Juan Nunez-Iglesias's Avatar

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. πŸ˜‚

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26.03.2024
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Latest posts by Juan Nunez-Iglesias @jni.codes

A cochlea imaged in light-sheet microscopy (right) with staining for spiral ganglion neurons (red) and inner hair cells (blue). You will develop AI-based methods to analyze these structures, for example via segmentation of the individual cells (right) that will support gene therapy development for hearing loss and a better overall understanding of the anatomy of hearing.

A cochlea imaged in light-sheet microscopy (right) with staining for spiral ganglion neurons (red) and inner hair cells (blue). You will develop AI-based methods to analyze these structures, for example via segmentation of the individual cells (right) that will support gene therapy development for hearing loss and a better overall understanding of the anatomy of hearing.

Looking for a PhD position at the intersection of AI, imaging, and gene therapy? Apply for this position in my lab: tinyurl.com/2a2v6tvx

Part of sfb1690.uni-goettingen.de to study hearing, vision, and more.

Plus, you can create pretty pictures as the one below :).

05.03.2026 10:25 πŸ‘ 18 πŸ” 14 πŸ’¬ 0 πŸ“Œ 1
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Igalia Coding Experience | Igalia - Open Source Consultancy and Development Igalia is an open source consulting firm specialised in the development of innovative projects and solutions. Our engineers have expertise in a wide range of technological areas, including browsers an...

Global remote, 🚨paid🚨 open source grant program from @igalia.com for folks to learn more about Linux, Graphics, JS DevTools, Multimedia + GStreamer or Web Standards.

- apply by April 3
- €7k for 450 hours over 3-6 months
- uni students or self directed learners

www.igalia.com/coding-exper...

04.03.2026 14:31 πŸ‘ 17 πŸ” 29 πŸ’¬ 1 πŸ“Œ 0
Screenshot from the Apple website for the MacBook neo. The text reads, β€œthe most colorful MacBook lineup ever,” while showing just four colours, of which one is near-white and another is near-black.

Screenshot from the Apple website for the MacBook neo. The text reads, β€œthe most colorful MacBook lineup ever,” while showing just four colours, of which one is near-white and another is near-black.

Straight up gaslighting on the site. (Yes I know the one in the OP is called an iBook.)

05.03.2026 08:32 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

PAPER OUT ✨ How can we make smart microscopy more interoperable? What are the technical and cultural challenges? 30+ people from academia and industry propose a roadmap: doi.org/10.1515/mim-... Also a review of applications and repo of implementations. Join the discussion! smartmicroscopy.github.io

03.03.2026 17:32 πŸ‘ 45 πŸ” 17 πŸ’¬ 2 πŸ“Œ 1
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Crick BioImage Analysis Symposium 2026

πŸ“£We’re back πŸ”¬πŸ‘€πŸ–₯️!
#CBIAS2026 returns 23–24 November 2026:
Join the bioimage analysis community to discuss advances in quantitative imaging & computational methods for image analysis. Great opportunity for early-career analysts & microscopists to present and connect.
#CBIAS2026 #BioimageAnalysis

25.02.2026 10:29 πŸ‘ 15 πŸ” 10 πŸ’¬ 0 πŸ“Œ 2
A two-column status table titled "Stage" and "Start Date" tracks the timeline of a manuscript submission from its preliminary data submission on October 8, 2025, to its eventual withdrawal on March 2, 2026. The log reveals a lengthy and repetitive administrative process, particularly between October 26, 2025, and February 19, 2026, where the status cycled more than ten times between "Contacting Potential Reviewers" and "Waiting for Reviewer Assignment," suggesting significant difficulty in securing peer reviewers. Following these numerous failed attempts to move into the active review phase, the final entry shows the manuscript was officially withdrawn on March 2, 2026, at 09:08:18.

A two-column status table titled "Stage" and "Start Date" tracks the timeline of a manuscript submission from its preliminary data submission on October 8, 2025, to its eventual withdrawal on March 2, 2026. The log reveals a lengthy and repetitive administrative process, particularly between October 26, 2025, and February 19, 2026, where the status cycled more than ten times between "Contacting Potential Reviewers" and "Waiting for Reviewer Assignment," suggesting significant difficulty in securing peer reviewers. Following these numerous failed attempts to move into the active review phase, the final entry shows the manuscript was officially withdrawn on March 2, 2026, at 09:08:18.

