Sign in

Daniel Krentzel

@danielkrentzel.bsky.social
202 followers 301 following 55 posts

Postdoc-ing in @virginieuhlmann.bsky.social's lab at UZH 🇨🇭 | Previously @pasteur.fr, @crick.ac.uk and @imperialcollegeldn.bsky.social

PostsRepliesMedia
Daniel Krentzel @danielkrentzel.bsky.social · 6h
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...
2206
Reposted by Daniel Krentzel
Marie Held @makaefer.bsky.social · 28/09/2026
Want to enhance your image analysis skills with napari? We’re running a two-day training event on how to use napari to effectively analyse your bioimaging data. 🕒 Applications close on 15 September. Learn more and apply 👇 www.crick.ac.uk/whats-on/cbi...
crick.ac.uk
01215
Daniel Krentzel @danielkrentzel.bsky.social · 28/09/2026
And here's a nice résumé of our @natcomms.nature.com paper for the grand public 👇 📃 www.nature.com/articles/s41...
nature.com
Deep learning recognises antibiotic modes of action from brightfield images - Nature Communications
Authors present a deep learning model that recognises antibiotic modes of action (MoA) directly from brightfield images. Their proposed method complements traditional growth inhibition assays in the s...
082
Daniel Krentzel @danielkrentzel.bsky.social · 28/09/2026
Super excited to see the first research article from my PhD @pasteur.fr out in @natcomms.nature.com! Here's a thread on the key results 🧵 @chzimmer.bsky.social @kelvinkho.bsky.social @curieuseny.bsky.social @awehenkel.bsky.social @ivo-boneca.bsky.social www.nature.com/articles/s41...
nature.com
Deep learning recognises antibiotic modes of action from brightfield images - Nature Communications
Authors present a deep learning model that recognises antibiotic modes of action (MoA) directly from brightfield images. Their proposed method complements traditional growth inhibition assays in the s...
141
Reposted by Daniel Krentzel
Christophe Zimmer @chzimmer.bsky.social · 10/09/2026
Can you tell how an antibiotic kills bacteria just by watching them under a regular microscope — without any dyes ? Yes, it turns out, at least if you are a deep neural net.
12316
Reposted by Daniel Krentzel
Nature Communications @natcomms.nature.com · 17/09/2026
#Antibiotics A deep-learning model recognises antibiotic modes of action using unlabelled brightfield images of drug-treated bacteria @chzimmer.bsky.social @pasteur.fr @uni-wuerzburg.de @danielkrentzel.bsky.social @kelvinkho.bsky.social @awehenkel.bsky.social #deeplearning #AI4AMR #microbiology
dlvr.it
Deep learning recognises antibiotic modes of action from brightfield images - Nature Communications
Authors present a deep learning model that recognises antibiotic modes of action (MoA) directly from brightfield images. Their proposed method complements traditional growth inhibition assays in the search for novel antibiotics.
031
Reposted by Daniel Krentzel
Gillen Tener Martin @gillenmartin.bsky.social · 20/08/2026
I wrote some words from a village below a wildfire that are out in the @washingtonmonthly.bsky.social today. washingtonmonthly.com/2026/08/20/h...
011
Reposted by Daniel Krentzel
Joel Lüthi @joelluethi.bsky.social · 14/08/2026
We're excited to announce the 2026 OME-Zarr hackathon 🎉 📅 Date: November 2nd - November 6th 2026 📍 Location: University of Zurich, Zurich, Switzerland 💻 Virtual participation: possible for Monday afternoon, 1:00 PM CET 6:00 PM CET biovisioncenter.notion.site/2026-ome-zar... (1/6 🧵)
2025 OME-Zarr hackathon
11414
Reposted by Daniel Krentzel
Guillaume Jacquemet @guijacquemet.bsky.social · 30/06/2026
Delighted to share our latest preprint "NucleiSky enables cross-scale multimodal registration of microscopy data using nuclei constellations" www.biorxiv.org/content/10.6... Code and App: github.com/CellMigratio...
37436
Reposted by Daniel Krentzel
Aafke Gros @aafkegros.bsky.social · 24/07/2026
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell. A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution
26827
Reposted by Daniel Krentzel
Joel Lüthi @joelluethi.bsky.social · 24/07/2026
Do you want to learn more about OME-Zarr viewers, where they stand today and what's being developed at the moment? On August 24th at 4pm CEST, we will hear about 3 different OME-Zarr viewers and user stories for each. www.biovisioncenter.uzh.ch/en/events/Up... (1/5 🧵)
biovisioncenter.uzh.ch
Open Bioimaging Practices Meetup August 2026
11511
Reposted by Daniel Krentzel
Spyros Lytras @spyroslytras.bsky.social · 23/07/2026
Come work on exciting AI for biology projects in Paris!! 🇫🇷 Details and application below, deadline sept 1st!
