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Jain_Akanksha_

@akanksha-jain.bsky.social
633 followers 1.2K following 42 posts

Ass. Prof. Of Neural MorphoGenomics @DMLS, Uni Zurich. •4D tissue morphogenesis •Human organoids •Developmental biology •Evolution of tissue mechanics. Previous @ETH @mpicbg @DBS-TIFR akankshajain2022.github.io/Akanksha…

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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵
doi.org
From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence
Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...
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Thibaut Brunet @thibautbrunet.bsky.social · 02/09/2026
🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️
biorxiv.org
Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals
Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...
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Shayan Shamipour @shamipourshayan.bsky.social · 20/09/2026
Excited to share that our **3D-4i multiplexed imaging method** is now out in @natcomms.nature.com 🎉 🔗 www.nature.com/articles/s41... Huge thanks to the reviewers and editor for their constructive feedback and smooth handling of the work!
nature.com
Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells - Nature Communications
The protein landscapes that underlie multicellular self-organization remain challenging to characterize across intact embryos at high spatial resolution. Here, the authors present 3D-4i, a high-throug...
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Development @dev-journal.bsky.social · 16/09/2026
Pathway to Independence – an interview with Nikhil Mishra In this interview, @nikhil-mishra.bsky.social discusses the evolution of his research interests from subcellular beginnings to whole-organism questions, and the importance of scientific security. doi.org/10.1242/dev....
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Joel Lüthi @joelluethi.bsky.social · 19/08/2026
Join the Open Bioimaging Practices Meetup all about OME-Zarr viewers on Monday, August 24th, 4pm CEST. Learn about ViZarr, napari & VolE & hear user stories on how they handle OME-Zarrs. More info here: www.biovisioncenter.uzh.ch/en/events/Up...
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epithelial mechanics fan club @epimechfc.bsky.social · 20/08/2026
Wu, P. H., Phillip, J. M., Du, W., Forjaz, A., Nair, P. R., & Wirtz, D. (2026). Methods to analyze cell migration data: fundamentals and practical guidelines. Nature methods, 23(1), 43–55. #EpithelialMechanicsReview buff.ly/WtqtEf4
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Cornelia Schwayer @cschwayer.bsky.social · 03/08/2026
I will be opening my research group at the Max Delbrück Center later this year to unravel the principles governing the unique context sensing capacity of the liver www.mdc-berlin.de/schwayer and am looking for enthusiastic PhD applicants.
mdc-berlin.de
Schwayer Lab
The mammalian liver possesses a regenerative capacity that is unmatched by any other organ. Following injury, liver epithelial cells can proliferate or even change their identity, enabling the organ t...
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Yanlan Mao @yanlanmao.bsky.social · 30/07/2026
This epic paper, which has been a heroic 10 year journey for the lead author, Ricardo Barrientos, is finally out in Cell today! Many thanks to all co-authors, especially Billie Meadowcroft and Andela Saric for their beautiful MD simulations www.cell.com/cell/fulltex...
cell.com
Basement membrane turnover controls cell shape
Basement membranes are scaffolds of proteins, like collagen, that give organs shape. During development, basement membranes must adapt to the growing organ. We infer how fast the basement membrane ada...
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paveltomancak.bsky.social @paveltomancak.bsky.social · 03/08/2026
#Twisting embryos and multiple #attachment sites in #Drosophila - now both available as #preprints. Proud of @giuliaserafini.bsky.social & @cuencam15.bsky.social, who worked together & established theory collaborations with @lepuslapis.bsky.social & @carldmodes.bsky.social @mpi-cbg.de at its best
Giulia SerafiniMarina Cuenca
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epithelial mechanics fan club @epimechfc.bsky.social · 26/07/2026
How do tissues safely remove cells? Join me, @marija-matejcic.bsky.social in this perspective on the past, present and future of epithelial cell extrusion 🧵 0/16
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The Daily Britain @thedailybritain.bsky.social · 26/06/2026
Analysis and video: thedailybritain.co.uk/polanski-dal...
thedailybritain.co.uk
Why aren't Britain's colonial history and the Balfour Declaration taught in schools? William Dalrymple joins Zack Polanski to explain
Historian William Dalrymple joins Zack Polanski on Bold Politics to explain how one corporation conquered India, how Britain created the conditions for the Nakba - and why none of it is on the school ...
