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Francesco Padovani

@padovaf.bsky.social
70 followers 101 following 8 posts

Research Scientist in Cell and Computational Biology at Helmholtz Munich | Creator of Cell-ACDC and SpotMAX | Excited about mitochondrial DNA and AI-driven bioimage analysis | Dad of 2

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Reposted by Francesco Padovani
MwahahahahahadScientist @mads100tist.bsky.social · 29/08/2026
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)
biorxiv.org
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...
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Fabrice Senger @senger.bsky.social · 31/08/2026
is spot detection still a thing ? Obviously, the answer is yes
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Francesco Padovani @padovaf.bsky.social · 31/08/2026
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!
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Francesco Padovani @padovaf.bsky.social · 30/06/2026
Fantastic collaboration! It's always rewarding to see #Cell-ACDC help enable exciting biological discoveries. Congratulations to all the authors!
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Ricardo Henriques @henriqueslab.bsky.social · 15/01/2026
📯👨‍🚀 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
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Florian Jug @florianjug.bsky.social · 28/12/2025
🚨 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/...
janelia.org
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.,
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AI4Life @ai4life.bsky.social · 23/12/2025
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...
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paveltomancak.bsky.social @paveltomancak.bsky.social · 13/12/2025
#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...
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Jean-Yves Tinevez @jytinevez.bsky.social · 10/12/2025
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 👇
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Ben Gallusser @bengallusser.bsky.social · 20/11/2025
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 🤖
imagej.net
TrackMate Trackastra
Trackastra integration in TrackMate.
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 20/11/2025
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!
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Arjun Raj @arjunraj.bsky.social · 14/11/2025
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...
cell.com
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...
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Rita Strack @ritastrack.bsky.social · 13/11/2025
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...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 13/11/2025
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)
A fluorescent embryo on black text, with the words 
Halfway to I2K: Virtual Tutorials on Image Analysis
November 17-19, 2025
Virtual Conference for beginners to developers
i2kconference.org
Image Credit - "Sweet Embryo",Travis D. Carney, BINA Image Contest 2024
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 10/11/2025
Applications close tomorrow - hope to see you in January! If not, stay tuned for future editions :)
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Iain Cheeseman @iaincheeseman.bsky.social · 07/11/2025
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...
wi.mit.edu
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...
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/11/2025
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...)
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 03/11/2025
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...
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 31/10/2025
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.
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GdR ImaBio 🔬 @gdrimabio.bsky.social · 03/10/2025
🔬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
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Kate Cavanaugh @katecavanaugh.bsky.social · 01/10/2025
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 🧵...
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Aafke Gros @aafkegros.bsky.social · 24/09/2025
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!
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 23/09/2025
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.
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John Ngo @johntngo.bsky.social · 22/09/2025
🚀 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/
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Anna Foix @afoix.bsky.social · 19/09/2025
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
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Aafke Gros @aafkegros.bsky.social · 19/09/2025
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender 😋 youtu.be/WPajSWX730o?... #bcon25
youtu.be
Microscopy Nodes: handling large biological volumes — Blender Conference 2025
YouTube video by Blender
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Fabian P. Schlottmann @fpschlottmann.bsky.social · 15/07/2025
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!
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Florian Jug @florianjug.bsky.social · 11/02/2025
🔬🎤 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! 🙏
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Martin Weigert @maweigert.bsky.social · 06/06/2025
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
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Albert Dominguez Mantes @albertdm.bsky.social · 06/06/2025
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)
rdcu.be
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...
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Arjun Raj @arjunraj.bsky.social · 07/05/2025
Wow, just implemented the new Cellpose-SAM from @computingnature.bsky.social in NimbusImage and it's *awesome*! Give it a try! nimbusimage.com
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AI4Life @ai4life.bsky.social · 17/04/2025
