Kyle Harrington

@shauna This resonates in the @napari community: https://napari.zulipchat.com/#narrow/channel/348229-randoms/topic/being.20in.20OSS.20v.20contributing/with/537903987

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...

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...

🚀 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 […]

One of the cartoons from Physics for Cats

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 […]

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.

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! 😃

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

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]

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?

Started

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!

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.

@shauna did you see this?

Are #Python folks I know (especially in the scientific computing area) using rootutils?

https://github.com/ashleve/rootutils

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 […]