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Kyle Harrington

@kisharrington.mastodon.social.ap.brid.gy
87 followers 1 following 6 posts

Computer scientist. Scientific computing, image analysis, and artificial life. Views are my own and do not reflect my employers. Web: kyleharrington.com 🌉 bridged from ⁂ mastodon.social/@kisharrington, follow @ap.brid.gy to interact

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Reposted by Kyle Harrington
napari @napari.fosstodon.org.ap.brid.gy · 11/03/2026
🔬 Registration is open for our pilot Introduction to napari Workshop! napari is a powerful open-source image viewer for scientific data analysis in Python. This hands-on workshop will get you exploring multi-dimensional datasets fast. ✅ Only $20 USD ✅ Limited to 20 people ✅ Perfect for […]
fosstodon.org
Original post on fosstodon.org
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Reposted by Kyle Harrington
Kyle Harrington @kyleharrington.com · 26/08/2025
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...
doi.org
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...
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Reposted by Kyle Harrington
napari @napari.fosstodon.org.ap.brid.gy · 10/07/2025
🚀 The napari team is excited to announce our brand new development roadmap — a community-informed vision for the future of napari. We’re laying the foundation for long-term sustainability, better docs, smoother releases, and exciting new features. 🔍 Read our blog to learn more about our roadmap […]
fosstodon.org
Original post on fosstodon.org
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Reposted by Kyle Harrington
Tom Gauld @tomgauld.bsky.social · 22/05/2025
One of the cartoons from Physics for Cats
Title: Soren Kierkegaard, 1843
 
 Image: A three panel comic strip that shows Mr Kierkegaard saying
 "Life can only be understood backwards" as he walks from right to left through the three frames (i.e. against the usual order in which these panels would be read)

A dog walks from left to right, saying: "But it must be lived forward"
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Reposted by Kyle Harrington
napari @napari.fosstodon.org.ap.brid.gy · 12/02/2025
Hi naparistas! A reminder that all are welcome at our next (Atlantic) community meeting, Feb 12, 8:30am SFO / 11:30am NYC / 5:30pm Paris. Agenda and details here: hackmd.io/BXWDZ3i8Q6OAEASrkaSNIQ Community meetings are for every napari user and developer. Get a chance to speak with […]
fosstodon.org
Original post on fosstodon.org
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Reposted by Kyle Harrington
Juan Nunez-Iglesias @jni.fosstodon.org.ap.brid.gy · 10/02/2025
Amazing new #Python #PEP to improve optional dependencies handling: 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! 😃
peps.python.org
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.
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Kyle Harrington @kisharrington.mastodon.social.ap.brid.gy · 05/02/2025
TL;DR installers are really challenging to make. The team made some tooling for @napari that was so fantastic that it is spreading across the scientific python ecosystem! labs.quansight.org/blog/napari-cond…
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Kyle Harrington @kisharrington.mastodon.social.ap.brid.gy · 29/12/2024
I made some updates to the tiled rendering branch in @napari. If you have uv installed, then this should open the mouse liver FIB-SEM dataset from OpenOrganelle: uv run atrium.kyleharrington.com/visualiza… s3 […] [Original post on mastodon.social]
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Reposted by Kyle Harrington
Kyle Harrington @kyleharrington.com · 08/12/2024
For the #ML and #CryoET folks out there: Are folks on here submitting to the CZII CryoET Object Identification competition: www.kaggle.com/competitions... ? The leaderboard is really interesting, and the forums are full of insights. How many of the latest picking models have been submitted?
kaggle.com
CZII - CryoET Object Identification
Find small biological structures in large 3D volumes
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Reposted by Kyle Harrington
Kyle Harrington @kyleharrington.com · 22/11/2024
If folks aren't aware (especially bioimaging folks), we have a cryoET particle picking competition running (with $$$ prizes): cryoetdataportal.czscience.com/competition We're at >3k entrants with >1k submissions right now. 2 months to go, and the leaderboard is quite interesting already!
cryoetdataportal.czscience.com
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Juan Nunez-Iglesias @jni.fosstodon.org.ap.brid.gy · 18/11/2024
Has someone built a masto instance that hoovers up all one's tweets from your personal data archive and reposts them, fully searchable, with the original tweet date? I'd love to be able to link to my old tweets without linking to that site. (And I'd love if others here did the same!)
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Kyle Harrington @kisharrington.mastodon.social.ap.brid.gy · 17/11/2024
dev-discuss.pytorch.org/t/pytorch-d… oof, pytorch conda channel is getting deprecated.
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Kyle Harrington @kisharrington.mastodon.social.ap.brid.gy · 13/11/2024
Are #Python folks I know (especially in the scientific computing area) using rootutils? github.com/ashleve/rootutils
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Reposted by Kyle Harrington
Bastian Greshake Tzovaras @gedankenstuecke.scholar.social.ap.brid.gy · 13/11/2024
Elsevier retracts two papers over missing software licenses. Better no one tell Adobe, otherwise a large parts of current academic literature will disappear. On the other hand, most of the folks fraudulently manipulating their images probably also run pirates Photoshop copies. Also: if anyone […]
scholar.social
Original post on scholar.social
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