⏳ Only 8 days left to register for the AI4Life Community Event in Helsinki! Day 1️⃣: Workshops for life scientists, software devs, AI researchers & image analysts Day 2️⃣: Talks, discussions & networking If that sounds like you, don’t miss it! 👉 ai4life.eurobioimaging.eu/event/ai4lif...
ai4life.eurobioimaging.eu
AI4Life Community Event – AI4Life
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Robert Haase @haesleinhuepf.bsky.social · 10/04/2025
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 🥳 github.com/haesleinhuep...
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Suliana Manley @sulianamanley.bsky.social · 06/04/2025
Our latest preprint www.biorxiv.org/content/10.1..., describes Willi Stepp’s project to make smart microscopy even gentler by doing event detection in phase contrast. We developed neural networks to detect mito-LD and mito-lysosome contacts, as well as mitochondrial pre-fission constrictions.
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Boyan Bonev @boyanbonev.bsky.social · 04/04/2025
Can a stem cell change its epigenome while proliferating? In collaboration with the lab of Amos Tanay, we demonstrate that yes, the epigenome of neural stem cells (NSCs) is continuously remodeled, across multiple layers, during mouse corticogenesis. 1/14 www.biorxiv.org/content/10.1...
biorxiv.org
Neural stem cell epigenomes and fate bias are temporally coordinated during corticogenesis
The cerebral cortex orchestrates complex cognitive functions, yet how its distinct temporal lineages are molecularly patterned during development remains unresolved. Here, we integrate single-cell tra...
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AI4Life @ai4life.bsky.social · 02/04/2025
At the @training.ebi.embl.org course on Microscopy Data Analysis: Machine Learning & @bioimagearchive.bsky.social, Dominik Kutra from @ilastik-team.bsky.social introduced ilastik and how it supports image analysis. Now, it's time for a hands-on session! 🚀 #BioImageAnalysis #MachineLearning
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AI4Life @ai4life.bsky.social · 25/02/2025
🗓️ Join us for the AI4Life Community in Helsinki Event on May 27-28 in Helsinki! Connect with researchers, developers, and industry leaders in bioimage analysis. Secure your spot now! 🔗 ai4life.eurobioimaging.eu/event/ai4lif...
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Constantin Pape @cppape.bsky.social · 21/02/2025
Because we have seen these improvements and due to popular demand, cc @ritastrack.bsky.social @jianxuchen.bsky.social, we have decided to start a call for community data submission to further improve our models: computational-cell-analytics.github.io/micro-sam/mi... . Looking forward to any feedback
computational-cell-analytics.github.io
micro_sam API documentation
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Florian Jug @florianjug.bsky.social · 17/02/2025
‼️🔬 We start!!! 🎉🤖 Super exciting!!! After years of teaching courses for #DeepLearning for Microscopy and Life Science application, we start today our first “advanced course” @embl.org! #EMBLDeepLearning
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Constantin Pape @cppape.bsky.social · 12/02/2025
After a long journey, Segment Anything for Microscopy is now published in Nature Methods! We significantly improve SAM for interactive and automatic segmentation in light and electron microscopy and build a user-friendly tool. www.nature.com/articles/s41...
Improvements in LM (top) and EM (bottom) of our micro-sam model (finetuned) compared to the default SAM model.
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Aafke Gros @aafkegros.bsky.social · 15/01/2025
With Microscopy Nodes, you can play with large volumes (this ExM dataset from Granita Lokaj is 49 GB total) and integrate this with all the cool tools in Blender, such as this #geonodes model of the centriole, made by @banterlegroup.bsky.social !
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Francesco Padovani @padovaf.bsky.social · 22/12/2024
🚨 New segmentation model alert! 🚨🥳 You can finally use InstanSeg in our #BioImageAnalysis software #CellACDC! InstanSeg is a fast and multi-channel cell segmentation model by Pete Bankhead, Thibaut Goldsborough, & co. The multi-channel ability is very interesting!
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German BioImaging @gerbi-gmb.de · 13/12/2024
🚀 We're hiring! Join the German BioImaging Team as a Software Developer! 💻 Build scalable #bioimaging solutions 🌍 Collaborate globally 🎯 Contribute to open science through #OMEZarr @openmicroscopy.org Remote, full-time. Apply by 31 Jan 2025: bit.ly/3Zrd4SR
bit.ly
Software Developer Wanted – Join the German BioImaging Team!
German BioImaging e.V. invites applications by 31. January for a remote position as Software Developer (m/f/d) (100 %, pay grade 13-14 TVöD depending on experience) Are you an enthusiastic open-...
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Biozentrum, University of Basel @biozentrum.unibas.ch · 13/12/2024
Entry-level position (80 - 100%) for bioimage analysis specialist at the Imaging Core Facility (IMCF) of the Biozentrum, University of Basel www.biozentrum.unibas.ch/open-positio... @unibas.ch #Biozentrum #Basel #research #science #joboffer #scientific
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Francesco Padovani @padovaf.bsky.social · 28/11/2024
The recording of the #Virtual #I2K2024 workshop about our #BioImageAnalysis software #CellACDC is now available on YouTube youtu.be/u1cQ2MH5uEQ?... Huge thanks to the organisers, this was a very useful conference!
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BioImaging North America @bioimagingna.bsky.social · 25/11/2024
Happy #MicroscopyMonday! The recordings of the #Virtual #I2K2024 workshops are available now tinyurl.com/VirtualI2K20... Thanks to all who presented! Please re-share! 2022 and 2023 content available too: www.youtube.com/@I2KConference
Virtual I2K Flyer notifying that the Recordings are available on the I2K YouTube channel: https://www.youtube.com/@I2KConference
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