Do you work with microscopy images and segment to quantify or track? Do you study cell biology? development? Gather round! Let me tell you about FOCUS-3D, a segmentation algorithm that is fast, accurate and can be used on any model. We used it here to study zebrafish development. 🧪 (thread)

FOCUS‑3D: Robust, generalizable volumetric cell segmentation for three‑dimensional fluorescence microscopy

Understanding how cells establish spatial organization within tissues is a fundamental question in life sciences. While modern three-dimensional fluorescence microscopy captures large-volume tissue ar...

biorxiv.org

is spot detection still a thing ? Obviously, the answer is yes

Francesco Padovani@padovaf.bsky.social · 3w ago

Very happy to see SpotMAX out in Science Advances! 🎉🔬 This has been a long and exciting journey, and I’m really grateful to everyone who contributed along the way. It certainly makes our microscopy analysis easier, so I hope it will make yours too!

Very happy to see SpotMAX out in Science Advances! 🎉🔬 This has been a long and exciting journey, and I’m really grateful to everyone who contributed along the way. It certainly makes our microscopy analysis easier, so I hope it will make yours too!

Epigenetics at Helmholtz Munich@epihmgu.bsky.social · 3w ago

Congratulations to Francesco Padovani, Kurt Schmoller, and colleagues on the publication of SpotMAX in Science Advances! An open-source AI framework making advanced microscopy image analysis easier, faster, and more accessible. #OpenScience #Microscopy www.science.org/doi/10.1126/...

Fantastic collaboration! It's always rewarding to see #Cell-ACDC help enable exciting biological discoveries. Congratulations to all the authors!

KunzLab@LMU@kunzlab.bsky.social · 3mo ago

Great team effort & our 1st #chlamy pub. Thx to many nice colleagues e.g., @jandevries.bsky.social @mackinderlab.bsky.social @lmu.de @padovaf.bsky.social #plantscience #GoPMF Conserved and Lineage-Specific Roles of KEA-Mediated Ion Homeostasis in Chlamydomonas academic.oup.com/plphys/artic...

📯👨‍🚀 Calling all #bioimage analysis aficionados. #EZInput is out! We wanted to bring #ImageJ’s capacity to record settings to the #Python ecosystem 🐍. It is a declarative library for generating UIs that just work. Done with @guijacquemet.bsky.social lab arxiv.org/abs/2601.08859 #ScientificComputing

🚨 Alarm!!! 🚨 AI/ML course for microscopy image analysis!!! 🧐 In 2026 at Janelia (@hhmijanelia.bsky.social), no tuition, housing and meals provided! Isn’t that borderline unbelievable?!? 20 students, ~14 TAs and lecturers 🗓️ June 4-18 2026 ✍️ Jan 15 2026 ✍️ 🔁 pls!! www.janelia.org/you-janelia/...

Deep Learning for Microscopy Image Analysis

Topics The following will be covered extensively during lectures, exercises, and project work: Image denoising and restoration (fully supervised and self-supervised) Image translation (e.g.,

janelia.org

As we wrap up the year, we’re 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. Here’s 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 🙃, 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 👇

Jean-Yves Tinevez@jytinevez.bsky.social · 10mo ago

We just released a new major version of TrackMate (v8), the cell and organelle tracking plugin of Fiji. It ships many new features, detailed below, but that are articulated around the following:

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 🤖

TrackMate Trackastra

Trackastra integration in TrackMate.

imagej.net

Jean-Yves Tinevez@jytinevez.bsky.social · 10mo ago

With an image with a proper background >.<

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...

Single-cell susceptibility to viral infection is driven by variable cell states

Not all cells that can be infected by a virus become infected with that virus. Single-cell clone tracing reveals intrinsic cell states with variable expression patterns that increase susceptibility to...

cell.com

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 :)

Beth Cimini 🔬💻📊@bethcimini.bsky.social · 11mo ago

Big news! Our week-long #bioimageanalysis bootcamp is BACK! Learn how to think about bioimage analysis like the pros do, learn what corrections you should (and shouldn't!) apply to your images, learn open source tools, and more. Apply NOW at broad.io/BAB3 for our January 2026 course!

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...

Alternate proteins from the same gene contribute differently to health and rare disease | Whitehead Institute

Iain Cheeseman and colleagues reveal the underappreciated role of single genes producing multiple proteins in atypical presentations of rare disease, and present case studies of affected patients thro...

wi.mit.edu

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...

BioImaging North America@bioimagingna.bsky.social · 11mo ago

#HappyFluorescenceFriday #microscopycommunity Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events! Submit by Oct 31: buff.ly/lMhK4vz Website: buff.ly/QP36RZB Register for the workshops: buff.ly/8nNAI18

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.

BioImaging North America@bioimagingna.bsky.social · 11mo ago

#HappyFluorescenceFriday #microscopycommunity Got an idea for an image analysis workshop? Share it at Halfway to I2K: Online Tutorials on Image Analysis (Nov 17–19, 2025), held with Zoom Events! Submit by Oct 31: buff.ly/lMhK4vz Website: buff.ly/QP36RZB Register for the workshops: buff.ly/8nNAI18

🔬For 22 years, we have been organizing #Mifobio "Functional Microscopy for Biology" the @cnrs.fr thematic school. 🎓 Courses, Seminars, Round Tables, Workshops. The overall theme concerns #biological_imaging in its most interdisciplinary aspects. 👉 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 🧵...

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 🤩 My workflow will be to autotrace and then manually correct the autotraces, reducing the time for our tracing significantly!

Eugene Katrukha 🇺🇦@ekatrukha.bsky.social · 12mo ago

New release of #BigTrace plugin is out. Together with @aafkegros.bsky.social from Simone Köhler group we added a fully automatic tracing mode. + more macro functions and bug fixes github.com/ekatrukha/Bi...

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.

BioImaging North America@bioimagingna.bsky.social · 12mo ago

#HappyFluorescenceFriday! #microscopycommunity- want to learn open source image analysis or share your knowledge to help others? We’ve got a FREE virtual workshop Nov 17-19! Now accepting workshop session applications! Learn more & sign up: buff.ly/esGIotD

🚀 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 ultra–low-background, single-mRNA imaging in live cells. 🔗 www.nature.com/articles/s41... 🧬 www.addgene.org/John_Ngo/

It’s 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 challenging👩🏻‍💻🔬🧬🦠 #bioimage #microscopy #interdisciplinary

Aafke Gros@aafkegros.bsky.social · 12mo ago

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25

Microscopy Nodes: handling large biological volumes — Blender Conference 2025

YouTube video by Blender

youtu.be

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!

🔬🎤 As pre-announced a few days ago... please let us proudly present to you: 𝑴𝒊𝒄𝒓𝒐𝕊𝒑𝒍𝒊𝒕 - your ticket to imaging more, imaging more gentle, and/or imaging more efficient. 🔬 doi.org/10.1101/2025... Like ❤️, repost 🔂, and most importantly... please send feedback ✉️ our way! 🙏

Florian Jug@florianjug.bsky.social · 2y ago

Immagine you could image two cellular structures in the same fluorescent channel and still reliably get them separated afterwards… What would you do with this? Now… what would you do if that also worked with 4 structures at once? 👇 #MicroSplit #preview🧵

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)

Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression

Nature Methods - Spotiflow uses deep learning for subpixel-accurate spot detection in diverse 2D and 3D images. The improved accuracy offered by Spotiflow enables improved biological insights in...

rdcu.be