02726
Reposted by Daniel Krentzel
Estibaliz Gómez de Mariscal, PhD @gomez-mariscal.bsky.social · 24/04/2026
Want to do a PhD in biomedical research and explore the exciting world of AI, microscopy and cell biology?👾🧠🧫🔬 In a research environment of high excellence🌟 and in beautiful Portugal🏄🌸? PhD fellowships are now open at #NIMSB from May-4 til June-5 👉 APPLY lnkd.in/eqkYreFi Reach out if interested!✉️
044
Reposted by Daniel Krentzel
Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
6226120
Reposted by Daniel Krentzel
Washington Monthly @washingtonmonthly.bsky.social · 30/03/2026
Trump’s bid to strip birthright citizenship from millions is a moral, administrative, and legal catastrophe that the Fourteenth Amendment was enacted to prevent. That’s why he’s pursuing it, writes Legal Affairs Editor @garrettepps.bsky.social.
washingtonmonthly.com
Birthright Citizenship: Supreme Court Could Create an Exploitable Noncitizen Class
Trump’s bid to strip birthright citizenship from millions is a moral, administrative, and legal catastrophe.
12317
Reposted by Daniel Krentzel
Levayer Lab @levayerr.bsky.social · 27/03/2026
Happy to share the heroic effort of @gaellel.bsky.social to reduce our segmentation pain through EpiCure (Epithelial Curation), a napari plugin easing the curation of epithelial segmentation developed with several groups of @devstempasteur.bsky.social. www.biorxiv.org/content/10.6... See more 👇
biorxiv.org
14218
Reposted by Daniel Krentzel
Carles Bosch @carlesbosch.bsky.social · 24/03/2026
#paper: Drying tissue samples enhances contrast in X-ray phase contrast imaging while largely preserving ultrastructure. 🧠🔬 doi.org/10.1107/S160... @safekhan.bsky.social @andreas-t-schaefer.bsky.social @crick.ac.uk @embl.org @imperialcollegeldn.bsky.social @esrf.fr @uclnpp.bsky.social
1126
Reposted by Daniel Krentzel
Institut Pasteur | 130 years of biomedical research @pasteur.fr · 23/03/2026
🧬 EMBO Workshop – The complexity of mycobacterial infections: from research to real-world impact 📅 14–18 Sept 2026, Paris Tuberculosis & non-tuberculous mycobacteria at the heart of discussions: evolution, host–pathogen interactions, drug resistance. 🔗 meetings.embo.org/event/26-myc...
Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains one of the deadliest infectious diseases worldwide. Meanwhile, non-tuberculous mycobacteria (NTM) are an increasing global health concern. NTM infections often resemble TB clinically, which can lead to misdiagnosis and inappropriate therapy. Additionally, drug-resistant strains of M. tuberculosis and NTM exacerbate the global antimicrobial resistance crisis. A better understanding of the biology of mycobacterial pathogens and of the mechanisms underlying disease pathogenesis and transmission is critical to reduce their burden worldwide.

This EMBO Workshop is the fourth in a successful series held at the Institut Pasteur in Paris, following the meetings organized in 2012, 2016, and 2022. It will bring together scientists, clinicians, public health experts, and representatives from industry and non-profit organizations, who will share recent insights into mycobacterial infections, from fundamental discoveries to translational research, and their practical implications. The program will cover mycobacterial evolution, physiology, metabolism, host–pathogen interactions, immune responses, mechanisms of drug evasion, therapeutic strategies, vaccines, and diagnostics. Emerging experimental models, computational approaches, and artificial intelligence will also be addressed, showing how recent technologies contribute to advancing mycobacterial research and interventions.
1911
Reposted by Daniel Krentzel
Juan Nunez-Iglesias @jni.codes · 16/03/2026
So… um… I (and Draga Doncila Pop and Eric Perlman and @joshmoore.bsky.social and @kevinyamauchi.bsky.social) started a thing! We are excited and terrified in equal measures, and look forward to working with you all in our amazing scientific imaging community! ❤️‍🔥 Read the linked post for the lowdown.
