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Octavio Reyes-Matte

@octavio-rm.bsky.social
450 followers 1.4K following 48 posts

PhD student Waterfowl appreciator 🦆🪿🦢 Bioimage analysis 🔬, Quantitative Biology📊 and Deep Learning 💻 Trying to understand the diversity of bacterial cell size and its evolution From 🇨🇱 in 🇩🇪 he/him

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Reposted by Octavio Reyes-Matte
Jean-Yves Tinevez @jytinevez.bsky.social · 03/09/2026
New version of #Mastodon-SC, the Fiji plugin to track and lineage cells in gigantic movies! What is Mastodon? 👉 in the preprint linked to the quote post What's new? 👇
liveimagetrackingtools.org
geff
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Octavio Reyes-Matte @octavio-rm.bsky.social · 30/08/2026
Tools like this keep making strong arguments to switch from 2D bugs 🦠 to 3D beasts 🐟🪰🪱. Can't wait to play with it! 🤩
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Reposted by Octavio Reyes-Matte
Aafke Gros @aafkegros.bsky.social · 24/07/2026
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell. A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution
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Biology Open @biologyopen.bsky.social · 14/07/2026
Are you an early-career researcher based in the Global South? Apply by 20 November 2026 for BiO Global South Conference Travel Grants to attend an international biological or biomedical conference. More information at www.biologists.com/grants/bio-g...
BiO Global South Conference Travel Grants. Supporting ECRs in the Global South to attend international biological and biomedical science conferences. Application deadline: 20 November 2026.
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Reposted by Octavio Reyes-Matte
Kaumudi Prabhakara @kaumudi.bsky.social · 26/06/2026
Excited to share that our paper is now published in Environmental Microbiology! It's open access. Read on to find out how functionally and taxonomically diverse microbial communities assemble on cellulose and glucose. enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources
Taxonomically and functionally distinct communities assemble on cellulose and its monomer, glucose. Although single carbon sources were provided, high and comparable diversity was maintained in both ....
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Reposted by Octavio Reyes-Matte
Mario Del Rosario @mariodelr.bsky.social · 05/06/2026
How do you know if a microscopy experiment can actually resolve a biological structure? Introducing VLab4Mic, a platform that predicts structural resolvability before you go to the microscope Led by Damián Martinez and Bruno Saraiva at @henriqueslab.bsky.social www.biorxiv.org/content/10.6...
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Jean-Yves Tinevez @jytinevez.bsky.social · 28/05/2026
Another outcome from the Appose processing hackathon: Cellpose simple tile processing in Fiji, with #imglib2 and #appose only. With @gaellel.bsky.social and @strigaud.bsky.social
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Communications Biology @commsbio.nature.com · 27/05/2026
🦠Featured on our homepage this week: MEDUSSA is a high-throughput method to measure bacterial cell size using deep-learning analysis of fluorescent membranes, revealing major size variation and genetic drivers of cell width. @mpi-evolbio.bsky.social 👇 www.nature.com/articles/s42...
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Reposted by Octavio Reyes-Matte
Jean-Yves Tinevez @jytinevez.bsky.social · 25/05/2026
Do you support people on the forum.image.sc or the forum itself? Do you want to feel good? forum.image.sc/t/i-finally-...
forum.image.sc
I finally got my PhD, thank you image.sc!
Hi everyone, I would like to make a small positive post. I finally got my PhD! The viva was actually on April 27th, but due to university paperwork, it only became official last Friday. A large par...
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Octavio Reyes-Matte @octavio-rm.bsky.social · 22/05/2026
Happy fluorescence friday! And I'm very excited to cellebrate it with my new paper "Deep-learning deconvolution and segmentation of fluorescent membranes for high-precision bacterial cell-size profiling", out yesterday in @commsbio.nature.com ! rdcu.be/fkg2G
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Guillaume Witz @guiwitz.bsky.social · 02/04/2026
I’m trying to figure out (like everyone else) how to reasonably use LLMs both for my work and teaching. This is fantastically written and clearly articulates a lot of ideas and concerns I had vaguely in mind. I’m considering suggesting this as a read to participants in my scientific coding courses.
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Octavio Reyes-Matte @octavio-rm.bsky.social · 05/05/2026
Figure 1 says it clearly, more structures per channel + more available channels -> more information from your images! Definitely would be cool for scaling virtual staining protocols. Congrats @ashesh-0.bsky.social and @florianjug.bsky.social !
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Reposted by Octavio Reyes-Matte