My first paper had to be mailed to Stockholm, Sweden, and then mailed to reviewers around the world. Everything by mail! It was submitted, reviewed, revised, typeset, and published in 3 months. I feel bad for early-career scientists who can't find a single reviewer after 5 months. It's gotta change.

03.03.2026 11:42 πŸ‘ 247 πŸ” 38 πŸ’¬ 13 πŸ“Œ 11

Hugs from Oz!

28.02.2026 16:08 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

Thank you! What do you mean by "play around" πŸ˜‚ any rough guidelines? (e.g. "I typically reduce saturation by about 20% and increase brightness by about 5%")

Also, any shenanigans with, e.g. you *have* to use a crappy Canon app and the connection is flaky? Or pretty seamless?

Thanks!

28.02.2026 08:25 πŸ‘ 0 πŸ” 0 πŸ’¬ 1 πŸ“Œ 0
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Accelerating Innovation in Biology HHMI’s $500 million over the next 10 years will support AI-driven projects and embed AI systems throughout the scientific process in labs across HHMI.

Join us in building foundational datasets and models for microscopy with @jakobtroidl.bsky.social and many others

AI Engineer Pre-Training: lnkd.in/eyEEV5nm
AI Engineer Post-Training: lnkd.in/eShVQ3y9
Data Engineer Data: lnkd.in/eCvm58xH
Data Engineer Pipelines: lnkd.in/ec6qGJkX

ai.hhmi.org

26.02.2026 16:15 πŸ‘ 14 πŸ” 8 πŸ’¬ 0 πŸ“Œ 0

I'm going on a long trip soon and I want to keep an analog journal with a photo per day. Anyone got experiences with portable photo printers? I'm looking at Fujifilm Instax Mini Link 3 and Canon CP1500 Selphy, but open to suggestions. Basically looking for reliable hardware that doesn't use Cloud.

27.02.2026 02:29 πŸ‘ 0 πŸ” 0 πŸ’¬ 2 πŸ“Œ 0
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🚨 Great news! The #SciPy2026 CFP deadline has been extended.
πŸ—“οΈ New CFP Deadline: March 4th, 2026.

πŸš€You have 1 more week to submit your proposal.
πŸ™‹β€β™€οΈDon’t miss this chance to present a tutorial, talk or poster at your favorite scientific Python conference!
πŸ‘‰οΈ Submit here: pretalx.com/scipy-2026/cfp

25.02.2026 20:27 πŸ‘ 4 πŸ” 5 πŸ’¬ 0 πŸ“Œ 2
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Federal funding for US biomedical research is moribund.

Since October 1 2025, NIH is -80% in new grants and -70% in values (total dollars).

Labs are closing down and researchers are leaving science.

To what end?

26.02.2026 15:48 πŸ‘ 70 πŸ” 57 πŸ’¬ 5 πŸ“Œ 12
The screenshot of the release notes reads:

A new version of TeX Live Utility is available!
TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now?
Release Notes:
Changes Since 1.54
β€’ Fix bug 137, homepage link in Help Book.
β€’ First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software.
β€’ Updated mirror list, which was three years out of date.
β€’ Added missing legacy mirrors, which was even more out of date.
β€’ Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database.
Thanks for nothing, guys. Bug 142 and 144.
β€’ Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models.
β€’ Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.

