I'm experimenting with reactive notebooks for spatial omics. Introducing the LandmarksWidget: draw regions on tissue and bring points straight back into your Python analysis, no tool‑hopping. Built on anywidget + marimo. What are your #spatialomics analysis pain points?

GitHub - ckmah/spatial-rx: Reactive spatial landmarks for matplotlib and marimo

Reactive spatial landmarks for matplotlib and marimo - ckmah/spatial-rx

github.com

Come check out cool demos with @marimo.io (reactive Python notebooks!) I’ll be doing a small demo at the next community call aug 25 on spatial omics. deets: luma.com/13c69h7x I'm also a new marimo ambassador! do reach out for event collabs in San Diego or Boston👋

marimo Community Call! · Luma

Hear directly from the developers of marimo at our Q3 community call! We'll share out some exciting new updates (hint: marimoHub 👀), as well as introduce you…

luma.com

It's been a minute but I found my way back to a conference; I'll be at AGBT this week representing @stellaromics.bsky.social to lend my experience communicating all things #spatialbio #bioinformatics #techbio #ai ! Looking forward to meeting new folks, please reach out if interested! 🧬🔬

Glad to be part of such an open and collaborative community pushing #SpatialBio forward! Thanks for inviting and hosting us @kevinyamauchi.bsky.social @lucamarconato.bsky.social & Giovanni Palla 🙏 I focused on the intro notebook and improving usability for first time users ⚒️ check it out! ->

scverse@scverse.bsky.social · 2y ago

Recently, we held the first #scverse SpatialData 3-day hackathon in Basel (Switzerland), where we brought together 20 developers from the Python, R, and web communities to work on interoperability, performance, and ergonomics for spatial omics data. Here is what we worked on!

Closing 2024, scverse celebrates growth and collaboration! Huge thanks to everyone on this journey and our core team & board (@fabiantheis.bsky.social, @francescafinotello.bsky.social, @steglelab.bsky.social, Nir Yosef, @panosroussos.bsky.social, @robp.bsky.social). Here's to an inspiring 2025!

Oof, software releases are always so nerve racking 😅 just updated bento-tools.readthedocs.io to v2.1.4 🥳 We now support 1-to-many spatial indexing for mapping cells to multiple organelles/subcellular domains, enabling the modeling of complex spatial relationships! #spatialbiology 🧪🧬🖥️

This looks amazing! Really appreciate the focus on documentation and usability.

Joshua Bull@joshuabull.bsky.social · 2y ago

Very pleased to announce that our package for Multiscale Spatial Analysis - MuSpAn - has landed! The preprint is on biorxiv now, but you can find a lot more details at www.muspan.co.uk, including documentation, worked tutorials (an ever-expanding list), install guides, and how to get the code!

that's a lot of git commits

Interactive Journalism@interactives.bsky.social · 2y ago

New on NBC News : “After years on the rise, ‘All I Want for Christmas Is You’ listenership is slipping”

I'm not in NLP or javascript, but found compromise.cool is a very cool example of "less is more" ❤️ #opensource

Jan Willem Tulp@tulpinteractive.com · 2y ago

Just came across compromise.cool which is a pretty cool and handy #NLP for #javascript. Just sayin'...

Sign of the times, no more bluebird on the biorxiv engagement tab..

Hey science folks 🧪! Trying to stay on top of #SpatialBiology convos, tech, studies, conferences, etc.? Well here's a feed for you! bsky.app/profile/did:...

oof, this was probably inevitable with the status quo. but also eLife's impact factor would simply drop over time to reflect the "lower quality" if it really is the case. seems like a hasty decision by Clarivate. 🧪 www.science.org/content/arti...

Open-access journal elife will lose its ‘impact factor’ over controversial publishing model

Web of Science index decides to strip key metric because elife’s unusual peer review doesn’t meet its criteria

science.org

Restarting a previous discussion on here: How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅 I see them used everywhere, but I don't know of any really good way to validate them... More importantly, I don't know of any *non-simulated* training data.