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Lucibee @lucibee.bsky.social · 30/06/2026
Fantastically interesting podcast - wide-ranging, nuanced, stuffed full of information that I no idea about (and I thought I was reasonably well read in this area). @willdalrymple.bsky.social talks to @zackpolanski.bsky.social #Palestine #India #Lebanon www.youtube.com/watch?v=13zQ...
youtube.com
The British Empire’s Downfall: From India to Palestine | William Dalrymple
YouTube video by Bold Politics with Zack Polanski
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Valentin Dunsing-Eichenauer @handle.invalid · 06/07/2026
Already out for a while as the final version: Our @elife.bsky.social paper presenting an experimental and computational pipeline for whole mount deep imaging and multi-scale analysis of organoid systems: elifesciences.org/articles/107... A great collaboration during my postdoc in Marseille.
elifesciences.org
A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales
The Tapenade pipeline enables single-cell, whole-mount 3D quantification in dense multilayer organoids, linking spatial gene co-expression and nuclear deformation to emerging tissue-scale organization...
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Jason Shepherd @jasonsynaptic.bsky.social · 06/07/2026
The @ibroorg.bsky.social World Congress program committee has finalized a 🔥 keynote and special lecture line up. Stay tuned! In the meantime, symposia submissions are still open. Join us in Cape Town next year for this unique global neuroscience meeting! ibroworldcongress.org/open-calls/c...
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Shayan Shamipour @shamipourshayan.bsky.social · 03/07/2026
🚀Excited to share our latest efforts in bringing highly multiplexed whole-mount imaging to intact multicellular systems! Shield-4i: an integrated platform to study multi-scale information flow in 3D embryos and embryo-like systems. Kudos to @rhornb.bsky.social for this major milestone in the lab!🚀
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Hanh Vu @hanhtkvu.bsky.social · 01/07/2026
Super excited that the first preprint from the lab is out! Led by an amazing student, Gaurav @gvaidya.bsky.social, jointly supervised with @mwdorr.bsky.social.
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Jain_Akanksha_ @akanksha-jain.bsky.social · 12/06/2026
Happy to share our perspective on Mechanobiology across scales! This started as a stimulating discussions at the N4M conference, Camogli 2 years ago and culminated through lots of discussions, edits and co-working!Special thanks to Daniel Müller and his lab for coordinating and driving this work 🍾📣
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Christopher Thomas @ovarylab.bsky.social · 20/04/2026
How does an ovarian follicle remodel in space and time to release an egg? 💥🥚 We have an exciting PhD project combining follicle culture, advanced imaging and quantitative analysis to understand the cellular dynamics of ovulation. 🔬 Co-supervised by me and @guignardlab.bsky.social. Please share! 🌱
An ovarian follicle poised for ovulation, with the oocyte at its centre. Cell membranes are shown in orange and DNA in blue.
