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Marvin Albert

@m-albert.bsky.social
547 followers 373 following 5 posts

Image Analysis and Data Management at the Department of Biosystems Science and Engineering of ETH Zürich in Basel

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Reposted by Marvin Albert
Daniel Krentzel @danielkrentzel.bsky.social · 28/09/2026
And here's a nice résumé of our @natcomms.nature.com paper for the grand public 👇 📃 www.nature.com/articles/s41...
nature.com
Deep learning recognises antibiotic modes of action from brightfield images - Nature Communications
Authors present a deep learning model that recognises antibiotic modes of action (MoA) directly from brightfield images. Their proposed method complements traditional growth inhibition assays in the s...
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napari @napari.org · 26/09/2026
🚀 napari is hiring Remote Developers-in-Residence! Join us to build the future of interactive n-dimensional data visualization in Python. 💻 60% Dev / 20% Maintenance / 20% Community & Outreach ⏱️ Contract, 14–35 hrs/wk 🌍 Global 100% Remote Learn more and apply today: napari.org/island-dispa...
napari.org
We’re hiring Developers-in-Residence! — napari blog documentation
Organization: napari (a NumFOCUS Sponsored Project) Position Type: Independent contractor agreement. Global, 100% Remote. Duration: One year, possibility to extend. Commitment: 0.4 to 1.0 FTE…
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Estibaliz Gómez de Mariscal, PhD @gomez-mariscal.bsky.social · 25/09/2026
🚨I have open PhD positions in my new lab at #NIMSB🚀!! Deadline Oct-16 nimsb.unl.pt/join-us/ 🌟I'm looking for motivated candidates who are eager to join a highly multidisciplinary team and study the intracellular dynamics of cancer cell migration using advanced computational methods and microscopy👾
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Josh Moore @joshmoore.bsky.social · 25/09/2026
ICYMI: OME-Zarr 0.6 is out! 🎉 This is big, years in the making. @bogovicj.bsky.social & @jo-soltwedel.bsky.social perseverance brought transformations into this next major step on the road to OME-Zarr 1.0. 👏👏👏 Huge congratulations to the Johns — and to everyone who helped get us here! 🥳🙌
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Johannes Soltwedel @jo-soltwedel.bsky.social · 23/09/2026
🚨New release: NGFF specification 0.6 🚨 Last week, we formally released the latest version of the NGFF specification: 0️⃣.6️⃣( ngff.openmicroscopy.org/specificatio...) Let's take a small tour through the things possible with #ome-zarr 0.6 now that this is out! 👇
ngff.openmicroscopy.org
Version 0.6 — NGFF documentation
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FMI science @fmiscience.bsky.social · 16/09/2026
We’re hiring! The FMI Computational Biology Facility is seeking a Computational Biologist with experience in proteomics data analysis. Join a collaborative team working with scientists across the FMI to turn complex datasets into biological insight. Apply by Oct 25: www.fmi.ch/education-ca...
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Hans-Rudolf Hotz @hrhotz.bsky.social · 16/09/2026
we have an opening in our group at @fmiscience.bsky.social - contact @mbstadler.bsky.social or me to get more details: www.fmi.ch/education-ca...
fmi.ch
Friedrich Miescher Institute, open position
Friedrich Miescher Institute, open position
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Tanja Stadler @tanjastadler.bsky.social · 15/09/2026
🚀 Interested in joining our Computational Evolution group at ETH Zürich in Basel @bsse.ethz.ch as a Postdoc? We will be hosting ETH AI Center's Postdoc Fellows on AI x evolution, AI x single cell biology as well as AI x public health. Apply now 👉 ai.ethz.ch/apply Deadline: Oct 27, 2026
ai.ethz.ch
Fellowship Programs
The application portal for the ETH AI Center Fellowship Programs is now closed. The deadline for submitting reference letters is 23:59 CET on November 14, 2025.
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Image Cooperative @image.coop · 09/09/2026
OME-Zarr Office Hours in <24h! Ask anything about OME-Zarr, and/or join Draga Doncila Pop and @kevinyamauchi.bsky.social working on oztest, which generates test cases for ome-zarr libraries. Thu Sep 10 @ 9am Paris / 5pm Melbourne github.com/German-BioIm... ngff.openmicroscopy.org/community/#o...
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Gaëlle Letort @gaellel.bsky.social · 03/09/2026
The final version of the paper presenting our tool EpiCure is now online: journals.biologists.com/dev/article/... !! Thanks again to all collaborators in this project
journals.biologists.com
EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation
Summary: EpiCure is a napari plugin designed to optimise epithelia segmentation and tracking curation through automatic errors detection and ergonomic correction while being easily interoperable with ...
