Kyle Harrington
@kyleharrington.com
Images, AI, ML, and ALife.
Former: @hampshirecolg
@brandeisuniversity.bsky.social
@harvardmed.bsky.social
@uidaho.bsky.social
@hhmijanelia.bsky.social
@mdc-berlin.bsky.social
@ORNL.
Now @chanzuckerberg.bsky.social.
Opinions are mine.
Former: @hampshirecolg
@brandeisuniversity.bsky.social
@harvardmed.bsky.social
@uidaho.bsky.social
@hhmijanelia.bsky.social
@mdc-berlin.bsky.social
@ORNL.
Now @chanzuckerberg.bsky.social.
Opinions are mine.
Pinned
Kyle Harrington
@kyleharrington.com
· Sep 22
Kyle Harrington
kyleharrington.com
Hi all, I'm a computer scientist. Currently I'm focused on computational work that connects to bioimaging data. You can find more about me at my personal page kyleharrington.com
Reposted by Kyle Harrington
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
GitHub - czimaginginstitute/zarr-particle-tools: Particle extraction and reconstruction from OME-Zarr tilt series.
Particle extraction and reconstruction from OME-Zarr tilt series. - czimaginginstitute/zarr-particle-tools
github.com
November 17, 2025 at 10:30 PM
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
I love the name!!! Looking forward to checking out🍦
Hey #TeamTomo …would you like to try some 🍦ICECREAM!? Our @unibas.ch colleagues over at the @ivandokmanic.bsky.social lab have developed a stunningly effective tool to de-noise and de-wedge your tomograms. The contrast and details will give you brain freeze! 🍨❄️🤯
Please try, we need feedback 🧪🧶🧬🔬
Please try, we need feedback 🧪🧶🧬🔬
Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧
October 23, 2025 at 6:19 PM
I love the name!!! Looking forward to checking out🍦
This is awesome! Way to go William!!!
Congratulations to 2025 #MacFellow William Tarpeh! The Stanford chemical engineer is working on sustainable and practical solutions to treat wastewater and recover valuable mineral resources.
🗞️: stanford.io/3IZIBqF
🗞️: stanford.io/3IZIBqF
October 9, 2025 at 4:18 AM
This is awesome! Way to go William!!!
Reposted by Kyle Harrington
#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/
October 7, 2025 at 8:24 PM
#geff v1 is released! 🎉 GEFF is a zarr-based Graph Exchange File Format with special support for tracking applications in Python and Java. Thank you to all the amazing developers who contributed at the Janelia 2025 Trackathon! liveimagetrackingtools.org/geff/
Howdy #arxiv folks, could someone please endorse my colleague Ambrose Carr on q-bio.QM for a preprint? Endorsement code O488JD
thank you!
thank you!
October 2, 2025 at 10:59 PM
Howdy #arxiv folks, could someone please endorse my colleague Ambrose Carr on q-bio.QM for a preprint? Endorsement code O488JD
thank you!
thank you!
Reposted by Kyle Harrington
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
September 10, 2025 at 12:50 PM
Save the date! The @pasteur.fr Pasteur course on image analysis is announced:
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
It will happen from the 1st of June to the 5th 2026.
This year there will be only one track: the Early Career Investigator track (beginners). 👇
Reposted by Kyle Harrington
A standardized, realistic phantom dataset consisting of ground-truth annotations for 6 diverse complexes serves as a community resource for benchmarking cryo-ET algorithms.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
www.nature.com
August 29, 2025 at 2:21 PM
A standardized, realistic phantom dataset consisting of ground-truth annotations for 6 diverse complexes serves as a community resource for benchmarking cryo-ET algorithms.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Caroline Hemphill also wrote up a great blog post about the competition: www.czbiohub.org/life-science...
August 26, 2025 at 9:49 PM
Caroline Hemphill also wrote up a great blog post about the competition: www.czbiohub.org/life-science...
Better ML for cryo-ET starts with better benchmarks.
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
doi.org
August 26, 2025 at 2:22 PM
Better ML for cryo-ET starts with better benchmarks.
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge.
The result: community models beat expert tools.
Read more in the @natmethods.nature.com article that just came out:
🔗 doi.org/10.1038/s415...
Reposted by Kyle Harrington
It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇
@napari.org @jni.codes is a finalist in the @ardc.edu.au Eureka Prize for Excellence in Research Software.
