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Joachim Goedhart

@joachimgoedhart.bsky.social
4.8K followers 1.3K following 870 posts

Scientist + Teacher UvA/Amsterdam | Cells | Molecules | Microscopy | Fluorescent Proteins | Biosensors | Lifetime imaging | Open Science | dataViz | R | web apps Homepage: joachimgoedhart.github.io DataViz Apps: huygens.science.uva.nl

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Reposted by Joachim Goedhart
Reto Fiolka @retof.bsky.social · 14h
Y’all 🤬☠️ www.linkedin.com/posts/wenlu2...
linkedin.com
#microscopymonday | Wen Lu | 29 comments
The Unicorn Is Still Waiting 🦄🔬 #MicroscopyMonday I created this cilia-“inspired” fluorescent unicorn last week, hoping Nikon Small World’s ongoing review would bring clarity and restore confidence i...
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Sebastian S. Cocioba @atinygreencell.bsky.social · 05/10/2026
I have a claude max account, a Prusa Mk4 printer, and i design in OpenSCAD which is a programming language for 3d design, a paradigm more familiar to LLMs than commercial CAD. Free to. I connect to printer wirelessly via PrusaLink (free) and tell claude what i need and feedback loop the fits/design
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Hetan Shah @hetanshah.bsky.social · 03/10/2026
Good piece from @jburnmurdoch.ft.com & @sarahoconnorft.ft.com on AI in science. It’s making some bits faster, but there is a new ‘verification tax’ taking up time. And there are heightened bottlenecks in physical experiments & data collection. AI is a workflow problem www.ft.com/content/4508...
ft.com
The AI Shift: Is AI supercharging science?
Productivity gains in analysis are getting stuck in physical-world bottlenecks
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Nicola Rennie @nrennie.bsky.social · 01/10/2026
If you missed today's @rinpharma.bsky.social workshop, here are a few of my favourite "quick fixes" for some common #ggplot2 issues 📊 1. Use {ggview} to preview plots at the same size and resolution as you want to save them with ggsave() to avoid the annoying resizing #RStats #DataViz
library(ggview)
ggplot(mtcars, aes(wt, mpg)) +
  geom_point() +
  canvas(
    width = 6, height = 4,
    units = "in",
    dpi = 300
  )
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Tim Carmody @tcarmody.bsky.social · 02/10/2026
This is the funniest thing I've seen today, possibly ever
A tweet by SarahStarberry that says "oh god read the vertical axis" on top of a chart measuring AI models' release dates and model numbers rather than any real capabilities
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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 02/10/2026
Happy #FluorescenceFriday. Single immune cell migration is fascinating. But these cells can also behave like a coordinated collective, like 🐝 from a hive. I captured some embryonic myeloid cells (🔴) displaying swarming behaviour in a migrating ectoderm cell sheet (🔵), like neutrophils in our body!
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Reposted by Joachim Goedhart
Jeremy Berg @jeremymberg.bsky.social · 01/10/2026
From a discussion of updating a department website...
A photo with baby Yoda and adult Yoda with the caption "Could it be time for a new photo?"
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Mill_lab @cilialab.bsky.social · 01/10/2026
While #NikonSmallWorldInMotion has been quiet over #CiliaGate, the story has broken mainstream media here in the UK just in time for #PCDAwarenessMonth www.bbc.co.uk/news/article...
bbc.co.uk
Tiny image sparks big backlash in Nikon photo contest
Dr Ning Xu denies he broke the rules of Nikon's annual Small World In Motion contest.
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Addgene @addgene.bsky.social · 30/09/2026
Scientists have been modeling proteins using machine learning for years. Advances in AI have made these models increasingly accurate, leading to modern tools like AlphaFold. Read an introduction to AlphaFold and how it can help you in our newest blog post!
twp.ai
blog.addgene.org
An Introduction to AlphaFold
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Barret Schloerke @schloerke.com · 30/09/2026
📦 Introducing shinyreact for R & Python Write your UI natively in React. Shrink your Shiny server to data-only logic. Agent Skills write the React for you. ✨ opensource.posit.co/blog/2026-09... This is the start! Tell us what you build and what breaks. #RStats #Python #Shiny #React
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Robert Arkowitz @robertarkowitz.bsky.social · 30/09/2026
www.biorxiv.org/content/10.6...
biorxiv.org
Fluorescent proteins misreport ribosome abundance under translation inhibition
Fluorescent proteins are widely used as quantitative reporters of protein abundance in living cells. Here we show that this relationship can break down under translation inhibition: the cellular ribos...
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Reposted by Joachim Goedhart
James Manton @jamesdmanton.bsky.social · 29/09/2026
I've been working on a fast, high-ratio image compressor to try and alleviate the data storage issues myself and some of my colleagues have recently been facing. Before I 'release' version 1, it'd be great to gain some feedback regarding performance and missing features. github.com/jdmanton/rad...
github.com
GitHub - jdmanton/radelta
Contribute to jdmanton/radelta development by creating an account on GitHub.
