Juan Nunez-Iglesias
@jni.codes
Co-founder, core developer, and steering council member of @napari.org
Also other FOSSy and Science-y things.
I prefer Mastodon (profile at https://fosstodon.org/@jni) but begrudgingly checking things out here. 😂
Also other FOSSy and Science-y things.
I prefer Mastodon (profile at https://fosstodon.org/@jni) but begrudgingly checking things out here. 😂
Reposted by Juan Nunez-Iglesias
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
BigVolumeBrowser: a new 3D multi volume/mesh/point clould (SMLM) data viewer
Hello everyone, I’d like to share with you another 3D viewer for FIJI, BigVolumeBrowser (full documentation link). It‘s a first initial public release, so there is still space for improvements. Le...
forum.image.sc
November 21, 2025 at 9:29 AM
Finally, the first public release of #BigVolumeBrowser, so after teasers, you can try it yourself. For details, please check the announcement post (1/2)
forum.image.sc/t/bigvolumeb...
forum.image.sc/t/bigvolumeb...
Reposted by Juan Nunez-Iglesias
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
November 20, 2025 at 1:03 PM
It's been great to present OME-Zarrs & Fractal for interoperable bioimage analysis at the 2025 @cytodata.bsky.social conference in Berlin today. Thanks a lot to the organizers & especially Christopher Schmied for having us!
Reposted by Juan Nunez-Iglesias
It’s now clear that information on U.S. government websites can no longer be trusted.
It’s both heartbreaking and infuriating to see how quickly this administration has undermined science, public health, and the credibility of our scientific institutions.
It’s both heartbreaking and infuriating to see how quickly this administration has undermined science, public health, and the credibility of our scientific institutions.
November 20, 2025 at 4:56 AM
It’s now clear that information on U.S. government websites can no longer be trusted.
It’s both heartbreaking and infuriating to see how quickly this administration has undermined science, public health, and the credibility of our scientific institutions.
It’s both heartbreaking and infuriating to see how quickly this administration has undermined science, public health, and the credibility of our scientific institutions.
Reposted by Juan Nunez-Iglesias
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:
It ships many new features, detailed below, but that are articulated around the following:
November 20, 2025 at 11:42 AM
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:
It ships many new features, detailed below, but that are articulated around the following:
Reposted by Juan Nunez-Iglesias
“Federal Science Minister Tim Ayres said the cuts were aimed at refocusing the efforts of the CSIRO towards research priorities, such as critical minerals, iron and steel production in Australia.”
🤬🤬🤬
www.abc.net.au/news/202csir...
🤬🤬🤬
www.abc.net.au/news/202csir...
CSIRO to cut up to 350 research jobs in major overhaul
After 440 positions were slashed last year, the CSIRO has announced more staff cuts across the country in a bid to remain financially viable.
www.abc.net.au
November 19, 2025 at 4:22 AM
“Federal Science Minister Tim Ayres said the cuts were aimed at refocusing the efforts of the CSIRO towards research priorities, such as critical minerals, iron and steel production in Australia.”
🤬🤬🤬
www.abc.net.au/news/202csir...
🤬🤬🤬
www.abc.net.au/news/202csir...
> The result has been an ineffectual "open source revolution" that maintains the status quo of our modern day hellscape by facilitating an upwards transfer of wealth and power […]. Open source "won" by aiding and abetting the already dominant owner-class.
💯 Go read this excellent piece.
💯 Go read this excellent piece.
Anti-fascistic software is made possible by pro-labor licensing.
I've been trying to write this piece for years. Every time I get started I'm just overwhelmed with paralyzing visions of the FOSS commentariat accusing me of WrongThink.
But I'm tired and we urgently need to get our shit together.
I've been trying to write this piece for years. Every time I get started I'm just overwhelmed with paralyzing visions of the FOSS commentariat accusing me of WrongThink.
But I'm tired and we urgently need to get our shit together.
Open Source Power
We have to talk about open source licensing.
blog.muni.town
November 19, 2025 at 1:33 AM
> The result has been an ineffectual "open source revolution" that maintains the status quo of our modern day hellscape by facilitating an upwards transfer of wealth and power […]. Open source "won" by aiding and abetting the already dominant owner-class.
💯 Go read this excellent piece.
💯 Go read this excellent piece.
Reposted by Juan Nunez-Iglesias
Anti-fascistic software is made possible by pro-labor licensing.
I've been trying to write this piece for years. Every time I get started I'm just overwhelmed with paralyzing visions of the FOSS commentariat accusing me of WrongThink.
But I'm tired and we urgently need to get our shit together.
I've been trying to write this piece for years. Every time I get started I'm just overwhelmed with paralyzing visions of the FOSS commentariat accusing me of WrongThink.
But I'm tired and we urgently need to get our shit together.
Open Source Power
We have to talk about open source licensing.
blog.muni.town
November 14, 2025 at 4:22 PM
Anti-fascistic software is made possible by pro-labor licensing.