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Michalis Averof @michalis-averof.bsky.social · 19/04/2026
These images show live embryos of animals (jellyfish, crustacean, worm, sea urchin, sea squirt, beetle) and one of animals closest single-celled relatives. They were captured taking advantage of fluorescent proteins localised on the outer membrane of cells, allowing us to observe cell outlines. 1/9
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Virginie Uhlmann @virginieuhlmann.bsky.social · 10/03/2026
If you've been wondering what our current obsession with OME-Zarr and lego blocks is about, I have good news for you: the Fractal preprint is out! Thanks to @joelluethi.bsky.social , all co-authors, and the Fractal developers and users community for making this beautiful project a reality ❤️
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Thomas Lecuit @thomaslecuit.bsky.social · 24/11/2025
And here is the link to access the whole pdf. Enjoy! I strongly believe that focusing on information & computation during Development provides an important framework, that encapsulates the genetic, chemistry & mechanics, but focusses on organisation, dynamics & logic. PDF: tinyurl.com/4hn34t8w
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 09/02/2026
1/ 🚀🧪🤖 Big update for #Omega — the LLM-powered autonomous agent for bioimage analysis in @napari.org ! Custom LLM endpoints, layer actions, plugin extensibility, agentic widget maker, modernized UI, & 30+ fixes. Here's what's new in version *2026.2.8.2*:
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Kevin Dean @kevin-dean.bsky.social · 05/02/2026
In @elife.bsky.social: A high-resolution, easy-to-build light-sheet microscope for subcellular imaging doi.org/10.7554/eLif...
doi.org
A high-resolution, easy-to-build light-sheet microscope for subcellular imaging
An accessible light-sheet microscope delivers subcellular-resolution, multicolor volumetric, and live-cell imaging, lowering barriers to state-of-the-art performance.
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Murawala Lab at MDI Bio Lab @murawalalab.bsky.social · 31/01/2026
Checkout this updated preprint-a tour de force and truly globe-spanning collaboration with an exceptional group of scientists.
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Carlo Colantuoni @carlocolantuoni.bsky.social · 23/01/2026
NEXT TUE: DDD seminar, Jan. 27, 2025 @ 1PM Eastern US: Nadezhda Azbukina @nazbukina.bsky.social (from Dr. Barbara Treutlein's group) will speak on "A systematic study of morphogen patterning and its reproducibility in human neural organoids". carlocolantuoni.org/seminar
carlocolantuoni.org
SeminarPage | Carlo Colantuoni
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Biomedical Picture of the Day BPoD @bpodaily.bsky.social · 12/01/2026
Open-source atlas of fruit fly development DynamicAtlas is a high-res framework for morphological studies 📹 M. F. Lefebvre, V. Jain-Sharma, N. Claussen & N. P. Mitchell et al @streichan.bsky.social lab University of California Santa Barbara in @natmethods.nature.com ➡️ bpod.org.uk/archive/2026...
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Jain_Akanksha_ @akanksha-jain.bsky.social · 08/01/2026
📣Registration deadline approaching !📣 Check out @embo.org @biologists.bsky.social workshop "biophysical & molecular mechanisms of animal homeostasis & repair" 6-10th April, with a fantastic lineup of speakers! meetings.embo.org/event/26-hom.... Register/Abstract submission by 10th January.
meetings.embo.org
Interfacing biophysical and molecular mechanisms of animal homeostasis and repair
The control of animal homeostasis and repair has been studied for decades, mostly from a molecular and biochemical perspective. Recent research shows that biophysical factors, such as mechanical forc…
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Brugues Lab @brugueslab.bsky.social · 07/01/2026
Excited to share Alison's @alisonkickuth.bsky.social paper from the lab out in @nature.com this week! We uncovered how a mechanical ratchet mechanism drives cytokinesis in early #zebrafish embryos. Read more in this thread 🧵 and at www.nature.com/articles/s41... 🤩 @poldresden.bsky.social @mpi-cbg.de
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Institute of Science and Technology Austria (ISTA) @istaresearch.bsky.social · 05/01/2026
In @natphys.nature.com, they demonstrated that the zebrafish embryo “reads” and correctly interprets the zygote’s geometry during the initial few minutes of its existence. They discovered ... 📷 C.-P.Heisenberg, N. Mishra, Y. I. Li (from left to right).