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Tessa Montague @tessamontague.bsky.social · 29/09/2026
I'm excited to share our new preprint: Generation of a transgenic cephalopod tinyurl.com/pc86jxz8 Cephalopods (cuttlefish, octopus & squid) are crazy critters that dynamically camouflage to their surroundings by changing the color, pattern, & texture of their skin, which they control w their brain.
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jmutterer.bsky.social @jmutterer.bsky.social · 29/09/2026
Because the source region is kept in the many panel metadata, it's now easy to highlight it in the original image in FigSpace. forum.image.sc/t/fig-space-...
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Reposted by Joachim Goedhart
Hao Yin @haoyin.bsky.social · 29/09/2026
Real-time in vivo measurement of cGMP in cGi500 (FRET-based cGMP sensor- CFP/YFP ratio) 🐭 skeletal muscle Arterioles Acetylcholine-induced arteriolar dilations are Not attenuated in sGC−/−🐭 How flow modulates precapillary arteriolar cGMP?😁 #ActaPhysiol 2026 onlinelibrary.wiley.com/doi/10.1111/...
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Louis Ates @mycolates.bsky.social · 28/09/2026
Hey all, If you're interested in the work we do on designing mRNA encoded TB vaccines at BioNTech, check out this webinar I gave recently for the @isv-news.bsky.social webinar series. youtube.com/playlist?lis...
youtube.com
ISV Webinar Series - YouTube
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Simon Bullock @simonbullock11.bsky.social · 28/09/2026
How are mRNAs linked to molecular motors in mammalian cells? In our new preprint, we show that FXR1/2 are RNA adaptors for the microtubule motor dynein. Our findings have also prompted us to rethink how activating adaptors contribute to motor-based transport (1/n)
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Joachim Goedhart @joachimgoedhart.bsky.social · 28/09/2026
Mapping the Functional Landscape and Viral Diversity of 2A Peptides by Eric Jan and team: www.biorxiv.org/content/10.6...
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Rachel Donka @racheldonka.bsky.social · 27/09/2026
🚨New paper alert: Excited to share our journey to contrast how multiple dopamine sensors respond to acute morphine treatment. We first compared changes in dopamine transients in rats prepared with VTA DA GCaMP6f, NAcLS dLight1.3b or GRABDA2h 1/5
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Joachim Goedhart @joachimgoedhart.bsky.social · 27/09/2026
or never made and used a calibration curve on grid paper
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Peter Carlton @carltonlab.org · 27/09/2026
Interesting! It was 193 frames, 1288x720 px when I obtained it; shasum-1 : 1bccd…. I scanned the other 30 hosted entries and found no SynthID watermarks.
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Kay Schink @kschink.bsky.social · 26/09/2026
It's actually quite easy to test. Go to SynthId (deepmind.google/models/synth...) , upload the video and ask it to test. I downloaded the video directly from Linkedin
deepmind.google
SynthID
SynthID is a tool to watermark and identify AI-generated content, helping to foster transparency and trust in generative AI.
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Caroline Bartman @cbartman.bsky.social · 26/09/2026
Are there key discoveries made with spatial RNA seq? Or what are your favorite spatial rna seq papers? Pls reski!
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Valentin Dunsing-Eichenauer @handle.invalid · 25/09/2026
#FluorescenceFriday: Given the recently grown interest in ciliary beating, here is a movie of beating cilia in a human airway model that I captured last week with lattice light-sheet microscopy. No AI „processing“, this is the raw data! Frame rate is ca. 170fps, displayed here at 25fps.
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Mia Konjikusic, PhD @konjikusicmia.bsky.social · 25/09/2026
To add to all the lovely videos of non-AI processes multicilia beating: ctenophore multiciliated cells! They can reach up to 1mm long, causing a rainbow light refraction effect with the correct light positioning! Taken by myself at MBL in 2019 embryology. Realtime frame-rate!
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Jonas Wietek @jwietek.bsky.social · 24/09/2026
Two cillia, no AI, enjoy.
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Joachim Goedhart @joachimgoedhart.bsky.social · 25/09/2026
Don't you just love the natural panning?
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Christophe 🔬 Leterrier @christlet.bsky.social · 25/09/2026
Here's a balanced account of where the microscopy community stands on AI use by this year's Small World in Motion winner. My main issue is that no one seems to have seen the original data despite requests (no mention of it being reviewed by the organizers) www.the-scientist.com/allegations-...
the-scientist.com
Allegations of AI Use in Nikon Competition Spark Controversy | The Scientist
Microscopists raise concerns about inappropriate AI usage in Nikon's microscopy contest-winning video. Nikon stands their ground, citing no policy breach.
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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 25/09/2026
Happy #FluorescenceFriday. The first time I imaged a 🐸 embryo, I didn't realise they had these ciliated cells on the outer surface. So you can imagine how surprised and curious I was! These cilia are similar to those found in the human airway. And yes, this is just a good old confocal + 🔥LUT!