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Pedro Escoll @pescoll.bsky.social · 04/09/2026
New preprint in the lab! "Single-cell metabolomics reveals infection-specific metabolic reprogramming of human macrophages". Led by Paula Martínez, with @cbuch.bsky.social , Sandrine Aros and @jytinevez.bsky.social How does Legionella pneumophila reshape host metabolism at the single-cell scale? 🧵👇
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Maite Freire @maitefreired.bsky.social · 03/09/2026
Nothing goes to waste in a choano♻️
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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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Juan Nunez-Iglesias @jni.fosstodon.org.ap.brid.gy · 02/09/2026
Job alert! This would be right up my alley which means it might be up *your* alley if you follow me: Software Engineer (Data Specialist) at the Australian National University's Centre for Advanced Microscopy: au.seek.com/job/94226839 #GetFediHired
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Marco Dalla Vecchia @marcodv.bsky.social · 27/08/2026
Interested in image analysis and a service role in a dynamic and growing facility? Come and joy our image analysis team! Feel free to reach out for any questions or doubts. ista.ac.at/en/job/?titl...
ista.ac.at
Job details
Job details
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Ben Barad @baradlab.com · 08/07/2026
My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...
Screenshot of MorphometricsX rendering mitochondrial membrane surfaces in chimera with color-by-quantification.
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Johannes Soltwedel @jo-soltwedel.bsky.social · 23/07/2026
Not going to be in Cracow for the big event so had to make do with a small impromptu @napari.org x @openmicroscopy.org #omezarr Hackathon in Bern 🔬🇨🇭 @m-albert.bsky.social @guiwitz.bsky.social
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FMI science @fmiscience.bsky.social · 13/07/2026
📢 We’re hiring a Cloud Platform Engineer to drive FMI’s transition to a modern hybrid cloud architecture. Help build the infrastructure supporting 20 research groups, advanced technology platforms and large-scale biomedical data analysis. Apply by August 31 at www.fmi.ch/education-ca...
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Levayer Lab @levayerr.bsky.social · 06/07/2026
After a quite long process, we are happy to share the last version of our article describing unexpected results regarding the coupling between local cell death and proliferation (heroic revision effort from @ralitzastaneva.bsky.social ) urldefense.com/v3/__https:/...
urldefense.com
A global response contributes to tissue size robustness upon local induction of apoptosis
Tissue resilience requires tight coupling between cell proliferation, growth, and death.1,2,3,4It is assumed to be based on compensatory proliferation…
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Image Cooperative @image.coop · 01/07/2026
Earlier in June, we had our first in-person meeting at @embl.org (thank you for hosting us!), joined by representatives from Glencoe, Fideus Labs, @gerbi-gmb.de, and @scalableminds.com (+Dundee & Janelia on zoom) to start our OME-Zarr 1.0 project. More details to come, but it was fun and productive!
OME-Zarr collaborators having lunch together at the EMBL cafeteriaOME-Zarr working group discussing in a meeting roomJuan talking about Image Cooperative at an EMBL seminar roomhackathon participants having dinner in Heidelberg
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Johannes Soltwedel @jo-soltwedel.bsky.social · 25/06/2026
Just the occasional this-thing-is-really-easy-in-ome-zarr-0.6 kind of post: Stitching in napari @napari.org with napari-stitcher (@m-albert.bsky.social) and napari-ome-zarr (@will-j-moore.bsky.social) (WIP) : (Sample data from the awesome big-stitcher tool github.com/JaneliaSciCo...)
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Jean-Yves Tinevez @jytinevez.bsky.social · 27/05/2026
The paper is now published in Current Protocols!! 🎉🥳 currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1... Some personal story below 👇 , and technical details in the linked post that featured the preprint 👉
currentprotocols.onlinelibrary.wiley.com
Automated Optimization of Bacterial Tracking Pipelines With TrackMate 8
Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, ...
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Simon F. Nørrelykke @simonfn.bsky.social · 06/05/2026
The SwissBIAS Annual Meeting is taking place on June 3rd in Bern. Registration deadline: Friday, May 15th, so make sure to secure your spot now! We look forward to seeing you all there for a fantastic day of science, networking, and inspiration. @swissbias.bsky.social tinyurl.com/SwissBIAS2026
eventbrite.com
SwissBIAS annual meeting 2026
It is the time of the year to make veterans meet new members, discuss to foster feedback on existing activities and promote new initiatives.
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John Bogovic @bogovicj.bsky.social · 30/04/2026
@davisvbennett.bsky.social gave a great talk on the present and future of #zarr, including extending the core github.com/zarr-develop... and #metadata.