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katja heuer @k4tj4.bsky.social · 27/07/2025
1 To predict the behaviour of a primate, would you rather base your guess on a closely related species or one with a similar brain shape? We looked at brains & behaviours of 70 species, you’ll be surprised! 🧵Thread on our new preprint with @r3rt0.bsky.social , doi.org/10.1101/2025...
Brain Surfaces of 70 primate species
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Jain_Akanksha_ @akanksha-jain.bsky.social · 24/12/2025
I am extremely happy to see this work online! Long discussions about which, when and how much of morphogens or combinations result in what neural cell type/brain patterning culminated in this wonderful story, powered by multiplexed single-cell RNAseq. Follow the thread for a concise intro 🎊📣
screens.by
n8n.io - Workflow Automation
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bioRxivpreprint @biorxivpreprint.bsky.social · 13/12/2025
Mastodon: the Command Center for Large-Scale Lineage-Tracing Microscopy Datasets www.biorxiv.org/content/10.64898/20…
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Jean-Yves Tinevez @jytinevez.bsky.social · 20/11/2025
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:
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Sergiu P. Pasca @sergiuppasca.bsky.social · 19/11/2025
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...
the-scientist.com
As Neural Organoid Research Accelerates, Scientists Discuss Ethics
Neuroscience experts convened in Asilomar to talk through guidelines around ethical research on human neural organoids.
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Mechanics of Life Leverhulme Doctoral Scholarship Programme @mechanicsoflife.bsky.social · 18/11/2025
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
Background of DNA strand with logos of King's College London and the Leverhulme Trust and text Coping with mechanical stress: tissue dynamics during development, homeostasis and repair Professor Yanlan Mao University College London Force Talks Mechanics of Life Leverhulme DSP seminar series
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Carlo Colantuoni @carlocolantuoni.bsky.social · 11/11/2025
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]
carlocolantuoni.org
SeminarPage | Carlo Colantuoni
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Jain_Akanksha_ @akanksha-jain.bsky.social · 07/10/2025
🧠 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.
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Gautam Dey @gautamdey.bsky.social · 04/10/2025
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
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Akankshi Munjal @akankshi.bsky.social · 26/09/2025
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
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Denis Jabaudon @djabaudon.bsky.social · 19/09/2025
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/...
science.org
Cell-extrinsic controls over neocortical neuron fate and diversity
Cell-extrinsic cues are key for neocortical cell identity and diversity.
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André Nadler @nadlerlab.bsky.social · 15/09/2025
This is absolutely a must read. We are in deep trouble and I am even less optimistic than the authors.
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Pierre Haas @lepuslapis.bsky.social · 08/09/2025
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
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Pierre Haas @lepuslapis.bsky.social · 08/09/2025
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.
nature.com
Regionalized tissue fluidization is required for epithelial gap closure during insect gastrulation - Nature Communications
The mechanics of embryonic tissue spreading over spherical eggs is not fully understood. Here, the authors show that during gastrulation in the red flour beetle, extraembryonic tissue epiboly is facil...
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BaCell3D @bacell3d.bsky.social · 08/09/2025
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!
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David Brückner @davidbrueckner.bsky.social · 04/09/2025
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!
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paveltomancak.bsky.social @paveltomancak.bsky.social · 04/09/2025
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)
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Max Planck Institute of Molecular Cell Biology and Genetics @mpi-cbg.de · 03/09/2025
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...
mpi-cbg.de
Mechanical forces drive evolutionary change
A small tissue fold present in fruit fly embryos buffers mechanical stresses and may have evolved in response to mechanical forces.
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Jain_Akanksha_ @akanksha-jain.bsky.social · 03/09/2025
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 🧠🔬🧬
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Virginie Uhlmann @virginieuhlmann.bsky.social · 25/08/2025
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!
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Joel Lüthi @joelluethi.bsky.social · 25/08/2025
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 🧵)
Visual of segmented human induced pluripotent stem cells with the key workshop dates: Symposium on November 10-11, Hackathon on November 12-14th in Zurich Switzerland
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