0156
Reposted by Daniel Krentzel
Caterina Fuster Barceló @cfusterbarcelo.bsky.social · 15/03/2026
Are FMs actually FMing? ⛓️🔬 Thrilled to share that our paper on Foundational Models for mitochondria segmentation in EM is heading to the @iclr-conf.bsky.social 2026 LMRL Workshop! 🚀 Check out the full work here: 📄 ArXiv: arxiv.org/abs/2602.08505 📄 OpenReview: openreview.net/forum?id=Bba...
arxiv.org
Are Vision Foundation Models Foundational for Electron Microscopy Image Segmentation?
Although vision foundation models (VFMs) are increasingly reused for biomedical image analysis, it remains unclear whether the latent representations they provide are general enough to support effecti...
195
Reposted by Daniel Krentzel
David Stansby @dstansby.bsky.social · 13/03/2026
The paper that sums up what I've been working on and running for the last three years was published this week 🎉 www.science.org/doi/10.1126/...
science.org
The Human Organ Atlas
The Human Organ Atlas provides open access to 3D images of human anatomy spanning whole organs to cellular scale resolution.
0198
Reposted by Daniel Krentzel
Joel Lüthi @joelluethi.bsky.social · 10/03/2026
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...
biorxiv.org
23217
Reposted by Daniel Krentzel
Thibaut Brunet @thibautbrunet.bsky.social · 28/02/2026
Final version @nature.com of our paper describing unconventional multicellular development in a choanoflagellate inhabiting an extreme environment. A ton of new data since the first @biorxivpreprint.bsky.social preprint (which we've kept updating). A brief 🧵 (carried over from the old place)
16382152
Reposted by Daniel Krentzel
SFM Microbial Pathogenesis @sfmpathogenesis.bsky.social · 25/02/2026
🚨 𝐀𝐈 𝐦𝐞𝐞𝐭𝐬 𝐓𝐁 𝐝𝐫𝐮𝐠 𝐝𝐢𝐬𝐜𝐨𝐯𝐞𝐫𝐲! Imaging 𝐶. 𝑔𝑙𝑢𝑡𝑎𝑚𝑖𝑐𝑢𝑚 (a model for 𝑀. 𝑡𝑢𝑏𝑒𝑟𝑐𝑢𝑙𝑜𝑠𝑖𝑠) + deep learning reveals known, unseen, and novel antibiotic modes of action from images alone, a leap for TB drug discovery. ✍️ @awehenkel.bsky.social & coll. 📖 shorturl.at/9QPDy #Tuberculosis #MicroSky
263
Reposted by Daniel Krentzel
Jean-Yves Tinevez @jytinevez.bsky.social · 24/02/2026
One week left to register to the Bioimage Analysis with AI course in Pasteur! This June, 1 - 5. I give a bit more details in the thread below 👇
14029
Reposted by Daniel Krentzel
Mark A. Hanson @hansonmark.bsky.social · 23/02/2026
Very excited to be advertising this project with the excellent cosupervision of Peter Mergaert through @i2bcparissaclay.bsky.social and @uniexecec.bsky.social. This position is open to international applicants and will involve stints in both Penryn UK and Paris France. Please share! Apply: adum.fr
An advertisement for a PhD position studying "Revealing the mechanistic basis of defence peptide antibacterial specificity." It shows fruit flies infected by green-fluorescent protein expressing bacteria, and describes the project and way to apply.
11825
Daniel Krentzel @danielkrentzel.bsky.social · 24/02/2026
Our preprint outlining a deep learning-based phenotypic screening approach for the discovery of new TB drugs is out on bioRxiv now 💊🦠 🔗 doi.org/10.64898/202... Thank you @awehenkel.bsky.social @chzimmer.bsky.social @spetrella.bsky.social @curieuseny.bsky.social and everyone else not on bsky (yet)🙏
Screenshot of the title and author list of the preprint entitled "Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria"
11810
Reposted by Daniel Krentzel
Gillen Tener Martin @gillenmartin.bsky.social · 28/01/2026
"In repeating that colleges have 'gone soft,' pundits are, in some sense, telling universities what they want to hear. Schools would much rather wring their hands over vague cultural 'softness' than admit the obvious: that their revenue-maximizing logic is actively undermining educational quality."
washingtonmonthly.com
The Real Cause of Grade Inflation
Grade inflation is the predictable result of how American universities now organize teaching, labor, and money.