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Tiago Lubiana @tiagolubiana.bsky.social · 28/04/2026
now Aastha Mathur presenting on all the interoperability brought by @gideproject.bsky.social #OME2026
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Talley Lambert @talley.codes · 06/02/2026
One of the funniest conversations I've ever had with Claude... stick with it through the third image to watch it slowly realize it's broken, try to "play it cool", fail spectacularly, then attempt self-aware commentary and immediately faceplant again. it's worth it, I promise.
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Johannes Soltwedel @jo-soltwedel.bsky.social · 28/04/2026
🚨ngff-spec release candidate out🚨 Just out: ngff specification version 0.6.dev4 (github.com/ome/ngff-spe...), which will be the last dev version (!) and mark the beginning of the 🚧spec-phase🚧 (see also forum.image.sc/t/ngff-weekl...) This means: let's develop some implementations 👷‍♀️👷‍♂️ #OME2026 👋
github.com
Release 0.6.dev4 · ome/ngff-spec
What's Changed fix: avoid non-unicode characters (dev) by @jo-mueller in #121 specification: Tie down possible output for coordinate transformation… by @jo-mueller in #109 Improve readability of m...
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Damian Dalle Nogare @damiandn.bsky.social · 28/04/2026
Roughly two weeks (until May 15th) left to apply and join our team! Bioimage Analyst: careers.humantechnopole.it/job/Bioimage... Rsearch Software Engineer: careers.humantechnopole.it/job/Research...
careers.humantechnopole.it
Fondazione Human Technopole - Viale Rita Levi-Montalcini, 1 - Area MIND - 20157 Milano Italy - C.F. 97821360159 - PEC: htechnopole@pec.fondazioneht.it
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NFDI4BIOIMAGE @nfdi4bioimage.bsky.social · 28/04/2026
Day 1 at #OME2026 is coming to an end with stimulating discussions during the poster session. It's been a wonderful first conference day. Looking forward to tomorrow with highlights including workshops and our keynote speaker Carole Goble. Stay tuned.
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Stefan Terjung @stefanterjung.bsky.social · 14/04/2026
We are looking for an experienced light microscopy specialist, motivated to support our users in the Advanced Light Microscopy Facility at EMBL Heidelberg. embl.wd103.myworkdayjobs.com/en-US/EMBL/j... -closing date 11 May 2026 @eurobioimaging.bsky.social @globalbioimaging.bsky.social
embl.wd103.myworkdayjobs.com
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Jean-Yves Tinevez @jytinevez.bsky.social · 16/02/2026
Another banger from Talley
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Talley Lambert @talley.codes · 16/02/2026
Rewrote my Python bioformats wrapper (from aicsimageio/bioio) as a standalone package: - fully bootstrapped Java setup (just pip install) - lazy, repeatably-indexable Array object - fully spec-compliant OME-Zarr group obj. - xarray/dask exports github.com/imaging-form... v0.0.rc1 on PyPI
github.com
GitHub - imaging-formats/bffile: Modern Bio-Formats wrapper with clean lazy Python API
Modern Bio-Formats wrapper with clean lazy Python API - imaging-formats/bffile
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Joel Lüthi @joelluethi.bsky.social · 26/03/2026
🔬 Next Open Bioimaging Practices Meetup (OBPM) – Mar 31, 16:00 CET Hybrid: FMI Basel & Zoom Talk by @jo-soltwedel.bsky.social : Transforming OME-Zarr: What’s coming in v0.6 Plus short updates from the BVC & time for discussion www.biovisioncenter.uzh.ch/en/events/Up...
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup: March 2026
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Florian Jug @florianjug.bsky.social · 30/03/2026
🚨Job Alert -- again!🚨 You are into disease risk prediction based on images or other data modalities? This is for you! 🫵 careers.humantechnopole.it/job/Postdoc-... Part of our Scientific AI Flagship @humantechnopole.bsky.social and part of our mission to benefit society via biomedical #AI solutions.
careers.humantechnopole.it
Postdoc on Multimodal AI for Disease Risk Prediction
Postdoc on Multimodal AI for Disease Risk Prediction
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eurobioimaging.bsky.social @eurobioimaging.bsky.social · 30/03/2026
🙌 Programme's out for the Image Data Community Days! Check out the amazing plenary sessions & workshops during our 5-day long online event! There's something for everyone - don't miss out. Registration is FREE & open to all⤵️ www.eurobioimaging.eu/events/image...
