Sign in

Antoine Le Gall

@antoinelegall.bsky.social
165 followers 220 following 6 posts

Biophysicist at CNRS/CBS studying bacterial chromosome secrets, motility, and collective behaviors using multiscale microscopy and bioimage magic.

PostsRepliesMedia
Reposted by Antoine Le Gall
Fabrice Senger @senger.bsky.social · 22/09/2026
Sounds great, could help people to use these approaches and maybe unify the calculations
111
Reposted by Antoine Le Gall
bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 17/09/2026
The construction and operation of type IV pili impose a variable energetic burden across phylogenetically distant bacteria www.biorxiv.org/content/10.64898/20…
021
Reposted by Antoine Le Gall
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.
24417
Reposted by Antoine Le Gall
Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 07/09/2026
Very happy to share my postdoc paper is out now in @natcellbio.nature.com titled "Tissue flow acts as a guidance cue for immune cell polarization and directional migration". If you love imaging and immune cells, this is for you! #microscopymonday www.nature.com/articles/s41... A 🧵: 1/n
18395107
Reposted by Antoine Le Gall
Arnaud Krebs @arnaudkr.bsky.social · 07/09/2026
Is activation of multiple enhancers and promoters coordinated? Short answer is yes. Check full story from @mathias-boulanger.bsky.social @kasitc.bsky.social leveraging long read single molecule sequencing to address this. @embl.org www.cell.com/molecular-ce...
15014
Reposted by Antoine Le Gall
Delarue Research @delarueresearch.bsky.social · 06/09/2026
Our collaborative paper, with Daria Bonazzi and @dumenillab.bsky.social is finally out in Nat Comms! Using microfluidic confiners, amazing Laure Leblanc found that confined growth of E. coli uncouples growth and division, as well as pressure and biomass production. tinyurl.com/4zdwrp39
2437
Reposted by Antoine Le Gall
Francesco Padovani @padovaf.bsky.social · 31/08/2026
Very happy to see SpotMAX out in Science Advances! 🎉🔬 This has been a long and exciting journey, and I’m really grateful to everyone who contributed along the way. It certainly makes our microscopy analysis easier, so I hope it will make yours too!
072
Reposted by Antoine Le Gall
Carballido-López's lab @carballido-lab.bsky.social · 25/08/2026
New preprint from the lab (link below), and first preprint from Matteo Gerard, who will soon be a doctor (and looking for a post-doc, just saying). Toolbox for fluorescent labelling of Pseudomonas aeruginosa across scales: from single cells to bacterial communities and host infection models.
2126
Reposted by Antoine Le Gall
Tobias Warnecke @tobiaswarnecke.bsky.social · 22/08/2026
Who needs chromatin anyway...? NOT THIS GUY! www.biorxiv.org/content/10.6... 1/n
biorxiv.org
Chromatin is dispensable for bacterial life
Inside cells, DNA is intimately associated with proteins, forming chromatin. The protein constituents of chromatin vary across the tree of life: histones are the principal building blocks of chromatin...
3231104
Reposted by Antoine Le Gall
Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
110545
Reposted by Antoine Le Gall
David Dulin @dulinlab.bsky.social · 17/08/2026
Finally out! I am super proud of this work that took 6 years to come to fruition, with many amazing people involved, in particular Sadegh, Ibrahim, Jelmer. #SadeghFeiz: all kudos for you to push this project through! Great Collab with Anssi Malinen from @utu.fi @vuamsterdam.bsky.social
193
Reposted by Antoine Le Gall
Kirsty Wan @micromotility.bsky.social · 17/08/2026
What does a single-celled organism tell us about the origins of complex behaviour? Delighted to see the final version of our paper: Embodied behavioural complexity in a ciliated microorganism out in@natcomms.nature.com (Funded by @erc.europa.eu ERC) doi.org/10.1038/s414... #cilia #protistsonsky
110035
Reposted by Antoine Le Gall
Jean-Yves Bouet @jyb-tlse.bsky.social · 10/08/2026
Happy to share our latest work: Fast assembly and in vivo coalescence of ParBf biocondensates involved in bacterial DNA partition academic.oup.com/nar/article/... Great thanks to all contributing authors and in particular Perrine Revoil and Linda Delimi for their fruitful collaborative interactions
academic.oup.com
Fast assembly and in vivo coalescence of ParBF biocondensates involved in bacterial DNA partition
Abstract. Faithful DNA segregation in bacteria relies on ParABS systems, in which ParB assembles into condensates at centromere-like parS sites, while the
042
Reposted by Antoine Le Gall
Cascales Lab @cascaleslab.bsky.social · 07/08/2026
Happy to share our latest review on the "Structure and function of the #T9SS for protein secretion and cellular motility" to be published in the incoming volume 80 of Annual Review in Microbiology. Kudos to Yaelle Aouizerate and @thicoz.bsky.social ! www.annualreviews.org/content/jour...
