Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets https://www.biorxiv.org/content/10.64898/2025.12.10.693416v1

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:

Some ideas and discussions from our recent Asilomar meeting on the ethics and societal implications of neural organoid and assembloid research www.the-scientist.com/as-neural-or...

Our next #ForceTalk is Prof Yanlan Mao @yanlanmao.bsky.social on "Coping with mechanical stress: tissue dynamics during development, homeostasis and repair" 🗓️ 26 Nov 2025 🕒 15:00 - 16:00 GMT Online & open to all 👉 www.kcl.ac.uk/events/force-talk-yanlan-mao #mechanobiology @kingsnmes.bsky.social

NEXT TUE: DDD seminar, Nov. 18, 2025 @ 1PM Eastern US: Continuing our focus on approaches to the study of many pluripotent stem cell lines, Dr. Michael Wells @mfwells.bsky.social will share his recent work on "cell villages". seminar info: carlocolantuoni.org/seminar [repost to spread the word]

🧠 Join us @uzh-ch.bsky.social ! We are a new lab looking for PhDs, Postdocs & Master’s students interested in studying how human neural systems emerge & go awry using brain organoids, light-sheet imaging & genomics. 🚀 Deadline for LSZGS 1st Nov! www.lifescience-graduateschool.uzh.ch/en.html.

If you’re applying to your dream lab for an internship/PhD/postdoc, always send a second email 1-2 weeks after the first one if you don’t hear back. I promise we will be grateful rather than annoyed. My email inbox is a disaster and I’m quite junior - and very few of us have secretarial support

Our latest preprint! Into morphogenesis, Yap, ECM, signaling, vertex models, feedbacks/robustness? There is something here for everyone. We discovered a positive feedback loop that extends inner ear canals, and a built-in mechanism that shuts it down when morphogenesis is done. tinyurl.com/464wsjhd

Ever wondered how robust cellular identity is to external perturbations? Here we disrupt cellular environmnent in vivo and in vitro, and find cell population specific sensitivities. Environment sculpts development yes, but not all cells are made of the same wood. www.science.org/doi/10.1126/...

This is absolutely a must read. We are in deep trouble and I am even less optimistic than the authors.

Another #preprint: "Elasticity and plasticity of epithelial gap closure", from the #PhD work of Maryam Setoudeh: arxiv.org/abs/2509.05110 This one required a lot of (I think) beautiful #mechanics! @mpipks.bsky.social @mpi-cbg.de @csbdresden.bsky.social

Our work is motivated by Tribolium serosa closure, a particularly simple instance of epithelial gap closure: nature.com/articles/s41467-020-19356-x @akanksha-jain.bsky.social @paveltomancak.bsky.social discovered tissue fluidisation near the gap and inhomogeneities of the contracting cable.

Join us on November 4th! The winners of our best short talk awards will be telling their research on the @isscr.org stage! Thank you @stemcellreports.bsky.social for co-organizing this webinar!

Super excited that our group will be supported by an ERC Starting Grant! In project "InfoFate" we will study how cells use information in dynamical, neighborhood & mechanical signals to make decisions. We'll have PhD and Postdoc positions available, please get in touch if interested!

We are all super happy and proud to see our work on the function and evolution of the #cephalic #furrow published in @nature.com. Let me say a few things about the background and history of this work on the #Evolution_of_Morphogenesis (1/12)

Dresden researchers @paveltomancak.bsky.social @bruvellu.bsky.social, Carl Modes, @cuencam15.bsky.social ‬ & colleagues published in @nature.com that a tissue fold in fruit fly embryos buffers mechanical stresses & may have evolved in response to mechanical forces. www.mpi-cbg.de/news-outreac...

