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Reposted by Francesco Padovani

GdR ImaBio @gdrimabio.bsky.social · 6d

🔬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 · 8d

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 · 16d

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 · 16d

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...

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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 16d

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 · 20d

#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

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Francesco Padovani @padovaf.bsky.social · 17d

That sounds fantastic, cannot wait to try them out, congratulations!

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John Ngo @johntngo.bsky.social · 17d

🚀 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 · 21d

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 · 21d

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

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Aafke Gros @aafkegros.bsky.social · 21d

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

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Fabian P. Schlottmann @fpschlottmann.bsky.social · Jul 15

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 · Feb 11

🔬🎤 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 · Jun 6

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 · Jun 6

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

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Arjun Raj @arjunraj.bsky.social · May 7

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 · Apr 17

⏳ 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...

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Robert Haase @haesleinhuepf.bsky.social · Apr 10

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 · Apr 6

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 · Apr 4

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...

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...

www.biorxiv.org

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AI4Life @ai4life.bsky.social · Apr 2

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 · Feb 25

🗓️ 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 · Feb 21

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

micro_sam API documentation

computational-cell-analytics.github.io

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Florian Jug @florianjug.bsky.social · Feb 17

‼️🔬 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 · Feb 12

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 · Jan 15

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 · Dec 22

InstanSeg repo: github.com/instanseg/in...
InstanSeg preprint: arxiv.org/abs/2408.15954

If you don't know what #CellACDC is, you can find the source code here: github.com/SchmollerLab... And do not hesitate to contact me with any questions!

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Francesco Padovani @padovaf.bsky.social · Dec 22

🚨 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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