034
Reposted by Daniel Krentzel
David Bikard @dbikard.bsky.social · 28/01/2026
🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...
research.pasteur.fr
Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research
The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...
07481
Reposted by Daniel Krentzel
Laura Cantini @cantinilab.bsky.social · 21/01/2026
Two postdoc positions opened in my team @pasteur.fr in Paris on the development of machine learning methods for single-cell multi-omics spatiotemporal data. See the announcement for all details emploi.cnrs.fr/Offres/CDD/U...
emploi.cnrs.fr
Portail Emploi CNRS - Offre d'emploi - Two Postdoctoral (M/F) Positions in the Development of Machine Learning Methods for Single-Cell Multi-Omics Spatiotemporal Data
Assurez-vous que votre profil candidat soit correctement renseigné avant de postuler
0810
Reposted by Daniel Krentzel
Daniel Krentzel @danielkrentzel.bsky.social · 15/11/2025
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr research.pasteur.fr/fr/job/open-...
research.pasteur.fr
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
02014
Reposted by Daniel Krentzel
Joel Lüthi @joelluethi.bsky.social · 17/11/2025
We had an amazing OME-NGFF hackathon last week, Wednesday to Friday, following the inspiring OME-NGFF symposium. What a fantastic week! It’s hard to describe how motivating it is to be surrounded by so many talented, curious & friendly people who care deeply about open, FAIR bioimaging data. 1/14 🧵
Hackathon participants group picture
24116
Reposted by Daniel Krentzel
Joel Lüthi @joelluethi.bsky.social · 17/11/2025
A great plugin prototype to run Fractal tasks interactively in napari: Making interoperable workflow tasks accessible directly in a viewer (8/14 🧵)
Daniel showing new napari Fractal task plugin
161
Daniel Krentzel @danielkrentzel.bsky.social · 15/11/2025
If you're interested in developing an open-source image analysis platform/plugin to profile bacteria with deep learning while living in the beautiful city of Paris 🇫🇷, check out this job ad from the @chzimmer.bsky.social lab @pasteur.fr research.pasteur.fr/fr/job/open-...
research.pasteur.fr
Open-Source Developer for Deep Learning Antibiotic Discovery Platform - Research
Introduction Antimicrobial resistance (AMR) is one of the most urgent global health threats projected to cause up to 10 million deaths per year by 2050. The AI4AMR project brings together teams from I...
02014
Reposted by Daniel Krentzel
Nature Communications @natcomms.nature.com · 16/10/2025
In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular #mycobacteria (doxycycline-loaded nanoparticles, zebrafish model of Mycobacterium marinum #infection) @lkremer1.bsky.social #DrugDevelopment
bit.ly
In vivo antimicrobial activity of engineered mesoporous silica nanoparticles targeting intracellular mycobacteria - Nature Communications
Current treatment options for Mycobacterium marinum infections are extensive and challenging. In this work, authors explore the potential of functionalized mesoporous silica nanoparticles as a carrier for delivery of drugs against M. marinum.
072
Reposted by Daniel Krentzel
Christophe Zimmer @chzimmer.bsky.social · 05/10/2025
** Now seeking postdocs ** Join our interdisciplinary and transnational team in Würzburg (Germany) or Paris (France) to drive projects in translational biology and antibiotic drug discovery. Backgrounds in computational biology, AI, physics, or microbiology are all welcome. Please spread the word.
195
Reposted by Daniel Krentzel
Institut Pasteur Education @pasteuredu.bsky.social · 13/10/2025
🚨 1 week left to apply for the Pasteur-Paris University International PhD Program (PPU)! Join an international community of scientists at the Institut Pasteur 🌍 Dedicated support, mentorship & world-class labs included. 📅Deadline: Oct 20, 2025 🎓Program start: October 2026 👉 Apply: bit.ly/CallPPU
01415
Reposted by Daniel Krentzel
Jean-Yves Tinevez @jytinevez.bsky.social · 07/10/2025
Job alert! We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? See also on the forum: forum.image.sc/t/research-e...
forum.image.sc
Research engineer in Bioimage Analysis for the researchers of the inIdEx FORMULA
Hi all We are looking for a bioimage analysis to work in an image analysis core facility in beautiful Paris. Can I ask you to share this opportunity with your networks? The position is in the Instit...