I've been trying to write this piece for years. Every time I get started I'm just overwhelmed with paralyzing visions of the FOSS commentariat accusing me of WrongThink.
But I'm tired and we urgently need to get our shit together.
I've been trying to write this piece for years. Every time I get started I'm just overwhelmed with paralyzing visions of the FOSS commentariat accusing me of WrongThink.
But I'm tired and we urgently need to get our shit together.
Reposted by Juan Nunez-Iglesias
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
GitHub - czimaginginstitute/zarr-particle-tools: Particle extraction and reconstruction from OME-Zarr tilt series.
Particle extraction and reconstruction from OME-Zarr tilt series. - czimaginginstitute/zarr-particle-tools
github.com
November 17, 2025 at 10:30 PM
Hi #teamtomo! Want to use OME-Zarr for your tilt series but can't integrate it with your existing sub-tomogram averaging pipelines?
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Try zarr-particle-tools - RELION-style extraction & reconstruction built for OME-Zarr-based workflows!
📦 pip install zarr-particle-tools
🔗 github.com/czimagingins...
Reposted by Juan Nunez-Iglesias
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵
1/14 🧵
November 17, 2025 at 1:24 PM
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data.
1/14 🧵
1/14 🧵
Reposted by Juan Nunez-Iglesias
Reposted by Juan Nunez-Iglesias
Have you ever wanted @astropy.org tutorials on:
– spectroscopic data reduction from a raw FITS image,
– computing galactic orbits from Gaia measurements,
– cross-matching astronomical catalogs?
Check out the redesigned learn.astropy.org! Announcement from @numfocus.bsky.social below. 🧪🔭 #astrocode
– spectroscopic data reduction from a raw FITS image,
– computing galactic orbits from Gaia measurements,
– cross-matching astronomical catalogs?
Check out the redesigned learn.astropy.org! Announcement from @numfocus.bsky.social below. 🧪🔭 #astrocode
Explore the Redesigned Learn.Astropy.org
A New Way to Learn Astronomy with Python
numfocus.medium.com
November 17, 2025 at 1:07 PM
Have you ever wanted @astropy.org tutorials on:
– spectroscopic data reduction from a raw FITS image,
– computing galactic orbits from Gaia measurements,
– cross-matching astronomical catalogs?
Check out the redesigned learn.astropy.org! Announcement from @numfocus.bsky.social below. 🧪🔭 #astrocode
– spectroscopic data reduction from a raw FITS image,
– computing galactic orbits from Gaia measurements,
– cross-matching astronomical catalogs?
Check out the redesigned learn.astropy.org! Announcement from @numfocus.bsky.social below. 🧪🔭 #astrocode
Reposted by Juan Nunez-Iglesias
🌀¡Miércoles, Git! Manejo de errores sin morir en el intento #LatinR2025
Aprendé a resolver 7 errores comunes en #Git desde #RStats
Maëlle Salmon, Yanina Bellini Saibene
📅 2 Dic, 10:00–12:00 UTC-3 – Online
💵 USD: Estudiantes 5, Academia 10, Industria 15
🔗 www.eventbrite.com.ar/e/1937068908...
Aprendé a resolver 7 errores comunes en #Git desde #RStats
Maëlle Salmon, Yanina Bellini Saibene
📅 2 Dic, 10:00–12:00 UTC-3 – Online
💵 USD: Estudiantes 5, Academia 10, Industria 15
🔗 www.eventbrite.com.ar/e/1937068908...
November 15, 2025 at 8:01 PM
🌀¡Miércoles, Git! Manejo de errores sin morir en el intento #LatinR2025
Aprendé a resolver 7 errores comunes en #Git desde #RStats
Maëlle Salmon, Yanina Bellini Saibene
📅 2 Dic, 10:00–12:00 UTC-3 – Online
💵 USD: Estudiantes 5, Academia 10, Industria 15
🔗 www.eventbrite.com.ar/e/1937068908...
Aprendé a resolver 7 errores comunes en #Git desde #RStats
Maëlle Salmon, Yanina Bellini Saibene
📅 2 Dic, 10:00–12:00 UTC-3 – Online
💵 USD: Estudiantes 5, Academia 10, Industria 15
🔗 www.eventbrite.com.ar/e/1937068908...
Reposted by Juan Nunez-Iglesias
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
research.pasteur.fr
November 15, 2025 at 9:22 AM
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr
research.pasteur.fr/fr/job/open-...
research.pasteur.fr/fr/job/open-...
Reposted by Juan Nunez-Iglesias
Want to help shape the SCENE collaboration?! Join us as an executive director: www.cam.ac.uk/jobs/scene-m...
SCENE Manager
The Simons Collaboration on Ecological Neuroscience (SCENE): SCENE is an international consortium of 20 leading researchers in the fields of Computational, Systems and Cognitive Neuroscience, and
www.cam.ac.uk
November 13, 2025 at 5:32 PM
Want to help shape the SCENE collaboration?! Join us as an executive director: www.cam.ac.uk/jobs/scene-m...
