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Nathan Day

@nthndy.bsky.social
809 followers 668 following 29 posts

cell biology // host pathogen interactions // image analysis // deep learning // object tracking

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Reposted by Nathan Day
Daniel Krentzel @danielkrentzel.bsky.social · 30/09/2026
The source code and datasets for this study can be found here 👇 💻 github.com/krentzd/morp... 🔬 www.ebi.ac.uk/biostudies/b...
github.com
GitHub - krentzd/morphoscreen: Source code for morphoscreen analysis
Source code for morphoscreen analysis. Contribute to krentzd/morphoscreen development by creating an account on GitHub.
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Daniel Krentzel @danielkrentzel.bsky.social · 30/09/2026
Our paper outlining a deep learning-based phenotypic screening method to discover new TB drugs is out in @science.org #ScienceAdvances 💊🦠 It's the result of a great collaboration between the labs of @chzimmer.bsky.social and @awehenkel.bsky.social at @pasteur.fr! 📃 www.science.org/doi/10.1126/...
science.org
Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria
To address drug-resistant tuberculosis, the leading single-pathogen infectious killer, drugs with novel modes of action (MoAs) are urgently needed. Phenotypic screening of chemical libraries can ident...
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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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Fared Al Mahlool | فريد المحلول @faredalmahlool.bsky.social · 19/09/2026
This video was filmed in Palestine. My heart struggles to comprehend such cruelty and the heartbreaking disregard for human life. No human being should have to endure this.
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Ricardo Henriques @henriqueslab.bsky.social · 15/09/2026
🔬🚀 Out now in Communications AI & Computing: mAIcrobe, our open-source napari plugin for high-throughput bacterial image analysis. Segmentation, morphological profiling and cell cycle classification, all in one place 👇 doi.org/10.1038/s44488-026-00022-y
Screenshot of the published article page. Software, Open access, published 15 September 2026. Title: mAIcrobe, an open-source framework for high-throughput bacterial image analysis. Authors: António D. Brito, Dominik Alwardt, Beatriz de P. Mariz, Sérgio R. Filipe, Mariana G. Pinho, Bruno M. Saraiva and Ricardo Henriques. Communications AI & Computing 1, article number 16 (2026), followed by the abstract.Diagram of the mAIcrobe workflow. Acquisition feeds into segmentation with StarDist, Cellpose and community models, then into morphological profiling and a three-class cell cycle classifier, ending in a feature-space scatter plot with three separated clusters.
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Nature Reviews Microbiology @natrevmicro.nature.com · 13/08/2026
ICYMI: New online! Mycobacterium tuberculosis outpaces antibiotic treatment
dlvr.it
Mycobacterium tuberculosis outpaces antibiotic treatment
Nature Reviews Microbiology, Published online: 06 August 2026; doi:10.1038/s41579-026-01357-0This study reports that fast-growing intracellular Mycobacterium tuberculosis evades antibiotic treatment.
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Nathan Day @nthndy.bsky.social · 07/08/2026
I'm converting an old chlorine-bleached fountain into a natural pond ecosystem. If you're curious about pond life, from alba lillies to aquatic snails, you can follow along here 🐸 nthndy.github.io/peasoup
A close up shot of a water lily with flower in full bloom, pale pink petals opening up radially in all directions with a yellow heart. The flower is surrounded by a few lily pads in a peasoup green pond.
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Nathan Day @nthndy.bsky.social · 28/07/2026
I hope you enjoy reading the paper and viewing the beautiful live-cell imaging behind it all. In the name of open source everything I made an interactive manuscript where you can view the rich images that contributed to every single-cell measurement at nthndy.github.io/macrohet_worldwide
nthndy.github.io
Fast-growing intracellular Mtb populations evade antibiotic treatment
An interactive manuscript exploring how fast-growing intracellular M. tuberculosis populations evade first-line antibiotic treatment.