The screenshot of the release notes reads: A new version of TeX Live Utility is available! TeX Live Utility 1.55 is now available-you have 1.54. Would you like to download it now? Release Notes: Changes Since 1.54 β€’ Fix bug 137, homepage link in Help Book. β€’ First release in a long time, since I don't use TeX anymore and resent the very idea of paying Apple annually for the privilege of giving away free and open-source software. Also, I'm really lazy. Please accept my apologies for all the annoying issues you've encountered in this mission-critical software. β€’ Updated mirror list, which was three years out of date. β€’ Added missing legacy mirrors, which was even more out of date. β€’ Added an alert on startup when user tries Homebrew's lobotomized MacTex, because those lunatics left timgr but removed its database. Thanks for nothing, guys. Bug 142 and 144. β€’ Use a custom user-agent to work around the Anubis bot trap on texlive.info. Can't wait to see what else breaks because of this, thanks to the profusion of degenerate Artificial Insemination fetishists scraping websites to feed their models. β€’ Lists of countries in Repository/Continent are now sorted. No idea how you people let me get away with that one for the last fifteen years.

There's a "is anyone even reading this" sort of honesty you get in the software update release notes from a project that's been around for a long time.

26.02.2026 20:44 πŸ‘ 1339 πŸ” 329 πŸ’¬ 19 πŸ“Œ 16
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Open Source Product Marketing Manager | Igalia - Open Source Consultancy and Development We’re looking for someone to help spread the word about our Open Source projects to the whole world.

My company @igalia.com is hiring an Open Source Product Marketing Manager. www.igalia.com/jobs/product...

Igalia is a worker-owned cooperative based in A CoruΓ±a, Spain. All positions are 100% remote. Igalia can potentially sponsor visas to emigrate to Spain.

23.02.2026 20:55 πŸ‘ 36 πŸ” 29 πŸ’¬ 0 πŸ“Œ 2
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Assistant/Associate/Full Project Scientist - Instrumentation Microscopy – Advanced Bioimaging Center – Department of Molecular and Cell Biology University of California, Berkeley is hiring. Apply now!

We are recruiting an instrumentation scientist.
aprecruit.berkeley.edu/JPF05253

24.02.2026 21:44 πŸ‘ 1 πŸ” 2 πŸ’¬ 0 πŸ“Œ 0
Interactive 3D Visualization of Multiple Volumes & Shapes in FIJI (BigVolumeBrowser)
Interactive 3D Visualization of Multiple Volumes & Shapes in FIJI (BigVolumeBrowser) YouTube video by Johanna M. Dela Cruz

In the #BigVolumeBrowser news, there is a new awesome video tutorial about it made by certified magician Johanna M. Dela Cruz.
Check it out: www.youtube.com/watch?v=c0fr... (1/2)

24.02.2026 22:01 πŸ‘ 20 πŸ” 10 πŸ’¬ 3 πŸ“Œ 0
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The Misuses of the University - Public Books Have the funds that might have trained the next generation of scholars at the nation’s first research university have been blown on ostentatious new buildings?

Even by the standards of modern university management (most of this was me nodding along to things I've sadly seen and heard about many times before), this took a breathtaking turn.

www.publicbooks.org/the-misuses-...

24.02.2026 08:49 πŸ‘ 0 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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Since last year, I've been making a RELION GUI that supports viewing, navigating and running jobs in a way completely compatible with the original RELION pipeline. Now it's working nicely for both SPA and tomography! Please try it out - github.com/hanjinliu/hi...

22.02.2026 20:10 πŸ‘ 84 πŸ” 28 πŸ’¬ 4 πŸ“Œ 0

This afternoon I took my mom to the ballet. She was as a dancer and choreographer for decades & has been in memory care for 8 years. She can’t recall many details of her past but danceβ€”and her identity as a dancerβ€”lives in her soul 1/
#alzheimers

23.02.2026 06:27 πŸ‘ 64 πŸ” 20 πŸ’¬ 6 πŸ“Œ 6
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Satellite proposals threaten the night sky In the United States, the Federal Communications Commission (FCC), the agency responsible for authorizing satellite launches and operations…

The FCC just opened public comments on SpaceX's plan to launch a million satellites to do AI compute in space. Under the current proposal, an environmental review won't be required. Please consider submitting a public comment to oppose this damaging plan.
darksky.org/news/two-sat...