24021
Reposted by Antoine Le Gall
FocalPlane @focalplane.bsky.social · 01/07/2026
Bringing together science & art, @manuelthery.bsky.social & the CytoMorpho lab describe their project on how cells adapt their shape to their environment using the Musée d’Orsay as their template! The full performance was presented over two nights at the museum earlier this year. #sciart #cellbio
focalplane.biologists.com
Living Architectures - FocalPlane
Living Architectures - Case studies
12011
Reposted by Antoine Le Gall
Jeunes microbiologistes de la SFM @jm-sfm.bsky.social · 04/06/2026
Ce mois-ci, Marie nous présente 𝗹'𝗮𝗿𝘁𝗶𝗰𝗹𝗲 𝗰𝗼𝘂𝗽 𝗱𝗲 ❤️ 𝗱𝘂 𝗥𝗲𝗝𝗠𝗶𝗙 : Vous êtes vous déjà demandé comment remporter la victoire dans une compétition inter-bactérienne ? 𝗣𝗮𝗶𝗹𝗹𝗮𝘁 𝗲𝘁 𝗮𝗹., oui ! Ils ont découvert la stratégie de 𝘍𝘭𝘢𝘷𝘰𝘣𝘢𝘤𝘵𝘦𝘳𝘪𝘶𝘮 𝘫𝘰𝘩𝘯𝘴𝘰𝘯𝘪𝘢𝘦 pour éliminer ses concurrents ! urlr.me/yAHSbK
085
Reposted by Antoine Le Gall
Maelle Paillat @maellepllt.bsky.social · 08/05/2026
Very happy to see the second story from my PhD out in @currentbiology.bsky.social An exciting project where we explored the roles of secretion systems and gliding motility in predatory behavior in F. johnsoniae. www.cell.com/current-biol...
cell.com
Type VI and type IX secretion systems and gliding motility contribute to facultative predation by Flavobacterium johnsoniae
Paillat et al. show that Flavobacterium johnsoniae combines type VI and type IX secretion systems with gliding motility to efficiently kill diverse bacterial competitors. They demonstrate that nutrien...
1186
Reposted by Antoine Le Gall
Jean-Yves Tinevez @jytinevez.bsky.social · 27/05/2026
The paper is now published in Current Protocols!! 🎉🥳 currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1... Some personal story below 👇 , and technical details in the linked post that featured the preprint 👉
currentprotocols.onlinelibrary.wiley.com
Automated Optimization of Bacterial Tracking Pipelines With TrackMate 8
Quantitative analysis of bacterial dynamics in time-lapse microscopy requires robust tracking pipelines, yet selecting and optimizing algorithms for specific experiments remains challenging. Indeed, ...
23616
Reposted by Antoine Le Gall
Marie Vasse @marievasse.bsky.social · 13/05/2026
What's predation like in the microbial world? Greg Velicer @usyseth.bsky.social and I take you on a tour in our new review! @ethz.ch @cnrs.fr
1265
Reposted by Antoine Le Gall
Chris Toseland @christoseland.bsky.social · 23/02/2026
Save the date! We have an exciting conference coming up next year for the UK Mechanobiology community!