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Nathan Day @nthndy.bsky.social · 28/07/2026
Very pleased to announce that my Crick postdoc work has just been published in Nature Communications: www.nature.com/articles/s41... Big thank you to @bpradel.bsky.social, @jaksonluk.bsky.social, @maxgg.bsky.social and the rest of the host-pathogen interactions in TB lab that made it all possible!
nature.com
Fast-growing intracellular Mycobacterium tuberculosis populations evade antibiotic treatment - Nature Communications
The slow growth displayed by Mycobacterium tuberculosis has been historically associated with pathogen’s persistence and drug tolerance. Unexpectedly, here the authors identify a rare subpopulation of...
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Juan Nunez-Iglesias @jni.codes · 07/07/2026
I don't know how much of my view is because "I've found a really cool hammer and now everything looks like a nail", but cooperative ownership and governance seems to me to be a great model for universities, newspapers, and platforms (music or otherwise).
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Zack Polanski @zackpolanski.bsky.social · 20/06/2026
“restrictions on pro-Palestinian speech and protest, when justified by invocations of Jewish safety, will backfire and weaken social cohesion and potentially increase antisemitism”. www.theguardian.com/news/2026/ju...
theguardian.com
Conflation of Jewish identity with Israel driving antisemitism, Jewish Council says in submission to royal commission
Progressive Jewish group calls for more focus on the threat from the far right and the recognition of a diversity of views within the community
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Emily Hunt @emily.space · 05/06/2026
I am SO sick of headlines like this. The public sees "AI" as being LLMs/ChatGPT, not an ML algorithm - and articles like this mislead the public into thinking that LLMs are discovering novel things. It's a cool thing! I'm excited! But it is lazy reporting to suddenly use "AI" as such a broad term
Headline that reads 'World-first' vaccine designed by artificial intelligence
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George Monbiot @georgemonbiot.bsky.social · 04/06/2026
In Doppelganger, @naomiaklein.bsky.social shows how white supremacists assume the victimhood of those they oppress, presenting the evils they do as evils done to them. In Britain, where black people are 7 times more likely than white people to die after police restraint, this is what we are seeing.
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Sarah Rose @thesarahrose.bsky.social · 13/05/2026
The good taxpayers of New York have given me a pair of Meta glasses because I am low vision disabled, and I seem to have used them more than a lot of people on here, so let me say a little about my experiences:
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mara🐦‍⬛ @mara.x0f.nl · 29/04/2026
so envious of LLMs i want to be able to invoke tool calls just by thinking a json structure too
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London Infection Network for/by ECRs (LINE) @londoninfectionecr.bsky.social · 28/04/2026
📢 Our SECOND LINE+ seminar will be on May 20nd at Imperial College. @nthndy.bsky.social will join us to share how he turns his machine learning approaches to understand Mtb persistence into accessible interactive datasets. Registration/info: tinyurl.com/2t56zfp8 More about Nathan: nthndy.github.io
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Chumbus @chumbus.bsky.social · 02/04/2026
Someone has probably said it but
A tweet from Tom Walker @tomwalkerisgood which takes the form of a dialogue as follows.
KOKOK: Koko birkin bag. Practical Koko possession bag
RESEARCHER: No, Koko. You can't have a Birkin bag.
KOKO: Good Birkin good Koko give beautiful Koko deserve gorilla
RESEARCHER: Koko, we simply can't afford a Birkin bag. It is an unjustifiable expense.
KOKO: jealousy professor
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Jessica Elgot @jessicaelgot.bsky.social · 31/03/2026
Strikes me as an absurd threat, either we need the 4000 new training places or we don’t
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Nathan Day @nthndy.bsky.social · 27/03/2026
tracking a single-cell mycobacterium tuberculosis infection across time
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The Great Pumpkin Papers 🎃🎃🎃 @professormusgrave.bsky.social · 24/03/2026
I am always with you, in spirit, to remind you that thou art mortal. profmusgrave.github.io/anotherday/
profmusgrave.github.io
One Day Closer to the End
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Emily R. Trunnell, Ph.D. @ertrunnell.bsky.social · 23/03/2026
☝️ Incl. work from our colleagues & exciting research from @jaksonluk.bsky.social, @maxgg.bsky.social, @nthndy.bsky.social, & @gabrielconway.bsky.social at @crick.ac.uk. Also papers by @simonjoosten.bsky.social, @tbimmunologytcd.bsky.social, @armesilla.bsky.social, & more! #EndTB #StopTB #IDsky
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Dr Dion Georgiou 🇨🇾❤️🇬🇾 @drdiongeorgiou.bsky.social · 23/03/2026
My grandfather worked at a Jewish restaurant in Golders Green for twenty years. When he was taken ill at work one day, this ambulance service rushed him to hospital. This is such a cowardly, immoral, hateful act.
