jwpylvanainen.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

4th day on the go for #neubiaspasteur2025 with a @biapyx.bsky.social practical course by @jwpylvanainen.bsky.social and a #cellpose #dask and RNA2Seg (doi.org/10.1101/2025...) course with @gaellel.bsky.social and Alice Blondel

submitted 30 days ago • 1 comment

Kick-starting the #neubiaspasteur2025 #BioImageAnalysis courses at @pasteur.fr and @pasteuredu.bsky.social

submitted 32 days ago • 1 comment

Just arrived to Institute Pasteur in Paris for Neubias Image analysis course. Todays opening talk about the future of bioimage analysis by @florianjug.bsky.social - very cool week ahead! #neubiaspasteur2025

submitted 32 days ago • 3 comments

Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching. A collaboration with @mh123.bsky.social 🚀 github.com/danionella/w...

submitted 33 days ago • 7 comments

🌍 GloBIAS is now open for members! Join our global community of scientists, developers & microscopists advancing BioImage Analysis. Let’s build tools, share knowledge & shape the field together. 🔗 More information: tinyurl.com/mtvjadex #BioImageAnalysis #GloBIAS #OpenScience

submitted 46 days ago • 0 comments

Second round of hashtag#GloBIAS Free Help (previously Call4Help) is happening in May. You can register for the sessions on our webpage: www.globias.org/activities/g... Registration deadline is 7. May 2025.

submitted 47 days ago • 2 comments

Joanna Pylvänäinen @jwpylvanainen.bsky.social Hanna Grobe and Guillaume Jacquemet @guijacquemet.bsky.social present their practical guidelines for data exploration in quantitative cell biology. journals.biologists.com/jcs/article/... #OpenAccess

submitted 61 days ago • 1 comment

Delighted to announce that @erinweisbart.bsky.social and I have teamed up to create a new bioimage analysis video podcast called Ask Erin/Dear Beth - you can check it out at the link below! It will highlight common challenges in #bioimageanalysis, as well as our favorite solutions to them. (1/x)

submitted 68 days ago • 1 comment

We wrote an opinion with simple, practical advice for building data exploration workflows in quantitative cell biology with @guijacquemet.bsky.social and @hanna09.bsky.social . I hope you find it useful!

submitted 67 days ago • 0 comments

Repost appreciated: Open #PhDposition in structural virology in my group! Join us in Umeå, 🇸🇪 to uncover how arboviruses remodel the cellular interior. In situ #cryoET combined with #virology, #cellbiology, and #biophysics. Deadline 4 May. More info: www.carlsonlab.se/join/

submitted 71 days ago • 1 comment

Jamie Hyneman's lecture on creative problem solving & climate innovation was packed, so we found a cozy spot in the streaming room to watch live with @ivanhcenalmor. @aboakademi.bsky.social

submitted 74 days ago • 1 comment

In their Essay, @jwpylvanainen.bsky.social, @guijacquemet.bsky.social and @lankylaste.bsky.social outline their practical recommendation for developing image analysis software for life science applications. journals.biologists.com/jcs/article/...

submitted 86 days ago • 0 comments

Excellent set of guidelines for anyone developing software for life scientists, from @jwpylvanainen.bsky.social, @lankylaste.bsky.social and @guijacquemet.bsky.social journals.biologists.com/jcs/article/...

submitted 87 days ago • 1 comment

Awesome to have @henriqueslab.bsky.social join us as a visiting professor!!!

submitted 89 days ago • 0 comments

Check this one out! This is a great read (I am bias). But Joanna and Stefania did an amazing job putting the article together.

submitted 89 days ago • 0 comments

And it’s out! Thanks to @bethcimini.bsky.social and all the participants in the @biologists.bsky.social “Effectively Communicating BioImage Analysis” workshop last year for the fruitful discussions that started the idea behind this paper. Get reading and let us know what you think!

submitted 89 days ago • 0 comments

Fresh from the press! @lankylaste.bsky.social, @guijacquemet.bsky.social and I put together a practical guide on how to develop software for life science applications.

submitted 89 days ago • 1 comment

Yet another throwback to my thesis work—digging into year-old data. For once, past me did future me a favor: everything nicely documented in one place! 💪🏻

submitted 129 days ago • 0 comments

To publish or not to publish? And where to publish? Hopefully @guijacquemet.bsky.social can answer some of these questions in his presentation today. @aboakademi.bsky.social

submitted 130 days ago • 1 comment

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 ⏬️

submitted 135 days ago • 3 comments

2025 is now well underway and we are happy to announce that ZIDAS is coming to Basel this year ! 2025.zidas.org

submitted 151 days ago • 1 comment

Great talks and hands-on sessions at @v4sdb.bsky.social's Winter School 2025 in beautiful Budapest! 🤗 Yesterday, @jekely.biologists.social.ap.brid.gy and @jwpylvanainen.bsky.social guided us through CATMAID, TrackMate, and CellTracksColab. 🧫 More imaging data analysis and programming ahead! 🧑‍💻

submitted 135 days ago • 0 comments

I put together a small guide on how to get started with Fiji. Please distribute to anyone who might benefit form this! zenodo.org/records/1477... #imageanalysis #fiji #imagej #training

submitted 135 days ago • 5 comments

Call 4 Help Pilot Event by GloBIAS, 22 Jan–5 Feb 2025! Offering life scientists a chance for hands-on guidance & support for #bioimage_analysis using Napari, Ilastik & CellProfiler. 💡 Details: www.globias.org/activities/c... 🔗 Sign up! Application until Friday 17 Jan: forms.gle/7hsJgramrFXB...

submitted 152 days ago • 0 comments

Yesterday we celebrated the lab's 5th anniversary (a few months late) and welcomed our new lab members 🎉🎉

submitted 155 days ago • 0 comments

From the Henriques lab comes NanoPyx, which optimizes bioimage analysis by dynamically selecting code variations based on input data and hardware to ensures maximum computational efficiency. www.nature.com/articles/s41...

submitted 162 days ago • 0 comments

Synchronized filopodial formation for #FluorescenceFriday 💥 #CellBiology #Microscopy @vucellimaging.bsky.social

submitted 182 days ago • 3 comments

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

submitted 180 days ago • 18 comments

Microscope image drifting is an everyday headache in my job. Why not try to find some beauty in it?! Also, it would be nice if microscopes were made stable 😜 #fluorescenceFriday

submitted 183 days ago • 0 comments

Sometimes, a simple message can inspire the development of a new custom image analysis tool. 🌟 Since our xCELLigence doesn't support standalone image analysis, we built one tailored to the research needs of @ivaskalab.bsky.social. github.com/CellMigratio... #Collaboration

submitted 183 days ago • 2 comments