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Zach Marin

@zacsimile.bsky.social
599 followers 841 following 69 posts

hardware x software in microscopy | zacsimile.github.io | 📍Vienna, Austria | he/him | views are graphical projections

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Reposted by Zach Marin
Jia Chen @chenjiajiachen.bsky.social · 06/10/2026
Fresh preprint from St Johnston lab in collaboration with Paluch lab. "Fast, 3D SMLM imaging modality, Intrinsic3D, which combines the speed and optical sectioning of oblique plane microscopy (OPM) with the nanometre resolution of SMLM using DNAPAINT". Amazing imaging, here is one of my favourite:
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Reposted by Zach Marin
pixelatedboat aka “mr bluesky” @pixelatedboat.bsky.social · 06/10/2026
Once again, the Nobel prizes have been given to a bunch of nerds while all the recent advances that jocks have made in football go unrecognised 😞
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Virginie Uhlmann @virginieuhlmann.bsky.social · 05/10/2026
Are you a biologist working with microscopy images? A computer scientist wanting to work with microscopy data? Their boss??? None of these, but curious how AI has transformed microscopy image analysis? 🔬🤖 This one's for you: 📄 doi.org/10.1146/annu... More in the thread! 🧵
doi.org
From Pixels to Discovery: Microscopy Image Analysis in the Age of Artificial Intelligence
Modern microscopy generates data volumes that far exceed human analytical capacity. Over the past decade, artificial intelligence (AI) has transformed microscopy image analysis into an engine for quan...
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Zach Marin @zacsimile.bsky.social · 30/09/2026
Not future-proof, but ExifTool reveals metadata differences between real and GPT-generated OME-TIFFs. GPT images also have smoother histograms, even when based on a reference. A labeled collection of real and AI-generated images could help test whether these signals support a useful discriminator.
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Reposted by Zach Marin
Anne Helen Petersen @annehelen.bsky.social · 30/09/2026
This is *the* piece. Kate Manne, professor of philosophy at Cornell, speaks truth to the totality of failures at the university — and why students protesting the war in Gaza have faced far harsher consequences than any of the Cornell 7: www.thecut.com/article/what...
thecut.com
What It Feels Like at Cornell Right Now
As a professor at the Ivy League school, Kate Manne has known many, many victims. There’s a palpable feeling on campus, she writes, that this is big.
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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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Reposted by Zach Marin
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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Reposted by Zach Marin
Jörg Enderlein @joergenderlein.bsky.social · 24/09/2026
An extremely well written evaluation of the case of Jason Arday and the underlying right-wing ideology and racism by @florianaigner.at www.florianaigner.at/blog/posts/2...
florianaigner.at
The Return of Race Science
A Black Cambridge professor is targeted by a self-proclaimed “race realist”. The case of Jason Arday—and what it means for science.
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Reposted by Zach Marin
Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Eoin Higgins @eoinhiggins.bsky.social · 20/09/2026
You’re right—that plane shouldn’t have gone there. That’s my fault, and I should have made sure there wasn’t a terminal in the landing path. Would you like me to call emergency services, or assist with lining up takeoffs?
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Christophe 🔬 Leterrier @christlet.bsky.social · 19/09/2026
Here's a way to get a pure science shot on Bluesky: a custom feed that only shows the posts from people you follow that are linked to a DOI bsky.app/profile/pape...
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Zach Marin @zacsimile.bsky.social · 17/09/2026
This was a joint effort of the Scheuder (@florianschueder.bsky.social) and Ries (@jonasries.bsky.social) labs. Thanks to my amazing colleagues: Amr Abouelezz, Nestor Castillo, @aminosarah.bsky.social, Fabian Hauser, Leia T. Köstinger, @anvitamanjunath.bsky.social, and @nicostuurman.bsky.social.
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Zach Marin @zacsimile.bsky.social · 17/09/2026
We used it to implement workflows for parameter optimization (e.g. for TIRF angle), troubleshooting, Exchange-PAINT imaging, finding and tracking kinesins in living cells, and looking for specific mitochondrial morphology.
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Zach Marin @zacsimile.bsky.social · 17/09/2026
MicroClaw advises on experiment- and system-specific parameters and approaches. It collaboratively plans and executes diverse, complex, and reusable imaging workflows across microscope platforms, without requiring expert knowledge.
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Zach Marin @zacsimile.bsky.social · 17/09/2026
Happy to share our publication on MicroClaw, an AI agent that turns natural language requests into operations on any microscope controlled by Micro-Manager: www.biorxiv.org/content/10.6.... The software is single-click installable (download and click install.bat) at github.com/Micro-Claw/m....
biorxiv.org
Microscope control with a natural language agent
Microscopy underpins modern biology, but acquiring high-quality data from complex experiments at scale remains challenging. Smart microscopy can standardize and automate data collection, but each expe...