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London Review of Books @lrb.co.uk · 14/01/2026
‘The value of the world’s top ten companies is $25.6 trillion. Of that, $15.1 trillion has accumulated since 30 November 2022 and is directly linked to the AI boom.’ John Lanchester on the AI bubble. www.lrb.co.uk/the-paper/v4...
lrb.co.uk
John Lanchester · King of Cannibal Island: Will the AI bubble burst?
Nvidia shares are the purest bet you can make on the impact of AI. The leading firms are lending money to one another in...
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Damian Dalle Nogare @damiandn.bsky.social · 05/01/2026
It's honestly a bit surprising how much more complex image analysis gets once you're in the regime of images too big to fit in memory. All of the solutions you do (use zarr! Split the image!) come with a whole host of issues that you've never had to think about until you run into them.
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The Francis Crick Institute @crick.ac.uk · 01/01/2026
Lab-grown lung models have traditionally been grown from a mixture of cells, making it hard to tell how a disease or treatment will affect an individual person. These new models by @maxgg.bsky.social’s team and AlveoliX are grown from a single person’s stem cells ⤵️ www.crick.ac.uk/news/2026-01...
crick.ac.uk
Built to breathe: mini ‘lungs’ recreate individual response to infection
Lung-on-chip device exposes earliest stages of tuberculosis infection, and opens doors to investigate diversity in disease progression and personalised treatment.
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Mr Roger Quimbly @rogerquimbly.bsky.social · 19/12/2025
He saw the light.
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Adam Bienkov @adambienkov.bsky.social · 13/12/2025
The fact is no presenter has ever had to leave the BBC for expressing conservative views, or even explicitly endorsing a right-wing party. Was never a problem for Jeremy Clarkson. Was never a problem for Andrew Neil. Was never a problem for Alan Sugar
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Jamie Fookes @jrfookes.bsky.social · 07/12/2025
This is such an extreme and deeply segregationist view to hold it should completely discredit her from her position. Stating that a group, clearly protected in the spirit and word of the equality act, where tricked into 'thinking they have rights" is unforgivable she must resign
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Dave Barry @david-j-barry.bsky.social · 25/11/2025
BIOIMAGE ANALYSTS ASSEMBLE!!! #CBIAS2025
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Lee D @leedon1982.bsky.social · 24/11/2025
Brilliant from the journalist. The most on-the-ropes I’ve ever seen Farage. His usual bluster tactic didn’t work. His uttering of ‘well, you wouldn’t’ when the journalist said ‘I don’t quite know what you mean’ was genuinely pathetic. More of this please.
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Phil Lewis @phillewis.bsky.social · 10/11/2025
WASHINGTON (AP) — Canada has lost its measles elimination status because of continued spread, international health experts say.
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Nathan Day @nthndy.bsky.social · 27/10/2025
This is what real leadership and integrity looks like!!!
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Sojourners @sojo.net · 07/10/2025
Even the most dramatic displays of defiance can sometimes carry less impact than the humbler acts of protection and preparation, writes Georgia Coley. sojo.net/articles/cul...
sojo.net
‘One Battle After Another’ Shows Christians How to ‘Work for the Peace of the City’
In Paul Thomas Anderson’s latest film, the best way to fight an endless series of battles is to play smart defense. Churches should take note.