02312
Reposted by Antoine Le Gall
Raphaël Clément @raphclement.bsky.social · 29/04/2026
The division Physics and Life of the French Physical Society (SFP) organizes its fourth annual meeting in Lyon, July 9th & 10th! Join us and register here: phys-life-2026.sciencesconf.org Abstract submission deadline: May 30th
0118
Reposted by Antoine Le Gall
George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 28/04/2026
JB Editor's choice: Sen, Shrivastava et al. review the shared mechanisms of bacterial gliding motility, despite using different motors. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology
152
Reposted by Antoine Le Gall
Claire Dessalles @clairedessalles.bsky.social · 22/04/2026
All you ever wanted to know about how to analyse the nematic nature of cellular tissues is right here 👀👇🏼! Bonus #1: we did it for many cell types and uncovered unexpected defect behavior 🐌 Bonus #2: for theoreticians looking for parameter values for your simulation🧑🏼‍💻 tinyurl.com/2s399yen
44418
Reposted by Antoine Le Gall
Xavier Trepat @xaviertrepat.bsky.social · 17/04/2026
Our latest work on shape-programmable tissues is out in @science.org. By positioning topological defects in cellular nematics, we encode frustrated 2D force fields that relax into predictable 3D shapes. Collaboration with Marino Arroyo’s lab, led by @pauguillamat.bsky.social at @ibecbarcelona.eu.
718464
Reposted by Antoine Le Gall
Nessa Carson @supersciencegrl.co.uk · 31/03/2026
How to make your own robot! A review of people making awesome lab robots out of commercial 3D printers. Thank you @vsaggiomo.bsky.social and Sander for inviting me to help write this paper in @digital-discovery.rsc.org. Beep boop! 🤖 #chemsky doi.org/10.1039/D5DD...
doi.org
Hacking 3D printers as laboratory robots
The emergence of affordable and reliable 3D printers has enabled laboratories to optimize setups, print custom parts, accelerate research, and rapidly prototype. A new movement has emerged in the past...
34220
Reposted by Antoine Le Gall
Ákos T Kovács @evolvedbiofilm.bsky.social · 28/03/2026
@commsphys.nature.com Collection open for submission on Bacterial physiology and self-organization through the lens of physics Editors: Eleonora Secchi, Anupam Sengupta & Kazumasa Takeuchi www.nature.com/collections/... #Bacterial_motility #Biofilm #Bacterial_interactions #Self_organisation
nature.com
Bacterial physiology and self-organization through the lens of physics
This Collection aims to bring together research from diverse aspects of physical biology, focusing on the interplay of physical laws and bacterial behaviour ...
0158
Reposted by Antoine Le Gall
Enrico Sandro Colizzi @escolizzi.bsky.social · 26/03/2026
How common is multicellularity in bacteria? And archaea? And how does it evolve? We wrote a short review "On the architecture and evolution of prokaryotic multicellularity". Preprint link: bit.ly/4ta06Gq Sharing and comments are much appreciated. 1/4
An overview of bacterial multicellular formations: biofilms, filaments, free-floating aggregates, motile collectives and fruiting bodies. For each form, we mention an analogous eukaryotic multicellular form (respectively animal epitelia, filaments in fungi, Volvox, Dictyostelium/social animals, Dictyostelium and other slime moulds)
413351
Reposted by Antoine Le Gall
Géraldine Laloux @lalouxlab.bsky.social · 20/11/2025
Apply now to attend the next EMBO Bacterial Networks meeting #EMBOBacNet 🗓️13-18 September 2026 📍Sant Feliu de Guixols, Spain 📝Program and registration info: meetings.embo.org/event/26-bac... 👩‍🔬Organised with co-chair @s-lab.bsky.social and ECR @coralietesseur.bsky.social #MicroSky
15737
Reposted by Antoine Le Gall
Horst Obenhaus @octoscience.bsky.social · 06/03/2026
BIG UPDATES! OCTRON now supports the new SAM3 models (alongside SAM2)! We’ve also added a global switch for Detection vs. Segmentation: Use the same annotations to train either lightweight detection or full segmentation models. Plus, we’ve added support for the new YOLO26 models. ⤵️ 1/12
22812
Reposted by Antoine Le Gall
Max Planck Institute of Immunobiology and Epigenetics @mpi-ie.bsky.social · 06/03/2026
🤗 Next week, we are happy to welcome Marcelo Nollmann from @cbsmontpellier.bsky.social | @cnrs.fr | @umontpellier.bsky.social. His lab develops single-molecule and advanced imaging methods to investigate DNA organization, segregation and transcription in multicellular organisms. Join us at 3pm. ⬇️
Sharepic for a seminar at the MPI-IE:

Green-blue gradient background. The top left shows the name of the Max Planck Institute for Immunobiology and Epigenetics and its logo. Below is the heading 'MAX PLANCK SEMINAR FREIBURG'. The center displays the lecture title: 'INSPECTING THE ROLES OF CHROMATIN ORGANIZATION IN TRANSCRIPTION REVEALED BY SPATIAL GENOMICS'. The lower left lists the date, time, and venue: 'WED, 11 MARCH 2026, 15:00', 'MPI-IE, LECTURE HALL', 'Stübeweg 51, 79108 Freiburg, Germany'. The lower right shows the speaker's name and affiliation: 'Marcelo Nollmann, Center for Structural Biology, CNRS/INSERM, University of Montpellier, France'.