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Sholto David @sholtodavid.bsky.social · 20/09/2026
Today I'm posting a video about Neurodigitech LLC which has provided clearly photoshopped neurons to research teams that published these images in Nature, JBC, and more. A year after I uncovered this only one paper has been corrected. It's in Frontiers. youtu.be/4g_1_AWOVpI
youtu.be
Faked Images of Neurons in Major Journals
YouTube video by Sholto David
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Joachim Goedhart @joachimgoedhart.bsky.social · 25/09/2026
A Chemigenetic Fluorescence Lifetime Biosensor for Dopamine Sensing by Hsin-Chih Yeh and team: www.biorxiv.org/content/10.6...
Rational designs of the chemigenetic dopamine sensors
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Reposted by Joachim Goedhart
Peter Carlton @carltonlab.org · 25/09/2026
I know, and they also swing down into what should be intracellular space?! Here's another one using Grid/Collection stitching (thanks @preibischs.bsky.social !) showing the whole movie.
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André Nadler @nadlerlab.bsky.social · 24/09/2026
Well, actually cilia are probably also hallucinations bsky.app/profile/joac...
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Joachim Goedhart @joachimgoedhart.bsky.social · 24/09/2026
Thanks for sharing this version, to me the most stunning part is the region where the cilia seem to appear (out of nowhere?)
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Jonas Wietek @jwietek.bsky.social · 24/09/2026
Glutamate 🧠
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Christophe 🔬 Leterrier @christlet.bsky.social · 24/09/2026
I think I'm going to lose it being lectured on microscopy image presentation integrity by the winner of the Small Artificial World in Motion competition
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 23/09/2026
Preparing my submission for the next year's "Nikon Small World in Motion". It should qualify, since I wrote it on a PC connected to a microscope. No AI, pure GLSL GPU code www.shadertoy.com/view/f333Dj
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Heather Brown-Harding @microscopyed.bsky.social · 23/09/2026
Anyone have any seen red autofluorescence in the agarose pad while imaging c. elegans
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Joachim Goedhart @joachimgoedhart.bsky.social · 23/09/2026
The scale bar makes me curious about the time per frame and total duration of the movie
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Andrey Klymchenko @aklymchenko.bsky.social · 23/09/2026
Pre-print alert: we are thrilled to report on rhodamine-derived ratiometric molecular rotor for ratiometric sensing of viscosity in mitochondria. Thanks to co-authors O. Kharchenko and P. Didier! @cnrs.fr, @unistra.fr and @agencerecherche.bsky.social. BioRxiv link: www.biorxiv.org/content/10.6...
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Christophe 🔬 Leterrier @christlet.bsky.social · 23/09/2026
As they are not active here, I left a comment on the LinkedIn post from Nikon Small World about the concerns I think I share with many (first screenshot is their post, second screenshot is my comment) lnkd.in/p/ecdT6saZ
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Joachim Goedhart @joachimgoedhart.bsky.social · 23/09/2026
Serpin-driven green camouflage and NIR fluorescence in frogs www.science.org/doi/10.1126/...
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Nicola Rennie @nrennie.bsky.social · 22/09/2026
A question for the #RStats and #ggplot2 hivemind: What things do you find most tricky or frustrating in ggplot2? It might be things like specific chart types, aspects of styling, your workflow, saving charts etc.
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Christophe 🔬 Leterrier @christlet.bsky.social · 22/09/2026
From the new info my bet is fluo labeling inference pushed to 11. Hallucinating nonsensical DAPI nuclei, mitochondria stain, membrane labeling from a kind of phase contrast image: wrong localization, wrong scale, wrong movement. Keeping this movie as SWiM winner is a disgrace to the competition
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Christophe 🔬 Leterrier @christlet.bsky.social · 22/09/2026
This is the updated part. Looks like the movie is an AI-generated fluorescence image from a non-labeled acquisition technique. No indication that the Small World jury and organizers have requested and verified the raw data (as mentioned as a possibility in the competition rules)
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Tonni Andersen @tonnigrubeandersen.bsky.social · 22/09/2026
Check out our new preprint: a very cool fluorescence tool developed by @samwalds.bsky.social www.biorxiv.org/content/10.6...
biorxiv.org
Intronised fluorophores improve reporter output and biosensor expression in plants
Genetically encoded biosensors are central to plant cell biology, but low reporter signal can limit their use. Here, we developed modular intronised fluorophores to improve reporter output in transien...
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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 21/09/2026
Happy #MicroscopyMonday. I found this very pretty COS-7 cell expressing LifeAct-mCherry from my old data. Look at how dense its actin network is. Also, many of the moving dots are endosomal to seemingly push them through the cytoplasm, similar to actin comet tail, but just a lot shorter.
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David Gaboriau @dgaboriau.bsky.social · 21/09/2026
OptoBadFigure
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Joachim Goedhart @joachimgoedhart.bsky.social · 21/09/2026
What is THIS? Source: doi.org/10.1016/j.cr...
Visual abstract of a scientific paper with hints of AI slop (e.g. microtubules depicted with too little or too many protofilaments)
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Karen Fisher, PhD @fisherke.bsky.social · 21/09/2026
Hey @healthcare.nikon.com Care to comment? Quite a few of us have questions
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