Learn more: youtu.be/0g_MkTa_NwQ
#EurekaPrizes
Learn more: youtu.be/0g_MkTa_NwQ
#EurekaPrizes
August 1, 2025 at 7:29 AM
It's hard to express how much gratitude I have to everyone involved in the journey, both mine and @napari.org's, that has led to this point. #EurekaPrizes A small attempt below: 👇
Reposted by Kyle Harrington
🚀The napari team is excited to announce our brand new development roadmap — a community-informed vision for the future of napari!
🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...
🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...
🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...
🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...
napari roadmap blog post — napari blog documentation
napari.org
July 10, 2025 at 8:03 PM
🚀The napari team is excited to announce our brand new development roadmap — a community-informed vision for the future of napari!
🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...
🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...
🔍Read the blog to learn about our process and priorities:
napari.org/island-dispa...
🗺️OR check out the roadmap itself on napari.org:
napari.org/stable/roadm...
Reposted by Kyle Harrington
when you discover new tools and ideas via biorixv, sometimes you don't even notice when it is published, some great stuff here :
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Polarity-JaM: an image analysis toolbox for cell polarity, junction and morphology quantification - Nature Communications
Studying cell polarity is often limited by the complexity and variety of image data. Polarity-JaM is a software suite streamlining cell polarity analysis with easy-to-use tools and interfaces demonstr...
www.nature.com
June 20, 2025 at 9:30 AM
when you discover new tools and ideas via biorixv, sometimes you don't even notice when it is published, some great stuff here :
www.nature.com/articles/s41...
www.nature.com/articles/s41...
There is a @napari.org hackathon at GloBIAS!
Be there or be square (or whatever layer type you'd like)
Be there or be square (or whatever layer type you'd like)
Reminder: if you go to the GloBIAS conference we can help you contribute to napari at the hackathon! A bunch of the team will be there! (Great thanks to the GloBIAS team for accommodating us!!!)
More details on the conference website.
More details on the conference website.
Deadlines extended - you can still register for the GloBIAS conference! We have extended most deadlines. Please check our webpage: tinyurl.com/mr3kx5a5! Looking forward to welcoming you to Kobe, for training, developing and discussing a broad range of BIA topics!
May 16, 2025 at 11:24 AM
There is a @napari.org hackathon at GloBIAS!
Be there or be square (or whatever layer type you'd like)
Be there or be square (or whatever layer type you'd like)
TFW you discover the internet in the conference venue isn't stable enough for a Google Slides presentation with videos 😅 luckily with >24hr warning
May 6, 2025 at 12:15 PM
TFW you discover the internet in the conference venue isn't stable enough for a Google Slides presentation with videos 😅 luckily with >24hr warning
Reposted by Kyle Harrington
And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵
a woman in a hat is crying and says " i 've traveled a good many miles to get here "
Alt: Charlotte from the Sanditon TV series, emotionally exclaiming, "I've traveled a good many miles to get here!"
media.tenor.com
May 1, 2025 at 2:08 PM
And it's finally here! napari 0.6.0 is out on PyPI and conda-forge! 🥳 We've had a few threads about this release already but let's recap with some highlights: 🧵
Reposted by Kyle Harrington
We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
April 23, 2025 at 8:47 AM
We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Reposted by Kyle Harrington
Yo #TeamTomo, check out our updated #MemBrain v2 preprint. And better yet, give it a whirl on your #CryoET membranes! Please send us your feedback! 🧪🧶🧬🔬
We have updated our #MemBrain v2 preprint with a lot more details about the MemBrain-pick and MemBrain-stats modules, as well as some application examples!
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
Stay tuned for the upcoming thread by lead author @lorenzlamm.bsky.social! 🧠🧵
#CryoET #TeamTomo
www.biorxiv.org/content/10.1...
April 24, 2025 at 9:35 PM
"no no, I said turn up the economy"
you know things are going well when they break out the turnip photos
April 7, 2025 at 8:52 PM
"no no, I said turn up the economy"
Check this out!!! The results from our CryoET particle picking competition are available, the full test data (public and private datasets) is available, and you can dive right into the data on the CZ CryoET Data Portal! Enjoy and please let us know what you think :)
Results from CZII's #cryoET object detection challenge on kaggle are in!
