Joergen Kornfeld @jmrko.bsky.social · 12/09/2026Absolutely, modular code is great for that! I was unhappy about the "not-invented-here" syndrome for a long time. Many people "reinvented" Knossos, despite it being open-source and fully supported by us. But many people prefer writing their own tools when they can. Just an observation. 110
Joergen Kornfeld @jmrko.bsky.social · 11/09/2026I would argue we still think and learn, just something else (eg, what to type into the prompt rather than trying to get programming language syntax right). But yes, the transition seems far more dramatic than, eg, assembler to Python, and it is totally unclear at the moment where this will lead. 100
Joergen Kornfeld @jmrko.bsky.social · 11/09/2026... and I thought Oxford when I saw the picture :) 010
Joergen Kornfeld @jmrko.bsky.social · 11/09/2026One can use a powerful tool to learn and create, or to stop thinking. It is still our choice, fortunately. 100
Reposted by Joergen KornfeldBoneJ @bonej.org · 11/09/2026LLMs have helped speed up and improve the quality of engineering new features and fixing bugs. For us, they're power tools that help skilled people work more effectively - in the same way that circular saws, nail guns and CNC machines help properly trained people build things in the physical world. 013
Joergen Kornfeld @jmrko.bsky.social · 11/09/2026I don't think this article was influenced in any way by me having co-founded ariadne. One has to declare shares, whether they play a role or not. 000
Joergen Kornfeld @jmrko.bsky.social · 11/09/2026This is a very negative interpretation? I've written open-source research software for 20 years "by hand" myself (knossostool.org, started around 2006). I am not sad at all that we can develop such tools faster now, and yes, quality matters. LLMs empower people when used responsibly.knossostool.orgKNOSSOS — 3D Image AnnotationKNOSSOS is a scientific application for 3D image data annotation. 120
Reposted by Joergen Kornfeldpaveltomancak.bsky.social @paveltomancak.bsky.social · 10/09/2026This article seems to celebrate the shift from poor support for #software #engineers in research to pretending they aren't needed at all. Did we spend 2 decades consolidating fragmented software ecosystems into platforms only to see them dissolve through "vibe coding"? www.nature.com/articles/s41...nature.comDisruption of the research software landscape through AI software generation - Nature MethodsSpecialized research software has historically been costly and time-consuming to create, but large language models (LLMs) have become capable enough at code generation to fundamentally change this. We... 7309
Reposted by Joergen KornfeldMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 17/08/2026How is AI changing biomedical research? 🤖🔬 In a new article, @jmrko.bsky.social & @neurofinch.bsky.social in the LMB’s Neurobiology Division explore how AI-assisted programming is transforming coding in biomedical research. Read more here: www.nature.com/articles/s41...nature.comDisruption of the research software landscape through AI software generation - Nature MethodsSpecialized research software has historically been costly and time-consuming to create, but large language models (LLMs) have become capable enough at code generation to fundamentally change this. We... 072
Reposted by Joergen Kornfeldalexandrarother.bsky.social @alexandrarother.bsky.social · 30/10/2025I am happy to share that the main story of my PhD is now available as a preprint! www.biorxiv.org/content/10.1... We analyses over 8500 neurons in a songbird basal ganglia dataset. To explore this and two other stories more interactively, also check out our website! www.songbird-connectomics.orgbiorxiv.orgThe songbird basal ganglia connectomeThe basal ganglia (BG) play an essential role in shaping vertebrate behavior, ranging from motor learning to emotions, but comprehensive maps of their canonical synaptic architecture are missing. In m... 073
Reposted by Joergen KornfeldCaitlin Gillespie @neurocait.bsky.social · 30/10/2025It was a privilege to develop the website to showcase the release of this basal ganglia connectome! Congratulations to everyone involved 😊🎉 Check out interactive 3D models, analysis you can perform in your browser, & our interactive matrices; all on the website! songbird-connectomics.org 0124
Joergen Kornfeld @jmrko.bsky.social · 01/10/2025Long story short: PRISM has the potential to solve the connectomics reconstruction bottleneck for good. Fantastic collaboration with E11, MIT, and the Crick! 061
Joergen Kornfeld @jmrko.bsky.social · 23/08/2025💀 Spent hours doing email archaeology? Same. So I built NeuralMail 📨: 🔓 Open-source 🔑 IMAP (works w/ Gmail, Outlook, etc.) 🤖 Bring your own LLM ⚡ Digs thru 100k+ emails + attachments github.com/jmrk84/neura... #NoMoreEmailArchaeology 030