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Reposted by Zach Marin
Christophe 🔬 Leterrier @christlet.bsky.social · 02/09/2026
Really cool! Smaller than GFP and reversibly binding last-generation rhodamine dyes. De novo pan-rhodamine binders for fluorescence microscopy from mammalian cells to extremophiles www.cell.com/cell/fulltex... Congrats @bohuang.bsky.social @rhodamine110.bsky.social @mullinslab.bsky.social et al
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Reposted by Zach Marin
Reese Richardson @reeserichardson.bsky.social · 25/08/2026
A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵
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Harmit Singh Malik @harmitmalik.bsky.social · 09/08/2026
I’ve often said (partly tongue in cheek) that spite can be a great motivator. But mudita (freudenfeude), the ability to be truly happy for others’ success, can be a much more reliable way to have a fulfilling career. Even if it can seem that way, science is not a zero sum game. Play the long game.
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Ali Shaib @alishaib.bsky.social · 07/08/2026
Exciting new preprint from Ignacio Vega Vásquez, Sauer lab, my team and collaborators: #Mega-ExM. From just ~20 NPCs imaged with a 10× objective on a confocal, we reconstructed the 3D structure at ~33 Å. A step toward optical structural biology in intact cells. www.biorxiv.org/content/10.6...
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Jason Nomburg @jnoms.bsky.social · 22/07/2026
Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
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Carl T. Bergstrom @carlbergstrom.com · 31/07/2026
Nature did a short piece on our preprint about how LLMs will affect the practice of science; my more detailed thread is below.
nature.com
Scientists using LLMs will ‘do more, less well’, modelling study predicts
Research suggests that the combination of incentives to publish and the use of large language models will lead to more papers, but they will be less refined.
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Hao Sha @haosha.bsky.social · 28/07/2026
[0/1] Excited to share our new preprint DECODE-Plex! After many people efforts, we developed a deep-learning framework for multi-channel SMLM, enabling simultaneous localization and color assignment of densely packed emitters across multiple channels. biorxiv.org/content/10.6...
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Derek Lowe @dereklowe.bsky.social · 23/07/2026
Thoughts on the various Trump administration proposals to revamp US science funding - and what they all have in common:
science.org
The Assault On Science Funding Continues
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Carl T. Bergstrom @carlbergstrom.com · 23/07/2026
1. The new Trump / Kratsios plan for US science appears explicitly designed to destroy US universities. Diverting money to tech donors is probably just a bonus. Gift link.
nytimes.com
Trump’s Plan for Science: More Money for A.I., Less for Universities (Gift Article)
Michael Kratsios, President Trump’s science adviser, proposed overhauling how the government funds research. Democrats said Mr. Trump’s actions had weakened science.
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Zach Marin @zacsimile.bsky.social · 24/07/2026
Listening to Music to Make Microscopes To Listen To Music To www.youtube.com/watch?v=qJ5D...
youtube.com
Big City (Everybody I Know Can Be Found Here)
YouTube video by Spacemen 3 - Topic
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Reposted by Zach Marin
Nature Methods @natmethods.nature.com · 23/07/2026
FlatMux: an optimized microscope system for multiplexed 2-photon imaging of neuronal activity with voltage sensors. www.nature.com/articles/s41...
nature.com
A versatile platform for two-photon neuronal population voltage imaging across cortical depths - Nature Methods
FlatMux is an optimized microscope system for multiplexed two-photon imaging of neuronal activity with genetically encoded voltage sensors. The flexible system is demonstrated in a variety of scenario...
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Reposted by Zach Marin
Jay Van Bavel, PhD @jayvanbavel.bsky.social · 18/07/2026
We need to change norms around sexual harassment Yesterday Tessa West spoke up about a sexual harassment complaint she filed against John Jost. Not only is he a senior colleague in the dept of psychology, but he is one of the most prominant figures in the field of social and political psychology.
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Bill @bill-of-lefts.bsky.social · 17/07/2026
the degree to which they want to destroy one of the jewels of the American republic—our exceptional research universities—is just gobsmacking
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Luke Lavis @rhodamine110.bsky.social · 17/07/2026
Excited to see this collaboration now in print. Dye chemistry meets AI-designed proteins. Three small, orthogonal tags; lifetime modulation; split versions. Request the free dyes at dyes.janelia.org www.science.org/doi/10.1126/...
science.org
De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging
Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostabilit...
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Zach Marin @zacsimile.bsky.social · 17/07/2026
As an AI hater, it's with deep regret I inform you that I agree. Claude Code is very useful.
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Zach Marin @zacsimile.bsky.social · 17/07/2026
The end of this article correctly touches on what Corey Doctorow calls reverse centaurism (www.theguardian.com/books/2026/j...), where humans end up working in service to AI rather than the other way around. By using LLMs to write articles, we force reviewers to screen for machine made errors.
theguardian.com
The Reverse Centaur’s Guide to Life After AI by Cory Doctorow review – the real price of artificial intelligence
A vivid and entertaining polemnic on the economics of the tech revolution, filled with righteous ire
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Reposted by Zach Marin
Barbara Mellone 🇺🇦 @centromellone.bsky.social · 16/07/2026
Manuscripts with women as corresponding authors are less frequently sent out for review at Science. The ones reviewed receive less favorable reviews by both male and female reviewers.