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Gavin Buckingham @drgbuckingham.bsky.social · 25/10/2025
For your enjoyment (by @jagarikin)
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Frances Ryan @francesryan.bsky.social · 08/10/2025
This is devastating but hard to think of more important journalism. 18,457 children have been killed in Gaza (many more not accounted for). Here, The Guardian prints their names and beautiful faces and tells us what they were like before Israel stole their lives. www.theguardian.com/world/ng-int...
theguardian.com
Young lives cut short on an unimaginable scale: the 18,457 children on Gaza’s list of war dead
Every name on a list compiled by health authorities in Gaza of the child victims of Israel’s offensive
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Noémie Matthey @noemiematthey.bsky.social · 13/11/2024
It's really nice to see the huge flow of new people coming here! Maybe it's time for a quick presentation. Hi 👋 I'm Noémie, I love science 🧬 and especially microbes 🔬 I do scientific illustrations for paper, cover or logo. And I'm the illustrator behind the Bacterial World blog: sarahs-world.blog
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Farrukh @implausibleblog.bsky.social · 29/09/2025
Krishnan Guru Murthy, "Isn't it a bit insulting to say to an Indian doctor who is working 60-70 hours a week that in order to get settled status he's got to volunteer?" Rachel Reeves, "We want people to contribute if they come to our country" Labour have gone utterly bonkers
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Megan Abbott @meganabbott.bsky.social · 25/09/2025
“You’ve got sadness in you, I’ve got sadness in me – and my works of art are places where the two sadnesses can meet, and therefore both of us need to feel less sad.” HBD, Mark Rothko ...
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Alex Hern @hern.bsky.social · 15/09/2025
What do we want? Musk to face consequences? When do we want it? Right after we’ve provided material support to Musk!
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bakoon @bakoon.bsky.social · 12/09/2025
they are so long
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Rob Delaney @robdelaney.bsky.social · 10/09/2025
The depths of evil www.bbc.com/news/article...
bbc.com
Anti-Islamic US biker gang members run security at deadly Gaza aid sites
BBC identifies members of Infidels MC gang hired as armed security at US and Israel-backed aid sites.
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Jim Waterson @jim.londoncentric.media · 03/09/2025
With Melvyn Bragg retiring, @tomwhyman.bsky.social introduced me to the best episode of In Our Time where Bragg just kicks off at the guest historian for --reasons--. (Skip to 14:40 if you don't have the patience to listen to the whole thing.) www.bbc.co.uk/sounds/play/...
bbc.co.uk
In Our Time - The Industrial Revolution - BBC Sounds
Melvyn Bragg and guests discuss the Industrial Revolution.
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Sarah, manic pixie dream MILF @goatsarah.org · 29/08/2025
I want to explain a few things and then it might be clearer why UK trans people are upset. In 2001 I married my wife, Sylvia. In 2005 I started medical transition. (1/13)
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Gareth Dennis @garethdennis.uk · 27/08/2025
Yet more evidence of the damage that the chronic lack of post-2020 ambition for UK high speed rail is having on transport inequality: platform edge doors were a key accessibility opportunity that HS2 offered by operating a uniform fleet. Now they've been abandoned.
ABANDONED - Phase One and
Phase Two Stations Platform
Edge Doors Framework
Agreement
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Jewish Voice for Peace @jvp.bsky.social · 21/08/2025
“These are the things you are to do: Speak the truth to one another, render true and perfect justice in your gates.” Zechariah 8:16
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Nathan Day @nthndy.bsky.social · 21/08/2025
💅💅💅
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Musa Okwonga @okwonga.bsky.social · 20/08/2025
Years ago there was video of Tommy Robinson in Italy physically attacking a black African man who had gone there as a refugee, and now he is doing this. Someone yesterday asked “why is Farage so successful” and the answer no one seemed to want to give was “a lot of people are very, very racist”
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damniel spookradski @self.agency · 17/08/2025
mei from totoro sticking out of one of the windows created by the sunlight on the cat in the quoted image
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Al Jazeera English @aljazeera.com · 12/08/2025
Ibrahim Noufal, brother of Al Jazeera staffer Mohammed Noufal who was killed in a deliberate Israeli strike on a journalists’ tent, hands out handmade bracelets to children amid ongoing attacks and forced starvation in Gaza.
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