Octavio Reyes-Matte
@octavio-rm.bsky.social
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
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
Pinned
Just realized that what I intended to upload as GIF was just as an image ): So here they are first going through the Z stacks
Reposted by Octavio Reyes-Matte
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.
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.
November 20, 2025 at 5:42 PM
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.
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.
Reposted by Octavio Reyes-Matte
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.
November 13, 2025 at 5:08 PM
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.
Reposted by Octavio Reyes-Matte
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
October 21, 2025 at 11:51 AM
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
How cool is that! Would be really interesting to see conserved patterns across veery different bugs 🤓🤓
Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
September 24, 2025 at 5:50 PM
How cool is that! Would be really interesting to see conserved patterns across veery different bugs 🤓🤓
as a cell shape/morphology enthusiast, just saying that this is super cool doesn't do it enough justice! enhorabuena Ana and the team!
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing
📄 arxiv.org/pdf/2507.01009 (1/N)
📄 arxiv.org/pdf/2507.01009 (1/N)
September 23, 2025 at 9:36 PM
as a cell shape/morphology enthusiast, just saying that this is super cool doesn't do it enough justice! enhorabuena Ana and the team!
Reposted by Octavio Reyes-Matte
#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
#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
September 19, 2025 at 4:08 PM
#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
#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
Time to get more into OMEZarr! 🤓💻🔬
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 🧵)
📅 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 🧵)
September 17, 2025 at 8:53 AM
Time to get more into OMEZarr! 🤓💻🔬
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! 😁💻
- 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! 😁💻
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...
www.nature.com/articles/s41...
February 13, 2025 at 7:12 PM
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! 😁💻
- 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! 😁💻
Absolutely beautiful work! One channel: multi structure separation? The amount of information you'll be able to extract with multiple fluorophores 🤩🤩🤩
🔬🎤 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! 🙏
doi.org/10.1101/2025...
Like ❤️, repost 🔂, and most importantly... please send feedback ✉️ our way! 🙏
February 11, 2025 at 7:16 PM
Absolutely beautiful work! One channel: multi structure separation? The amount of information you'll be able to extract with multiple fluorophores 🤩🤩🤩
Reposted by Octavio Reyes-Matte
"Scientists collaborate — funders must, too"
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/2024...
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/2024...
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
www.statnews.com
December 4, 2024 at 10:21 AM
"Scientists collaborate — funders must, too"
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/2024...
@dartar.bsky.social & @k8hert.bsky.social
www.statnews.com/sponsor/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
November 29, 2024 at 8:34 PM
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
Reposted by Octavio Reyes-Matte
🎨 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
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
November 23, 2024 at 3:50 PM
🎨 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
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
Definitely a cool read!
Just out! Exploring the Impact of Variability in Cell Segmentation and Tracking Approaches. Published in Microscopy Research and Technique. Thanks #BBSRC for funding.
see: doi.org/10.1002/jemt...
@laurawiggins13.bsky.social @globias.bsky.social @eurobioimaging.bsky.social
see: doi.org/10.1002/jemt...
@laurawiggins13.bsky.social @globias.bsky.social @eurobioimaging.bsky.social
Exploring the Impact of Variability in Cell Segmentation and Tracking Approaches
While manual segmentation and tracking of cells from microscopy images remain common practices in biological studies, our work demonstrates the inter- and intra-user variability that can arise from t...
doi.org
November 22, 2024 at 12:47 PM
Definitely a cool read!
Reposted by Octavio Reyes-Matte
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 !
November 20, 2024 at 1:55 PM
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 !
Hi everyone! Looking to connect (back) with the people from the bird site! Always down to chat about imaging, science and music in general 👋
November 18, 2024 at 3:50 PM
Hi everyone! Looking to connect (back) with the people from the bird site! Always down to chat about imaging, science and music in general 👋