@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. 😂
If you've been wondering what our current obsession with OME-Zarr and lego blocks is about, I have good news for you: the Fractal preprint is out!
Thanks to @joelluethi.bsky.social , all co-authors, and the Fractal developers and users community for making this beautiful project a reality ❤️
Thanks to #Appose hackaton with @jytinevez.bsky.social, @ctrue.bsky.social, @nkiaru.bsky.social, @msphan.bsky.social, @strigaud.bsky.social, Carlos, Thomas and Julie, DeXtrusion can be **INSTALLED** and run to detect cell extrusions directly from Fiji 🤩! Appose is amazing
Let's get ready for a full month of training in image analysis in @pasteur.fr , this summer!
Are you interested in learning how to do bioimage analysis? For light microscopy? for cryo-EM? And for cellular cryo-EM?
Stay tuned, Pasteur offers access to THREE courses, this June.
👇🎓
We’re excited to share our latest preprint on Fractal: our approach towards FAIR bioimage analysis at scale with OME-Zarr-native workflows.
Fractal defines interoperable tasks on OME-Zarr and provides a platform for TB-scale image analysis.
(1 / 10🧵)
www.biorxiv.org/content/10.6...
🔊 The Carpentries is calling for volunteers from the Data Carpentry community to become Lesson Program Governors (LPGCs) for the project.
⏰ Applications close by the end of Tuesday 10th March 2026 (anywhere on Earth).
Find out more about and details on how to apply: carpentries.org/blog/2026/02...
🔬🌿Official launch of the #AGILE_project, an MSCA doctoral network funded by the European Union. #AGILE aims to train a new generation of plant scientists.
Team CODED @igred.fr is looking for 15 international doctoral students. For more information and/or to apply :
👉 www.msca-agile.eu
Thanks! I’d seen Guido’s post and indeed working with intervals in Python is so much nicer than in Matlab or R. I like John’s post because it speaks to non-CS folks: who hasn’t been annoyed trying to keep their centuries straight in history class! And it all could have been avoided with 0-indexing!
An oldie but a goodie: "Why computer scientists count from zero", from @johndcook.bsky.social
www.johndcook.com/blog/2008/06...
Charlie conspiracy meme image: Charlie from Always Sunny in Philadelphia looking insane in front of a pinboard with disheveled papers and red lines connecting them.
Image semantic similarity score: 96.9%
You are mistaken, we do not respond to legal requests from anywhere other than the Swiss authorities.
It is unlikely that one could build a business through ignoring the laws of the jurisdiction that it is in. The mail provider you're moving to included.
The best open source projects happen when industry needs meet community vision.
As Ralf Gommers shares, we help connect the two, funding flows to what communities want to build anyway.
Everyone wins. That's sustainable open source.🌱
#OpenSource #Community
Scikit-learn just took a leap toward GPU-accelerated machine learning, and the Python community made it happen. 🚀
The latest Quansight blog by Lucy Liu gives the full update: buff.ly/RCcPty1
#ScikitLearn #MachineLearning #OpenSource #Python #GPU #ArrayAPI #DataScience #MLOps
BIG UPDATES!
OCTRON now supports the new SAM3 models (alongside SAM2)!
We’ve also added a global switch for Detection vs. Segmentation: Use the same annotations to train either lightweight detection or full segmentation models. Plus, we’ve added support for the new YOLO26 models. ⤵️
1/12
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 :).
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...
Screenshot from the Apple website for the MacBook neo. The text reads, “the 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.)
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
📣We’re back 🔬👀🖥️!
#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
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.
Hugs from Oz!
Thank you! What do you mean by "play around" 😂 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!
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
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.
🚨 Great news! The #SciPy2026 CFP deadline has been extended.
🗓️ New CFP Deadline: March 4th, 2026.
🚀You have 1 more week to submit your proposal.
🙋♀️Don’t miss this chance to present a tutorial, talk or poster at your favorite scientific Python conference!
👉️ Submit here: pretalx.com/scipy-2026/cfp
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?
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 • Fix bug 137, homepage link in Help Book. • 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. • Updated mirror list, which was three years out of date. • Added missing legacy mirrors, which was even more out of date. • 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. • 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. • 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.
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 Coruña, Spain. All positions are 100% remote. Igalia can potentially sponsor visas to emigrate to Spain.
We are recruiting an instrumentation scientist.
aprecruit.berkeley.edu/JPF05253
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)
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-...