26380
Reposted by Daniel Krentzel
Anna Foix @afoix.bsky.social · 23/09/2025
Happy to share that ShapeEmbed has been accepted at @neuripsconf.bsky.social 🎉 SE is self-supervised framework to encode 2D contours from microscopy & natural images into a latent representation invariant to translation, scaling, rotation, reflection & point indexing 📄 arxiv.org/pdf/2507.01009 (1/N)
37126
Reposted by Daniel Krentzel
The Company of Biologists @biologists.bsky.social · 12/09/2025
We're excited to announce the first of two prize winners in our #biologists100 #sustainable #travel blog competition. Read Lea’s experience of travelling via four trains from France to Liverpool. www.biologists.com/stories/my-j... Stay tuned for next week’s post from winner two. #Sustainability
biologists.com
My journey from Paris to Liverpool in four trains
8 September 2025 by Léa Manke My journey to the Biologists @ 100 conference began early on Saturday morning. Clutching my thermos filled with coffee, I made my way to the major train station in…
052
Reposted by Daniel Krentzel
Romain F. Laine @lainebioimaging.bsky.social · 11/09/2025
Beautiful work from @danielkrentzel.bsky.social here! Correlative EM-LM made easy! Really grateful to be part of the team.
131
Reposted by Daniel Krentzel
Nature Methods @natmethods.nature.com · 11/09/2025
CLEM-Reg automates the 3D alignment of volume correlative light and electron microscopy data. www.nature.com/articles/s41...
095
Reposted by Daniel Krentzel
Ricardo Henriques @henriqueslab.bsky.social · 10/09/2025
Awesome to see this out. Thank you for bringing us in the journey @em-stp.bsky.social and @martinjones.bsky.social. Keep rocking @danielkrentzel.bsky.social!
0163
Reposted by Daniel Krentzel
Jean-Yves Tinevez @jytinevez.bsky.social · 10/09/2025
Save the date! The @pasteur.fr Pasteur course on image analysis is announced: It will happen from the 1st of June to the 5th 2026. This year there will be only one track: the Early Career Investigator track (beginners). 👇
35228
Reposted by Daniel Krentzel
Carles Bosch @carlesbosch.bsky.social · 10/09/2025
#preprint: We optimised the preparation of tissues for #X-ray phase contrast imaging. Drying tissue samples (instead of embedding them) brings more signal in #X-ray phase contrast images. The process largely preserves #ultrastructure. @safekhan.bsky.social @andreas-t-schaefer.bsky.social
1104
Daniel Krentzel @danielkrentzel.bsky.social · 10/09/2025
Super happy to see CLEM-Reg out in @natmethods.nature.com! A short thread on the algorithm behind it and how to try it out for yourself🧵(1/9) www.nature.com/articles/s41...
nature.com
CLEM-Reg: an automated point cloud-based registration algorithm for volume correlative light and electron microscopy - Nature Methods
CLEM-Reg automates the three-dimensional alignment of volume correlative light and electron microscopy datasets by leveraging probabilistic point cloud registration techniques for fast and accurate re...
24219
Reposted by Daniel Krentzel
Institut Pasteur | 130 years of biomedical research @pasteur.fr · 01/09/2025
🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry. Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, PPU-@ox.ac.uk, PPU-EID @upcite.bsky.social & more 🧬 Register now ✍️ www.pasteur.fr/en/education...
Pasteur-Paris University International Doctoral Programme, The call for enrollment of students in October 2026 will be open from September 1st to October 20th, 2025
03334
Reposted by Daniel Krentzel
Ricardo Henriques @henriqueslab.bsky.social · 10/07/2025
🚨Join us! We're soon opening 3 postdoctoral positions in #AIDrivenBiology. Seeking biologists (especially microbiology and infection biology), computer scientists, and microscopy developers. Ideal candidates are those eager to use or develop next-gen tech for cell biology. Get in touch (DM/email)
15031
Reposted by Daniel Krentzel
Martin Weigert @maweigert.bsky.social · 10/07/2025
Do you like developing new AI vision methods for microscopy image analysis? You love theory & implementation? 1 week left to apply for a fully funded PhD position in our lab in Dresden 🇩🇪! Topics: object detection/tracking, multimodal models & more. DM/email for details! #PhD #AcademicJobs #GPUsgoBrr
verw.tu-dresden.de
Vacancy ID 12244
12520
Reposted by Daniel Krentzel
Tom Cumming @tomcumming.bsky.social · 21/05/2025
The effector caspases drive cell death, but their activation can often be survived, so how do cells make this decision? Our new preprint from @levayerr.bsky.social shows that instantaneous caspase activity is important, but past activation has a key role to play! www.biorxiv.org/content/10.1...
13014