This is hard to hear. A lot more cuts to Federal science funding are likely in the offing. We need to find new/better/more ways to drive interdisciplinary collaboration and cooperation in science 🧪

Carl Percival@carlpercival.bsky.social · 2y ago

What a horrible day again, 2nd time this year. Slowly finding out which of our colleagues have been let go, we have lost some good people from the Science Division today 🧪😢 💔 www.space.com/nasa-jpl-lay...

Now that more of the spatial community is here, I've put together a feed for #SpatialBiology! Check it out here: bsky.app/profile/did:... Also, if you think it's missing posts, msg me the post and I'll see how I can improve things 🧪🖥️🧬

cue Python vs R 🧪

Marco Trizzino@marcotrizzino.bsky.social · 2y ago

For this to really look like ~2015 Twitter, we need the following: 1) Discussion about postdoc salaries in the US 2) Discussion about how many hours per week should a tenure-track prof work (in the US) 3) Lior fighiting with Manolis 4) Michale Eisen fighting Elsevier

Safety of these individuals is also a concern of mine, as I’ve mentioned on another thread 🥲 But as we expand our own networks with new voices, hopefully we can brainstorm together how to protect everyone from harm 🧠 These online spaces are communities, and we gotta look out for one another 💕

Michelle Franc Ragsac, PhD 🇵🇭🇺🇸@mragsac.com · 2y ago

In addition to the change in ✨ good vibes ✨, I’m also concerned about how starter packs might make individuals (especially minorities) easier to potentially target 🥲 Hopefully there’s a quiet opt-out or “starter pack invitation” feature in the future? 😅

So.. according to this umap, what cell type are you? 🧬🖥️

⏧@syntacrobat.xyz · 2y ago

new map of every account on BlueSky just dropped :) aurora.ndimensional.xyz

Agreed, reminder to myself to be mindful of inclusivity, biases and echo chambers when curating my own feed. 💡Related; I'm putting together a #spatialbiology starter pack, please let me know if you would like to be included!

Catherine Breslin @catherinebreslin.bsky.social · 2y ago

Starter packs are a great way to find people. But I followed a few tech/AI starter packs, and now have a sizeable gender skew in who I'm following. To counteract, I started collecting this list. Who else should I be following & add? 👇 go.bsky.app/LaGDpqg

Feeling blessed to be able to travel for science 😊 Shout-out to #scverse for hosting the SpatialData Workshop in Basel this week!

Genomics, evolution, and more starter pack! Help build community with this starter pack. This list is currently incomplete. Want to be included? Reply and I will remedy that! go.bsky.app/JjvzkWU

Another helpful resource for people to check out is @clearsky.app by @thieflord.dev: clearsky.app 🌐✨ You can use the site to look up who’s blocking a user 🛑, who that user is blocking 🙅🏽‍♀️, any lists the user is a part of 👥, and their message history (if authorized) 🦋!

Michelle Franc Ragsac, PhD 🇵🇭🇺🇸@mragsac.com · 2y ago

Cheers to @mubashariqbal.com for making the @blueskydirectory.com tool and the Starter Pack page! Check it out here: blueskydirectory.com/starter-pack... 🌐 For other #Science 🧪 folx migrating from the other place, this may prove a valuable resource!

Great list of curated individuals in the space! Though I recommend checking out who exactly is included 🧐 you can either "follow all" or follow accounts individually

Stephen Turner@stephenturner.us · 2y ago

I created a genomics+bioinformatics starter pack. If I left you off, *please* reply and I'll add you! go.bsky.app/B5YYBfq

Thanks for all the recent follows, I'm happy to see many familiar faces 😊 I'd like to briefly introduce myself here. I am a #bioinformatics scientist in #SanDiego building methods for #spatialbiology. I love building open source tools for the community and am excited to meet all of you!