Participation exceeded our expectations with 931 Teams from 76 countries competing, generating over 27,000 submissions. For an overview check out our post-competition page: cryoetdataportal.czscience.com/competition
Participation exceeded our expectations with 931 Teams from 76 countries competing, generating over 27,000 submissions. For an overview check out our post-competition page: cryoetdataportal.czscience.com/competition
March 6, 2025 at 5:18 PM
Check this out!!! The results from our CryoET particle picking competition are available, the full test data (public and private datasets) is available, and you can dive right into the data on the CZ CryoET Data Portal! Enjoy and please let us know what you think :)
Awesome! So glad to see my former RL professor Andy Barto get this recognition (and Rich is too!)
ACM A.M. Turing Award Honors 2024: Andrew Barto and Richard Sutton Recognized as Pioneers of Reinforcement Learning
awards.acm.org/about/2024-t...
awards.acm.org/about/2024-t...
Andrew Barto and Richard Sutton are the recipients of the 2024 ACM A.M. Turing Award for developing the conceptual and algorithmic foundations of reinforcement learning.
Andrew Barto and Richard Sutton as the recipients of the 2024 ACM A.M. Turing Award for developing the conceptual and algorithmic foundations of reinforcement learning. In a series of papers beginning...
awards.acm.org
March 5, 2025 at 12:56 PM
Awesome! So glad to see my former RL professor Andy Barto get this recognition (and Rich is too!)
Last night we were doing a family dance party...
My smartwatch gave a notification...
You've been running for 5 minutes...
I feel judged.
My smartwatch gave a notification...
You've been running for 5 minutes...
I feel judged.
February 12, 2025 at 2:18 PM
Last night we were doing a family dance party...
My smartwatch gave a notification...
You've been running for 5 minutes...
I feel judged.
My smartwatch gave a notification...
You've been running for 5 minutes...
I feel judged.
Reposted by Kyle Harrington
Amazing new #python #pep to improve optional dependencies handling:
https://peps.python.org/pep-0771/
The PEP is very thorough and well-written, and it perfectly uses @napari as a motivating example. We were not involved but we fully endorse it! 😃
https://peps.python.org/pep-0771/
The PEP is very thorough and well-written, and it perfectly uses @napari as a motivating example. We were not involved but we fully endorse it! 😃
PEP 771: Default Extras for Python Software Packages
PEP 508 specifies a mini-language for declaring package dependencies. One feature of this language is the ability to specify extras, which are optional components of a distribution that, when used, install additional dependencies. This PEP proposes a mechanism to allow one or more extras to be installed by default if none are provided explicitly.
peps.python.org
February 10, 2025 at 4:26 AM
Amazing new #python #pep to improve optional dependencies handling:
https://peps.python.org/pep-0771/
The PEP is very thorough and well-written, and it perfectly uses @napari as a motivating example. We were not involved but we fully endorse it! 😃
https://peps.python.org/pep-0771/
The PEP is very thorough and well-written, and it perfectly uses @napari as a motivating example. We were not involved but we fully endorse it! 😃
Reposted by Kyle Harrington
Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall:
February 6, 2025 at 11:02 AM
Hey #teamtomo, if you often find yourself using the excellent membrain-seg from @lorenzlamm.bsky.social et al., you might find my napari plugin "napari-segselect" useful. Let's say your tomogram contains the edges of two bacterial cells, each with a membrane and cell wall:
I just want to take the opportunity to remind everyone that the Hamster Dance still exists. You can even find 10 hour long videos of it. YW
February 5, 2025 at 1:25 PM
I just want to take the opportunity to remind everyone that the Hamster Dance still exists. You can even find 10 hour long videos of it. YW
Reposted by Kyle Harrington
There's a Korean soap opera on Netflix (When the Stars Gossip) which has *Drosophila courtship in space* as a major plot point (Ep 2). They have Michael Reiser & lab's flight arenas (you can see Janelia & MIchael's initials on the panels). Great way to learn about Drosophila courtship!
February 5, 2025 at 1:51 AM
There's a Korean soap opera on Netflix (When the Stars Gossip) which has *Drosophila courtship in space* as a major plot point (Ep 2). They have Michael Reiser & lab's flight arenas (you can see Janelia & MIchael's initials on the panels). Great way to learn about Drosophila courtship!