22.02.2026 19:21 πŸ‘ 3494 πŸ” 2687 πŸ’¬ 123 πŸ“Œ 397
a windows 11 menu showing "convert to adobe pdf", "ask copilot", and 4 more options that take time to load

a windows 11 menu showing "convert to adobe pdf", "ask copilot", and 4 more options that take time to load

windows 11 update: for the first time in my life, simply right clicking a file has a load time. unreal

19.02.2026 21:25 πŸ‘ 7185 πŸ” 1412 πŸ’¬ 207 πŸ“Œ 284

One of my websites is crumbling under a flood of traffic from thousands of different IP addresses this evening. They retrieve only HTML (no images, JS, CSS, etc.), and they claim to be all kinds of different user agents. CloudFlare can't really help here. I guarantee this is some AI-training thing.

14.02.2026 01:02 πŸ‘ 143 πŸ” 21 πŸ’¬ 16 πŸ“Œ 4
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GitHub - melissawm/open-source-ai-contribution-policies: A list of policies by different open source projects about how to engage with AI-generated contributions. A list of policies by different open source projects about how to engage with AI-generated contributions. - melissawm/open-source-ai-contribution-policies

Hi folks, I'm trying to put together a list of AI generated contribution policies for different open source projects. Do you have any you can link to me here?

You can also directly submit a PR to
https://github.com/melissawm/open-source-ai-contribution-policies

19.02.2026 14:42 πŸ‘ 6 πŸ” 4 πŸ’¬ 0 πŸ“Œ 0

Apply to join us this July for a crash course on Python & bioimage analysis tailored specifically for beginners! Applications due May 18th πŸ”¬πŸ’» #BoBiAC2026 bobiac.github.io

03.02.2026 21:42 πŸ‘ 9 πŸ” 5 πŸ’¬ 0 πŸ“Œ 0

"Consumer electronics" = more or less what the majority of scientific research gets done with.

17.02.2026 23:14 πŸ‘ 20 πŸ” 7 πŸ’¬ 2 πŸ“Œ 0

Honestly, AI slop PRs are becoming increasingly draining and demoralizing for #Godot maintainers.

If you want to help, more funding so we can pay more maintainers to deal with the slop (on top of everything we do already) is the only viable solution I can think of:

fund.godotengine.org

16.02.2026 15:33 πŸ‘ 1890 πŸ” 857 πŸ’¬ 51 πŸ“Œ 43
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Es hora de que la "IA" haga un fork - Less is Less No mΓ‘s exhortaciones para que los mantenedores de proyectos de cΓ³digo abierto hagan esto o aquello

Me explayo sobre el ΓΊltimo drama en el mundo del cΓ³digo abierto (un agente generΓ³ un artΓ­culo de blog insultando a un mantenedor que habΓ­a cerrado su pull request), por quΓ© debemos rechazar la urgencia para adoptar la "IA" como proponen @interacciones.org y D. Monett, y cuΓ‘l es la alternativa.

16.02.2026 20:10 πŸ‘ 6 πŸ” 4 πŸ’¬ 0 πŸ“Œ 1
Research Group Leader Tenure Track - Structural Studies - LMB 2775 - Medical Research Council Location: Cambridge. Vacancy: Research Group Leader Tenure Track - Structural Studies - LMB 2775. Closing Date: 16/03/2026, 23:55

Please spread the word: the Structural Studies Division @mrclmb.bsky.social is looking for a new tenure-track, independent group leader with an exciting plan in any area of Structural (Molecular & Cell) biology, in discovery biology and/or methods development. πŸ₯³

mrc.tal.net/vx/mobile-0/...

16.02.2026 12:09 πŸ‘ 83 πŸ” 106 πŸ’¬ 1 πŸ“Œ 2
Email from LinkedIn with the subject: "Bored? Solve today's puzzle (puzzle emoji)". First line is "672 colleagues from your company already solved LinkedIn puzzle games"

Email from LinkedIn with the subject: "Bored? Solve today's puzzle (puzzle emoji)". First line is "672 colleagues from your company already solved LinkedIn puzzle games"

Wow LinkedIn is really getting desperate in its struggle for relevance…

16.02.2026 23:37 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0
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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

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

16.02.2026 21:06 πŸ‘ 60 πŸ” 23 πŸ’¬ 1 πŸ“Œ 1