Thrilled to share 🎉 I’m starting my lab at University of Zurich, DMLS as Assistant Professor (tenure track) from Jan 2026! The Neural MorphoGenomics & Developmental Dynamics Lab will be exploring how genes + morphogenesis shape brain development with organoids, imaging & spatial genomics 🧠🔬🧬

Once is an exception, twice is a trend, thrice is a tradition! Save the date for our now-traditional annual OME-NGFF extravaganza in Zurich! Whether you’ve just heard about OME-NGFF and are curious to learn more or if you are working with it every day, there is something for everyone this year!

We're happy to announce the 2025 International OME-NGFF workshop 🎉 📅 Dates: - Symposium: Nov 10–11, 2025 - Hackathon: Nov 12–14, 2025 📍 Location: Zurich, Switzerland Full details & registration: www.biovisioncenter.uzh.ch/en/events/Up...  #bioimaging #openscience #OMENGFF #OMEZarr (1/x 🧵)

🧬🔬🧪 🎉 Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! 📦 Ultrack — robust, scalable nD cell tracking 🌐 inTRACKtive — a beautiful, open-source web viewer for lineage exploration Let’s dive in! 👇 www.nature.com/articles/s41... www.nature.com/articles/s41...

A continued highlight of the year for me, right from the first @embo.org #LISH. Always a fantastic course, impressive student projects, advanced lightsheet imaging for various samples AND data analysis in two weeks. Plus I get to visit my beloved Dresden, with CBG and #LISH veterans. Bis bald!

Out today in @nature.com: Together with the Honigmann, Shevchenko, Drobot and Hof labs, we present a general workflow for imaging the localization and transport of individual lipids in cells and mapping their metabolism. www.nature.com/articles/s41...

Honored to receive the @isrbio.bsky.social Rising Star Award for our work in regeneration biology! Grateful to the committee and our colleagues for the recognition. A huge motivation for the lab. Excited to give the award talk in Madison next week and connect with everyone! 😎🥳🍾 shorturl.at/LnkSt

Day three of #LISH25 beginning with a bang by @akanksha-jain.bsky.social talking about lightsheet-powered understanding of Morphogenesis of #insects (done with me @mpi-cbg.de) and brain #organoids which is also the future of Akanksha’s newly minted independent lab.

Nostalgia and Deja vu! Listening to @maweigert.bsky.social back at the incredible @mpi-cbg.de for @embo.org #LISH2025. Here after six years, the gray auditorium reminds of my thoughts when I sat here for my PhD selection interviews that included him!

We are today kicking off the two-week @embo.org practical course on #Lightsheet # Microscopy at @mpi-cbg.de in #Dresden. This is the fifth iteration of the course. Hashtag #LISH2025 meetings.embo.org/event/25-lsm

Looks like private funders, HHMI,CZI etc., are not going to “save” US research. Europe is setting up mechanisms to attract US researchers & it may work. But, common, target junior talent, don’t shower money on superstars who will be flying professors & return to US when the science winter passes.

🤩 Very excited to share our new work! We have derived euploid and aneuploid trophoblast organoids and extra-embryonic mesoderm cell lines from early human embryos. In doing so, we have characterised the tissue requirements for their specification. If you want to know more, continue reading….

Out now! Our very first [email protected], an impressive feat by @tobyandrews.bsky.social where we show how a developing heart grows and scales up its morphological complexity to keep beating...an excellent summary below ⬇️ www.cell.com/developmenta...

Very happy that the first article from my postdoc work in the Tomancak lab is now published @PNAS! www.pnas.org/doi/10.1073/.... We studied the self-organization of actin in aggregates made from Hydra cells. Thread below (1/9)

To recognise and celebrate @svobodalab.bsky.social's pivotal contribution to Woodstock Bio2 + Night Science, #TCTeAC, I am starting this "What Petr Svoboda did at Woodstock?" thread. If you were there - #contribute and #retweet. "Petr Didn’t Submit an Abstract. #TCTeAC Submitted to Him."

Stretching the immortal Hydra. Publication by @paveltomancak.bsky.social group with Carl Modes @mpi-cbg.de & @zechnerlab.bsky.social shows how cells can create a new organism from scratch by coordinating their mechanical properties. @anaisbailles.bsky.social @pnas.org www.mpi-cbg.de/news-outreac...