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STAT @statnews.com · 15/07/2026
An analysis of public comments on a White House proposal to change the way federal contracts and grants are doled out shows widespread opposition. www.statnews.com/2026/07/15/t...
statnews.com
Flood of comments on White House grantmaking overhaul is largely negative, analysis shows
An analysis of public comments on a White House proposal to change the way federal contracts and grants are doled out shows widespread opposition
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Zach Marin @zacsimile.bsky.social · 15/07/2026
I have taken the powermeter that was on the optics table and which you were probably saving for later Forgive me it was useful so sensitive and so fast
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Altmetric @altmetric.com · 10/07/2026
Thanks for the kind words, but equal (if not greater) credit goes to @benpatrickwill.bsky.social for helping us by identifying the AI slop to begin with. Highly recommended read - particularly for the unbelievably disgraceful use of GenAI faces. nobreakthroughs.com/the-scientis...
nobreakthroughs.com
The Scientists That Don't Exist
Ghostly websites publishing science press releases are filling up with AI-generated content — and the ghosts of scientists that don't exist.
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Zach Marin @zacsimile.bsky.social · 10/07/2026
Hunh. AI search becomes a lot less useful if you can't access to 20% (blog.cloudflare.com/application-...) of all websites. Are we heading back to web directories? www.adweek.com/media/publis...
adweek.com
Publishers Are Preparing to Opt Out of Google Search
The nuclear option is gaining traction as web traffic collapses and Google refuses to negotiate with content creators
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BWJones @bwjones.bsky.social · 03/07/2026
When I explain to peeps how much we do in research labs for how few $$, they simply don’t believe me. I once explained it to a famous person from Pixar, he looked me square in the eye and said “You mean all the cancer, vision, and Alzheimer’s grants work that way? You’ve gotta be %#ing kidding me!”
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Ran Blekhman @blekhman.bsky.social · 27/06/2026
I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...
open.substack.com
My Peer Review of The 1%
I wanted to like QED's new 1% ranking. I don't.
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WIRED @wired.com · 28/06/2026
A newly identified species of fungus attacks the famous “zombie mushrooms” that control ants.
wrd.cm
The ‘Parasite of Parasites’ Has Been Discovered in the Tropical Forests of Borneo
A newly identified species of fungus attacks the famous “zombie mushrooms” that control ants.
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Reese Richardson @reeserichardson.bsky.social · 06/06/2026
Thermo Fisher now has a page up in response to our observations. They flatly deny that images were manipulated or fabricated while repeating that images were "optimized for presentation and clarity on the website", no lie, six times. www.thermofisher.com/us/en/home/l...
thermofisher.com
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Sandrine Lévêque Fort 🔬 @slfort.bsky.social · 05/06/2026
🔬 Happy to share our new paper showing that fluorophore brightness open a new dimension in SMLM microscopy ! Thanks to all authors @laurent-le.bsky.social S. K. Sreenivas @emmanuelfort.bsky.social ! @ismolab.bsky.social @instlangevin.bsky.social @cnrs.fr rdcu.be/fmIeD doi.org/10.1038/s415...
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Zach Marin @zacsimile.bsky.social · 06/06/2026
Thermo Fishy
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Ricardo Henriques @henriqueslab.bsky.social · 05/06/2026
🔬🚀 It's out! Run 100s of imaging experiments before touching a microscope. #VLab4Mic reproduces them in silico from PDB/AlphaFold to help you image right first time. From rockstars Damián Martínez & Bruno Saraiva, inaugural preprint of @mariodelr.bsky.social new lab www.biorxiv.org/content/10.6...
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James Manton @jamesdmanton.bsky.social · 02/06/2026
We present: Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution www.biorxiv.org/content/10.6...
Image of first two pages of manuscript.
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Ali Shaib @alishaib.bsky.social · 01/06/2026
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
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Andrew G. York @andrewgyork.bsky.social · 29/04/2026
Meet MagLuc: a magnetically-controlled luminescent protein. This is a foundational tool for remote control of biological processes, also known as "magnetogenetics". Can you tell when the magnetic field turns on and off? From @mariaingaramo.bsky.social and the team at @nonfictionlabs.bsky.social
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Fiona Tribe @fionatribe.bsky.social · 23/04/2026
Yes, Swiss scientist Fritz Zwicky coined the term “dark matter” which is impressive, but he also coined the term “spherical bastard” to describe people who are bastards no matter which way you look at them, and I think that should be celebrated more.
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Zach Hensel @zachhensel.bsky.social · 23/04/2026
This isn’t the first time. He told someone he was “feeling blue” about the results of this study - www.nytimes.com/2020/04/15/s... - and then he didn’t publish them. As far as I know this hasn’t come up in congressional oversight. Pretty wild.
nytimes.com
M.L.B. Employees Become the Subjects of a Huge Coronavirus Study (Published 2020)
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