Florian Jug @florianjug.bsky.social · 23/04/2026
🤩 Now... THIS is a nice video about what @humantechnopole.bsky.social stands for! youtu.be/okWehgenNMM I feel well represented! 🤩 If you like what you see... why don't you check our open positions and join us?! Or... repost/send to people who might want to work with us?! 🙏 👍
youtu.be
Human Technopole: Connecting Science Across Scales
YouTube video by Human Technopole
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Florian Jug @florianjug.bsky.social · 02/04/2026
We've spent the last year building something at @humantechnopole.bsky.social that we think is genuinely needed: #AI that works across biological scales and data modalities, not just within them. A thread on what we're doing, why, and who we're looking for. A 🧵... 1/9
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 20/11/2025
Python notebook from a two year old paper: Oh, no, I cannot run, there is a slight mismatch of a logging library. ImageJ plugin from 2001 running on Quantum Java 51 in 2078: Your 100 petabyte temporal hologram was successfully thresholded.
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Virginie Uhlmann @virginieuhlmann.bsky.social · 13/11/2025
We wrapped up the symposium part of our 2025 International OME-NGFF workshop on Tuesday. What a phenomenal two days! I'm humbled by the incredible positive energy, talent, and enthusiasm that filled this event.
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MadScientist @mads100tist.bsky.social · 21/10/2025
For instance, have you wondered what would happen if Anthropic decided that trans authors's work was going to be cited less? Or the global south? Because you can definitely do that (Musk did that with Grok and we all know what happened. Those are the things that worry me, as a scholar and a person
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Octavio Reyes-Matte @octavio-rm.bsky.social · 24/09/2025
How cool is that! Would be really interesting to see conserved patterns across veery different bugs 🤓🤓
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Octavio Reyes-Matte @octavio-rm.bsky.social · 23/09/2025
as a cell shape/morphology enthusiast, just saying that this is super cool doesn't do it enough justice! enhorabuena Ana and the team!
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Reposted by Octavio Reyes-Matte
BioImaging North America @bioimagingna.bsky.social · 19/09/2025
#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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Octavio Reyes-Matte @octavio-rm.bsky.social · 17/09/2025
Time to get more into OMEZarr! 🤓💻🔬
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Octavio Reyes-Matte @octavio-rm.bsky.social · 13/02/2025
Cannot really emphasize how amazing this tool is! For me, it checks many important boxes: - feels intuitive - powerful - customizable - flexible Many congratulations to @anwaiarchit.bsky.social , @cppape.bsky.social and the whole team! Looking forward to play with it and push its limits! 😁💻
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Octavio Reyes-Matte @octavio-rm.bsky.social · 11/02/2025
Absolutely beautiful work! One channel: multi structure separation? The amount of information you'll be able to extract with multiple fluorophores 🤩🤩🤩
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Josh Moore @joshmoore.bsky.social · 04/12/2024
"Scientists collaborate — funders must, too" @dartar.bsky.social & @k8hert.bsky.social www.statnews.com/sponsor/2024...
statnews.com
New report highlights the scientific impact of open source software
Two of the scientists who won this year’s Nobel Prize for cracking the code of proteins’ intricate structures relied, in part, on a series of computing
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Octavio Reyes-Matte @octavio-rm.bsky.social · 29/11/2024
While my main focus is bacteria (for now), for my first #FluorescenceFriday I couldn't resist posting these beautiful neural crest immunofluorescence images of an embryo, by my fellow PhD student Elio Escamilla
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Jon Lim, FRCP PhD @drjonlim.bsky.social · 23/11/2024
🎨 In case anyone need… The NIH BioArt Source is an awesome library of *free* professionally drawn illustrations for scientific presentations or figures. Downloadable in HD. Thank you NIH for this invaluable tool 🙏! Check it out 👇 bioart.niaid.nih.gov
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Octavio Reyes-Matte @octavio-rm.bsky.social · 22/11/2024
Definitely a cool read!
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Reposted by Octavio Reyes-Matte
Nicolas Chiaruttini @nkiaru.bsky.social · 20/11/2024
Direct streaming of an #OMERO dataset in #BigDataViewer from the public server omero-tim.gerbi-gmb.de (dataset from the Workshop 35). Thank you Tom and @gerbi.bsky.social !
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Octavio Reyes-Matte @octavio-rm.bsky.social · 18/11/2024
Hi everyone! Looking to connect (back) with the people from the bird site! Always down to chat about imaging, science and music in general 👋
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