A fantastic opportunity! Please repost :) #Lightsheet #Microscopy #BioImage #ImageAnalysis

My postdoc work at Treutlein lab and @graycamplab.bsky.social with @jasperjanssens.bsky.social is out in @science.org ! We screen for neuron subtypes using pro-neural TFs + morphogen combinations + scRNA-seq and profiled over 700,000 cells in 480 conditions. www.science.org/doi/10.1126/...

Congratulations to Dr. @akanksha-jain.bsky.social, Gilles Gut, and the Treutlein Lab and @graycamplab.bsky.social on their work live imaging brain #organoid growth! @nature.com article: go.nature.com/4la2yZh Episode with discussion: bit.ly/4nzLrCp

Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr

Sign up to attend our next Development presents... webinar on early #embryogenesis, featuring talks from @lakshmib02.bsky.social, @dias-andre.bsky.social ‬and @nikhil-mishra.bsky.social 📅Wed 9 July 15:00BST (UTC+1) Register here: us02web.zoom.us/webinar/regi... #DevBio @dev-journal.bsky.social

On cell extrusion in the #intestine! After 80 years of observations, we finally took a deeper look thanks to 2D #organoids. We report: 3D #forces, #extrusion still only in the villus even without curvature, #lamellipodia generate 3D force.. and more. Have a look! www.biorxiv.org/content/10.1...

Hot off the press, our latest review of RNA-lipid interactions -> The secret life of RNA and lipids: "There is no life without RNA or lipids. But could there be life with only RNA and lipids?" @tcjea.bsky.social @bcube-tud.bsky.social be-tud.bsky.social www.tandfonline.com/doi/full/10....

Very happy to share it’s online! If you read the preprint, updates include tracking cells and tissue flow, Histo4i timecourse (69 Abs) comparing spatial patterning emergence and a new WLS KO ipsc line establishing mechanosensing via YAP-WLS/WNT caudalizes organoids www.nature.com/articles/s41...

Muhammad Jalal— "Powerful words from historian William Dalrymple on Gaza, exposing how Britain’s colonial legacy played a key role in creating this injustice. The suffering in Gaza didn’t start yesterday, it was engineered long ago. #Gaza #Palestin🇵🇸" Sorry, had to split video for BlueSky—1/2

OUTTAKES of my figure checklist (www.nature.com/articles/s41...) - many important and good references that explain why we do things the way we do in charts - e.g. why #rainbowcolors were replaced with #viridis. helenajamborwrites.netlify.app/posts/25-7_c... PS outtakes or directors cut?

Join the challenge, get the data, contribute your solution!!! 🎉

Thrilled to announce that our lab is relocating to the Friedrich Miescher Laboratory of the Max Planck Society @mpi-bio-fml.bsky.social in winter 2025. We’ll have open positions— please help us spread the word and stay tuned for more updates! 🐸 🐁 🥳

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 ⏬️

Spotiflow allows training detection models that generalize across imaging conditions w/o manual parameter tuning. Since the preprint we added lots of things, fast inference for large volumes + many use cases. Check it out at github.com/weigertlab/spotiflow . We hope it will be useful for people!

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

See Organoids Organise: Tracking brain organoid development from fluorescent human induced pluripotent stem cells over weeks using live light-sheet microscopy 📹 @akanksha-jain.bsky.social, Gilles Gut et al Treutlein lab @ethz.ch in @natcomms.nature.com ➡️ bpod.org.uk/archive/2025...

You cannot beat us in style, especially when it comes to FOOD and the local Basel favorite hangouts. Yes we booked and an entire giant restaurant and the tournament was very competitive!

⚠️ I am really excited to share the work of Anastasios Balaskas, an excellent PhD candidate in the lab, with the wider world. Tasos made a significant advance: generating a stem cell-based embryo model that contains both posterior and anterior neural tissues of the late-stage gastrulating embryo.