Reposted by Juan Nunez-Iglesias
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
November 12, 2025 at 5:00 PM
This is what hacking *actually* looks like. #OME_NGFF_Hackathon
Reposted by Juan Nunez-Iglesias
What is the most profitable industry in the world, this side of the law? Not oil, not IT, not pharma.
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
November 12, 2025 at 10:31 AM
What is the most profitable industry in the world, this side of the law? Not oil, not IT, not pharma.
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
It's *scientific publishing*.
We call this the Drain of Scientific Publishing.
Paper: arxiv.org/abs/2511.04820
Background: doi.org/10.1162/qss_...
Thread @markhanson.fediscience.org.ap.brid.gy 👇
Reposted by Juan Nunez-Iglesias
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
UZH: Head of the Center for Microscopy and Image Analysis (Core Facility)
The Center for Microscopy and Image Analysis (ZMB) is a nationally and internationally recognized Core Facility at the University of Zurich (UZH), providing access to state-of-the-art light and electr...
jobs.uzh.ch
November 12, 2025 at 6:42 PM
The Center for Microscopy and Image Analysis at the University of Zurich is seeking a new Head:
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
jobs.uzh.ch/job-vacancie...
It is super fun to work with them, tons of expertise and cutting edge instrumentation in ❄️🔬
Application deadline: December 15, 2025.
Reposted by Juan Nunez-Iglesias
Fantastic to see Igor Tatarnikov, Senior Research Software Engineer at SWC, collecting the 2025 International Prize from
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
November 11, 2025 at 3:48 PM
Fantastic to see Igor Tatarnikov, Senior Research Software Engineer at SWC, collecting the 2025 International Prize from
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
@theneuro.bsky.social Irv and Helga Cooper Foundation on behalf of the @brainglobe.info Initiative!
#OpenScience
Read more: sainsburywellcome.org/web/research...
Reposted by Juan Nunez-Iglesias
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
📢 Open 4-year PhD Position in Deep Learning for Bioimage Analysis! | CVPD Research group
The Computer Vision and Pattern Discovery (CVPD) group at the University of the Basque Country (UPV/EHU) is offering a fully funded 4-year PhD position within the recently awarded project TOSBI: Towar...
cvpd.github.io
September 30, 2025 at 11:01 AM
📣 We’re hiring, please RT! Fully funded 4-year PhD position in our CVPD group at @informatikaehu.bsky.social!
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Research at the intersection of AI, deep learning & bioimage analysis. 🧠🔬
📅 Applications open Oct 6 (deadline: ~Oct 27)
📍 San Sebastian, Spain.
👉 cvpd.github.io/post/2025-09...
Reposted by Juan Nunez-Iglesias
🪰 A new ‘Eyemap’ developed by a team led by Arthur Zhao & @michaelreiser.bsky.social reveals how visual information detected by the fly’s eye shows up in neurons deep in the brain. Remarkably, the eye’s shape determines how flies see motion.👁️
🔗 hhmi.news/4kSZjou
🔗 hhmi.news/4kSZjou
July 23, 2025 at 3:18 PM
🪰 A new ‘Eyemap’ developed by a team led by Arthur Zhao & @michaelreiser.bsky.social reveals how visual information detected by the fly’s eye shows up in neurons deep in the brain. Remarkably, the eye’s shape determines how flies see motion.👁️
🔗 hhmi.news/4kSZjou
🔗 hhmi.news/4kSZjou
Reposted by Juan Nunez-Iglesias
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
You might have noticed lots of activity in the napari project recently! 🚀 We're grateful for a grant from CZI that's keeping us going, but grants don't last forever: we're trying to figure out sustainable long term funding. Read our blog post to find out how you can help:
napari.org/island-dispa...
napari.org/island-dispa...
November 10, 2025 at 1:23 PM
Remember that survey about how we can sustain napari development? We extended the deadline until the 16th, AoE! Blog post: napari.org/island-dispa...
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Survey: napari.typeform.com/sustainability
If you use napari at all we would be super grateful if you filled it in! 🙏
Reposted by Juan Nunez-Iglesias
Hi Fans of Feedback Microscopy,
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
November 7, 2025 at 7:23 PM
Hi Fans of Feedback Microscopy,
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?
Btw, it works as well in Fiji&ImageJ :-)
Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.
Reposted by Juan Nunez-Iglesias
This is one of the best learning experiences I’ve had so if you want to dive into deep learning go for it!
📢 Apply now for the first DL@Janelia Bootcamp (June 4–18, 2026)! 2 weeks of hands-on deep learning for microscopy: train models on your own data, Python needed (no ML experience), housing + meals included, no registration fee
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
📍 Janelia Research Campus, VA
🗓️ Apply by Jan 15, 2026
🔗 shorturl.at/j4sgY
November 6, 2025 at 11:06 PM
This is one of the best learning experiences I’ve had so if you want to dive into deep learning go for it!
Reposted by Juan Nunez-Iglesias
