π―π¨βπ Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJβs capacity to record settings to the #Python ecosystem π. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab
arxiv.org/abs/2601.08859 #ScientificComputing
π¨ Alarm!!! π¨
AI/ML course for microscopy image analysis!!! π§
In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isnβt that borderline unbelievable?!?
20 students, ~14 TAs and lecturers
ποΈ June 4-18 2026
βοΈ Jan 15 2026 βοΈ
π pls!!
www.janelia.org/you-janelia/...
As we wrap up the year, weβre reflecting on what AI4Life delivered and what continues beyond the project.
AI4Life concluded in August 2025, but its outcomes remain central to FAIR, accessible AI-powered bioimage analysis.
Hereβs where to start:
www.eurobioimaging.eu/news/ai4life...
#Mastodon, the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets, is finally heading for publication (well, let's see). To #cite or not to cite shall no longer be the question π, because the #preprint. Software is available in every #Fiji near you.
www.biorxiv.org/content/10.6...
The new version of TrackMate, the v8.1 has just been released. It builds upon the recent v8, linked below, and offers two main improvements π
Trackastra is part of the brand-new TrackMate v8.
It is the first deep-learning-based ("AI") drop-in replacement for TrackMate's regular LAP-Track algorithm.
Tracks out of the box for many types of datasets (bacteria, fluorescent nuclei, phase contrast cell culture etc), zero parameters to tune π€
MASSIVE thank you to everyone involved in this year's I2K meeting - 32 SUPER sessions from our volunteer presenters, and so many super-engaged participants.
HUGE shoutout to Aditi from @bioimagingna.bsky.social for being the organizational wizard!
See you in the recordings and at next year's!
So awesome to have this great paper from Sam Reffsin and Sara Cherry out! In it, we use retrospective clone tracing to show that there are particular single cell states that are more susceptible to viral infection (both SARS-CoV-2 and flu)!
www.cell.com/cell/fulltex...
I won't talk about NMeth @natmethods.nature.com forever (probably), but I do want to brag a bit about the November focus issue on cell segmentation and tracking, which is many ways is my last hurrah (and final editorial) for the journal. I am so proud of these papers!! www.nature.com/nmeth/volume...
Just 4 days until the start of I2K and its 33 totally free image analysis tutorials and events! Please share with your "home networks", especially early career researchers - the videos will be amazing and high-impact no matter how many people attend live, BUT (1/x)
Applications close tomorrow - hope to see you in January! If not, stay tuned for future editions :)
From an accidental discovery of hidden biology to a new framework to understanding and diagnosing rare disease. Thrilled to share the most recent work from our lab and the amazing Jimmy Ly.
wi.mit.edu/news/alterna...
Seeing our good old AURA-Net from 2021 (doi.org/10.1109/ISBI...) end up 2nd on a 2025 U-Net variants leaderboard was not on my bingo card for this year, but here we are
(source: doi.org/10.48550/arX...)
Do you want to learn more about 25+ bioimage analysis tools, 100% for free? Sign up to attend Halfway to I2K today! tinyurl.com/Halfway-to-I...
Wishing you'd submitted a tool or workshop but missed the deadline? GREAT NEWS, we just extended one week! Submit by Friday - airtable.com/app2zpB8d82r...
Registration for Halfway to I2K is now OPEN! And workshop submission is still too (for a bit)! Join 20+ presenters and counting, and hundreds of attendees in learning about image analysis, whether you're a complete beginner or a total pro.
π¬For 22 years, we have been organizing #Mifobio "Functional Microscopy for Biology" the @cnrs.fr thematic school.
π Courses, Seminars, Round Tables, Workshops. The overall theme concerns #biological_imaging in its most interdisciplinary aspects.
π Program: imabio-cnrs.fr
#GDRImaBio #Mifobio2025
See this? This = implanting mouse embryo. Usually this happens inside its mother and is invisible to us, but we can actually watch implantation ex vivo with the hope of understanding why implantation goes awry in embryos of older women. A π§΅...
Automatic filament tracing in 3D data is now only a few clicks (or one macro) away! In the amazing #BigTrace FIJI plugin by @ekatrukha.bsky.social π€©
My workflow will be to autotrace and then manually correct the autotraces, reducing the time for our tracing significantly!
Halfway to I2K is BACK, friends of all kinds! Last year, 650 people attended 30+ TOTALLY FREE image analysis workshops of all kinds, across many timezones.
If you make image analysis software and want to teach it, workshop submissions are open now! We'd love to have your tool highlighted.
That sounds fantastic, cannot wait to try them out, congratulations!
π Our new paper is out @natmethods.nature.com!
Kuffer & Marzilli engineered conditionally stable MS2 & PP7 coat proteins (dMCP & dPCP) that degrade unless bound to RNA, enabling ultraβlow-background, single-mRNA imaging in live cells.
π www.nature.com/articles/s41...
𧬠www.addgene.org/John_Ngo/
Itβs crucial that the bioimage community joins spaces long dominated by computer vision/CS to highlight challenges in microscopy data and how we tackle them. Brilliant talk from @aafkegros.bsky.social showing how biology is both exciting and challengingπ©π»βπ»π¬π§¬π¦ #bioimage #microscopy #interdisciplinary
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender π youtu.be/WPajSWX730o?... #bcon25
No second chance for a first post - so I made it count:
Finished my PhD on glucose signaling in yeast's G2 phase.
Thanks to the whole Ewald lab and our fantastic collaborators!
π¬π€ As pre-announced a few days ago... please let us proudly present to you: π΄πππππππππ - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. π¬
doi.org/10.1101/2025...
Like β€οΈ, repost π, and most importantly... please send feedback βοΈ our way! π
Out today in @natmethods.nature.com : Spotiflow, our transcript localization method for imaging-based spatial transcriptomics. Led by amazing PhD student @albertdm.bsky.social, joint work w @gioelelamanno.bsky.social at EPFL / @scadsai.bsky.social
www.nature.com/articles/s41...
rdcu.be/epIB7
Spotiflow, our deep learning based spot detection method for microscopy, is now published in @natmethods.nature.com!
Since the pre-print, we have added many features, notably native 3D detection!
@maweigert.bsky.social @gioelelamanno.bsky.social @epfl-brainmind.bsky.social
Paper: rdcu.be/epIB7
(1/N)
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try!
nimbusimage.com
β³ Only 8 days left to register for the AI4Life Community Event in Helsinki!
Day 1οΈβ£: Workshops for life scientists, software devs, AI researchers & image analysts
Day 2οΈβ£: Talks, discussions & networking
If that sounds like you, donβt miss it!
π ai4life.eurobioimaging.eu/event/ai4lif...
During the workshop earlier this week we discussed how important it is to inspect histograms of image regions in some projects. Thus, here comes stackview.histogram() - new in stackview 0.15.0 π₯³
github.com/haesleinhuep...
