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: 👇

🚀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...

If you post the frames in a thread then we can try scrolling really fast

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...

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...

bsky.app/profile/wais...

There is a @napari.org hackathon at GloBIAS!

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

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!"

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: 🧵

We have a suite for studying cell polarity in Python polarityjam.readthedocs.io feel free to post an issue if you need any more functionality

Figure 4. MemBrain v2 end-to-end workflow detects periodic phycobilisome organization. A: Raw tomogram slice of EMD-31244. B: Out-of-the-box MemBrain-seg segmentation (light blue). C: A single membrane instance can be visualized in Surforama and manually annotated with GT phycobilisome positions (magenta). D: MemBrain-pick localizes particles (trained with data from C) on all membranes in the tomogram. E: MemBrain-stats computes Ripley’s O statistic using the positions from D with a bin size of 5nm. The distance between peaks (35 nm) was measured to estimate chain unit spacings.

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...

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! 🧪🧶🧬🔬

"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 :)

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.

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! 😃

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

Screencap of Drosophila courtship, caption "The male is flapping his wings"

Screencap showing Drosophila flight arena

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!

TL;DR installers are really challenging to make. The team made some tooling for @napari.fosstodon.org.ap.brid.gy that was so fantastic that it is spreading across the scientific python ecosystem!

Senior Research Scientist, AI x Imaging, Science Redwood City, CA (Open to Flex)

🚨Looking for a new opportunity at the intersection of #AI and #bioimaging? Want to work with an awesome team?

We have multiple open research scientist positions @cziscience.bsky.social. Please RT!

boards.greenhouse.io/chanzuckerbe...

boards.greenhouse.io/chanzuckerbe...

We just released and uploaded a new version of *Mastodon*, the large-scale tracking and track-editing framework for large, multi-view images.

Mastodon is available via Fiji, via a dedicated update site.
mastodon.readthedocs.io/en/latest/do...

Below is a thread that survey some of the novelties ⏬️

It was the user's fault for not signing up sooner.

🤣

is the strategy for getting gemini users to have pop up windows in google apps?

AI startup recruiting emails these days:
"Our company coming out of stealth mode w new capital. We need a founding engineer for our startup that is focused on developing foundation models of founding engineers. Our plan for monetization is replacing founding engineers in post-stealth mode companies"

For some reason it feels very judgy when my smart watch says "Good job being active again" when I was sitting at my desk scratching my head.

I feel your pain. I had to scavenge some emergency J48s a couple of weeks ago.

Extending API support for use in bpy · Issue #84 · oanegros/MicroscopyNodes Hihi! I'm following up from the bluesky exchange: https://bsky.app/profile/kephale.bsky.social/post/3lfrxatxsjk2y It would be great to have some example scripts of using MicroscopyNodes w/ bpy, esp...

Perfect, you've got it!
github.com/oanegros/Mic...

This is beautiful!!! Do you happen to have some scripts for using Microscopy Nodes w/ bpy in python?