @royalmicrosoc.bsky.social “Introduction to image analysis” workshop are now open!
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Join us for 3 days in Cardiff in May to learn the foundations of #bioimageanalysis using Fiji, Python and @napari.org
www.rms.org.uk/rms-event-ca...
Reposted by napari
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
November 20, 2025 at 1:03 PM
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
Reposted by napari
Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration:
www.i2kconference.org/workshops
www.i2kconference.org/workshops
November 18, 2025 at 12:13 PM
Last-minute advert for the Convpaint workshop at I2K by Roman Schwob! Interactive segmentation in @napari.org. Today 2:00 PM CET. Free registration:
www.i2kconference.org/workshops
www.i2kconference.org/workshops
Reposted by napari
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
November 10, 2025 at 1:23 PM
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
November 10, 2025 at 1:23 PM
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Reposted by napari
Hi Fans of Feedback Microscopy,
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
November 7, 2025 at 7:23 PM
Hi Fans of Feedback Microscopy,
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
Reposted by napari
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Adventures in Code VII: getting started with napari – quantixed
quantixed.org
November 4, 2025 at 10:00 AM
I'd only dabbled with napari, but needed to use it for a paper we're writing. This is a quick post about getting started: from installation to a folder full of thousands of processed images, with gotchas along the way.
quantixed.org/2025/11/04/a...
quantixed.org/2025/11/04/a...
Reposted by napari
Save the date! The Open Software Summer School returns August 17-28 2026 in London, U.K.
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
October 31, 2025 at 3:25 PM
Save the date! The Open Software Summer School returns August 17-28 2026 in London, U.K.
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
There will be four separate tracks on animal behaviour, extracellular electrophysiology, anatomy and handling large data.
Applications open Dec 1st.
More details:
neuroinformatics.dev/open-softwar...
Happy Halloween from the napari team!
October 31, 2025 at 2:20 PM
Happy Halloween from the napari team!
Reposted by napari
It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!
Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!
October 30, 2025 at 4:14 PM
It was a fantastic opportunity to finally meet the people behind this software that I have been using for years and is so important for my work! A big thank you to all core developers who were so welcoming, and patiently guided participants in their attempts to contribute back to napari!
Reposted by napari
I truly appreciate the organizers, core contributors, and all attendees for this wonderful opportunity! I enjoyed learning and working on napari in a welcoming environment.
Those interested in talking about and contributing to napari, let’s join the regular community meeting together!
Those interested in talking about and contributing to napari, let’s join the regular community meeting together!
October 31, 2025 at 3:16 AM
I truly appreciate the organizers, core contributors, and all attendees for this wonderful opportunity! I enjoyed learning and working on napari in a welcoming environment.
Those interested in talking about and contributing to napari, let’s join the regular community meeting together!
Those interested in talking about and contributing to napari, let’s join the regular community meeting together!
Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!
October 30, 2025 at 6:53 AM
Longer wrap-up to come, but in the meantime: we had a fantastic and productive time at the napari hackathon at @globias.bsky.social 2025 conference! Thanks to all the participants and to the GloBIAS team for hosting us!
Do you use napari and love @xarray.bsky.social? Or use Xarray but cry when napari ignores the axis names? Read how we will improve this in the future! 🤝
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
Xarray ❤️ napari — napari blog documentation
napari.org
October 24, 2025 at 3:34 PM
Do you use napari and love @xarray.bsky.social? Or use Xarray but cry when napari ignores the axis names? Read how we will improve this in the future! 🤝
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
napari.org/island-dispa...
Co-authored by @ianhi.bsky.social and @timmonko.bsky.social, powered by the @scipyconf.bsky.social sprints!
Reposted by napari
Filling out the attached survey and reading this blog will really help bring you up to speed with our progress as a team. Most importantly, we want to guide this project in the direction that sustainably supports the community -- and that's why we'd like your help!
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
October 21, 2025 at 4:40 PM
Filling out the attached survey and reading this blog will really help bring you up to speed with our progress as a team. Most importantly, we want to guide this project in the direction that sustainably supports the community -- and that's why we'd like your help!
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
October 21, 2025 at 2:32 PM
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...