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napari @napari.fosstodon.org.ap.brid.gy · 24/03/2026
napari 0.7.0 is available now! 🚀🎉 It's a BIG release so read the full release notes, with highlights: napari.org/stable/release/release_0… We want to thank everyone who has worked incredibly hard on this release including our 11 new brilliant […] [Original post on fosstodon.org]
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Levayer Lab @levayerr.bsky.social · 27/03/2026
Happy to share the heroic effort of @gaellel.bsky.social to reduce our segmentation pain through EpiCure (Epithelial Curation), a napari plugin easing the curation of epithelial segmentation developed with several groups of @devstempasteur.bsky.social. www.biorxiv.org/content/10.6... See more 👇
biorxiv.org
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Gaëlle Letort @gaellel.bsky.social · 27/03/2026
I'm happy to present our new tool, EpiCure, a napari plugin to ease correction of segmentation and tracking of epithelia movies, developed in @devstempasteur.bsky.social
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Thibaut Brunet @thibautbrunet.bsky.social · 27/03/2026
Interesting study in @science.org: asking chatbots for advice in social interactions decreases prosocial behavior: www.science.org/doi/10.1126/... (basically, chatbots will always affirm your reactions in social situations; on the long run, this makes you more selfish and self-righteous)
science.org
Sycophantic AI decreases prosocial intentions and promotes dependence
Despite rising concerns about sycophancy—excessive agreement or flattery from artificial intelligence (AI) systems—little is known about its prevalence or consequences. We show that sycophancy is wide...
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Florian Jug @florianjug.bsky.social · 25/03/2026
🚨 We are hiring! Personally, I think this is a fantastic job, good salary, and fun work place with exceptional colleagues. ⚠️ Warning, I’m quite biased… but still right! 😜 Join us! Apply!!! 🎉 careers.humantechnopole.it/job/AI-Exper...
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Johannes Soltwedel @jo-soltwedel.bsky.social · 09/01/2026
🚨Gearing up for #NGFF 0.6! 🚨 Help us give this a final push over the finish line and join us in ironing out the last flaws on the way! More information here 👇 forum.image.sc/t/ngff-weekl...
forum.image.sc
NGFF weekly dev update thread
🏁 Sprint to 0.6 🏁 Dear NGFF-community, it's been some time since the last release of a mjor version of the NGFF-specification. Since then, many of you engaged with the community which resulted in a lo...
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napari @napari.org · 10/03/2026
napari needs your help! Has napari helped you make cool and groundbreaking discoveries? We'd love to highlight that in our docs. Please tell us about it! You can fill in this survey: napari.typeform.com/to/vTCKeTKv and/or, as ever, drop by our chat room or meetings: napari.org/dev/community/ 🙏
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Lucien Hinderling @lhinderling.bsky.social · 16/03/2026
Recording of talk for the french bioimaging network RTmfm. My PhD work in @olivierpertz.bsky.social lab (closed-loop optogenetics, microfabrication, image analysis w/ Convpaint). On smart microscopes: the issue of interoperability and some preliminary results on LLM control :) youtu.be/Gvaw2kWsVIk
youtu.be
Smart microscopy for automation of optogenetic targeting
YouTube video by miti rtmfm
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Image Cooperative @image.coop · 16/03/2026
Hello, world! We are starting a worker cooperative to build, maintain, teach, and support open source scientific imaging software. image.coop/blog/posts/2...
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D-BSSE, ETH Zurich @bsse.ethz.ch · 16/03/2026
#JobAlert 🚨 at D-BSSE: Great opportunity for a Research Data Management expert to run our new facility in #Basel and build a forward-looking infrastructure for excellent research 👇🏽 > jobs.ethz.ch/job/view/JOP... Thanks for sharing!
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Virginie Uhlmann @virginieuhlmann.bsky.social · 15/03/2026
Check out @cfusterbarcelo.bsky.social's latest cool work! Domain shift, we are watching you 👀👀👀
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Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 15/03/2026
Are FMs actually FMing? ⛓️🔬 Thrilled to share that our paper on Foundational Models for mitochondria segmentation in EM is heading to the @iclr-conf.bsky.social 2026 LMRL Workshop! 🚀 Check out the full work here: 📄 ArXiv: arxiv.org/abs/2602.08505 📄 OpenReview: openreview.net/forum?id=Bba...
arxiv.org
Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Although vision foundation models (VFMs) are increasingly reused for biomedical image analysis, it remains unclear whether the latent representations they provide are general enough to support effecti...
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David Stansby @dstansby.bsky.social · 13/03/2026
The paper that sums up what I've been working on and running for the last three years was published this week 🎉 www.science.org/doi/10.1126/...
science.org
The Human Organ Atlas
The Human Organ Atlas provides open access to 3D images of human anatomy spanning whole organs to cellular scale resolution.
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Daniel Krentzel @danielkrentzel.bsky.social · 24/02/2026
Our preprint outlining a deep learning-based phenotypic screening approach for the discovery of new TB drugs is out on bioRxiv now 💊🦠 🔗 doi.org/10.64898/202... Thank you @awehenkel.bsky.social @chzimmer.bsky.social @spetrella.bsky.social @curieuseny.bsky.social and everyone else not on bsky (yet)🙏
Screenshot of the title and author list of the preprint entitled "Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria"
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