Kyle Harrington
@kisharrington.mastodon.social.ap.brid.gy
Computer scientist. Scientific computing, image analysis, and artificial life. Views are my own and do not reflect my employers. Web […]
[bridged from https://mastodon.social/@kisharrington on the fediverse by https://fed.brid.gy/ ]
[bridged from https://mastodon.social/@kisharrington on the fediverse by https://fed.brid.gy/ ]
Reposted by Kyle Harrington
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
🚀 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 […]
🔍 Read our blog to learn more about our roadmap […]
Original post on fosstodon.org
fosstodon.org
July 10, 2025 at 8:08 PM
🚀 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 […]
🔍 Read our blog to learn more about our roadmap […]
Reposted by Kyle Harrington
One of the cartoons from Physics for Cats
May 22, 2025 at 1:51 PM
One of the cartoons from Physics for Cats
Reposted by Kyle Harrington
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:
https://hackmd.io/BXWDZ3i8Q6OAEASrkaSNIQ
Community meetings are for every napari user and developer. Get a chance to speak with […]
https://hackmd.io/BXWDZ3i8Q6OAEASrkaSNIQ
Community meetings are for every napari user and developer. Get a chance to speak with […]
Original post on fosstodon.org
fosstodon.org
February 12, 2025 at 4:22 AM
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:
https://hackmd.io/BXWDZ3i8Q6OAEASrkaSNIQ
Community meetings are for every napari user and developer. Get a chance to speak with […]
https://hackmd.io/BXWDZ3i8Q6OAEASrkaSNIQ
Community meetings are for every napari user and developer. Get a chance to speak with […]
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! 😃
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!
https://labs.quansight.org/blog/napari-conda-constructor-menuinst
@napari that was so fantastic that it is spreading across the scientific python ecosystem!
https://labs.quansight.org/blog/napari-conda-constructor-menuinst
February 5, 2025 at 8:19 PM
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!
https://labs.quansight.org/blog/napari-conda-constructor-menuinst
@napari that was so fantastic that it is spreading across the scientific python ecosystem!
https://labs.quansight.org/blog/napari-conda-constructor-menuinst
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 https://atrium.kyleharrington.com/visualization/napari-tiled-zarr/0.0.3.py s3 […]
[Original post on mastodon.social]
If you have uv installed, then this should open the mouse liver FIB-SEM dataset from OpenOrganelle:
uv run https://atrium.kyleharrington.com/visualization/napari-tiled-zarr/0.0.3.py s3 […]
[Original post on mastodon.social]
December 29, 2024 at 6:47 PM
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 https://atrium.kyleharrington.com/visualization/napari-tiled-zarr/0.0.3.py s3 […]
[Original post on mastodon.social]
If you have uv installed, then this should open the mouse liver FIB-SEM dataset from OpenOrganelle:
uv run https://atrium.kyleharrington.com/visualization/napari-tiled-zarr/0.0.3.py s3 […]
[Original post on mastodon.social]
Reposted by Kyle Harrington
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?
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?
CZII - CryoET Object Identification
Find small biological structures in large 3D volumes
www.kaggle.com
December 8, 2024 at 5:18 PM
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?
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?
Reposted by Kyle Harrington
If folks aren't aware (especially bioimaging folks), we have a cryoET particle picking competition running (with $$$ prizes):
cryoetdataportal.czscience.com/competition
We're at >3k entrants with >1k submissions right now. 2 months to go, and the leaderboard is quite interesting already!
cryoetdataportal.czscience.com/competition
We're at >3k entrants with >1k submissions right now. 2 months to go, and the leaderboard is quite interesting already!
Started
cryoetdataportal.czscience.com
November 22, 2024 at 8:01 PM
If folks aren't aware (especially bioimaging folks), we have a cryoET particle picking competition running (with $$$ 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/competition
We're at >3k entrants with >1k submissions right now. 2 months to go, and the leaderboard is quite interesting already!
Reposted by Kyle Harrington
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!)
November 18, 2024 at 4:47 AM
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!)
https://dev-discuss.pytorch.org/t/pytorch-deprecation-of-conda-nightly-builds/2590 oof, pytorch conda channel is getting deprecated.
November 17, 2024 at 2:12 AM
https://dev-discuss.pytorch.org/t/pytorch-deprecation-of-conda-nightly-builds/2590 oof, pytorch conda channel is getting deprecated.
Are #python folks I know (especially in the scientific computing area) using rootutils?
https://github.com/ashleve/rootutils
https://github.com/ashleve/rootutils
November 13, 2024 at 2:08 PM
Are #python folks I know (especially in the scientific computing area) using rootutils?
https://github.com/ashleve/rootutils
https://github.com/ashleve/rootutils
Reposted by Kyle Harrington
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 […]
On the other hand, most of the folks fraudulently manipulating their images probably also run pirates Photoshop copies.
Also: if anyone […]
Original post on scholar.social
scholar.social
November 13, 2024 at 11:14 AM
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 […]
On the other hand, most of the folks fraudulently manipulating their images probably also run pirates Photoshop copies.
Also: if anyone […]