0116
Reposted by Antoine Le Gall
Lucien Hinderling @lhinderling.bsky.social · 03/03/2026
PAPER OUT ✨ How can we make smart microscopy more interoperable? What are the technical and cultural challenges? 30+ people from academia and industry propose a roadmap: doi.org/10.1515/mim-... Also a review of applications and repo of implementations. Join the discussion! smartmicroscopy.github.io
Screenshot of the abstract:
Smart microscopy is transforming life sciences by automating experimental imaging workflows and enabling real-time adaptation based on feedback from images and other data streams. This shift increases throughput, improves reproducibility, and expands the functional capabilities of microscopes. However, the current landscape is highly fragmented. Academic researchers often develop custom solutions for specific scientific needs, while industry offerings are typically proprietary and tied to specific hardware. This diversity, while fostering innovation, also creates major challenges in interoperability, reproducibility, and standardization, which slows progress and adaption. This article presents a collaborative effort between academic and industry leaders to survey the current state of smart microscopy, highlight representative implementations, and identify common technical and organizational barriers. We propose a framework for greater interoperability based on shared standards, modular software design, and community-driven development. Our goal is to support collaboration across the field and lay the groundwork for a more connected, reusable, and accessible smart microscopy ecosystem. We conclude with a call to action for researchers, hardware developers, and institutions to join in building an open, interoperable foundation that will unlock the full potential of smart microscopy in life science research.Screenshot of Figure 5: Interoperable smart microscopy ecosystem. Concept of a modular architecture for smart microscopy, where standardized experiment descriptions (e.g. useq-schema) and open data formats (e.g. OME-Zarr) allow integration of diverse microscopes, analysis tools, and user interfaces. Core components such as segmentation [76], [77], tracking [79], [80], and experiment logic are decoupled from specific hardware, enabling reuse across platforms. The system supports multiple input modalities (code, GUI, or natural language) and can be extended with additional devices like fluidics or environmental control modules. This structure enables flexible, feedback-driven acquisition strategies and cross-platform reproducibility.Screenshot of figure 4: Strategies for hardware abstraction that allow smart microscopy workflows to run across different microscope systems, illustrated with example implementations collected on the SMWG website. (A) Software communication layers: Image analysis and experiment logic are implemented in a platform-independent manner, while platform-specific adaptors control acquisition through proprietary microscope software via macros, APIs, or other interfaces. Custom GUIs allow users to configure analysis, while the vendor-provided software manages hardware and acquisition settings. By developing additional adaptors, these workflows can be extended to support microscope systems from other vendors. Example implementation: AutoMicTools , Supplementary Information S3. (B) Device-level standardization (e.g. μManager-based workflows) bypasses proprietary GUIs and provides a unified API for direct device control across manufacturers. This API abstracts vendor-specific differences, enabling consistent control of a growing collection of supported hardware. Example implementation: UU_smart_microscopy , Supplementary Information S2. (C) Event-based standardization decouples experimental design from hardware by describing acquisition events (e.g. acquire frame at x, y, t with channel c) in a structured format (e.g. useq-schema). Control software interprets these definitions and translates them into device-specific commands, enabling the use of vendor-specific features and optimizations during execution. Example implementation: rtm-pymmcore, Supplementary Information S1.
14315
Reposted by Antoine Le Gall
Marie Vasse @marievasse.bsky.social · 23/02/2026
Interested in microbial predation? Join us in Ticino Switzerland on July 27-31, 2026! More info at microbialpredation.ethz.ch #predation #ecology #evolution #microbes
11212
Reposted by Antoine Le Gall
AI-driven Optical Biology Lab @aiopticalbiolab.bsky.social · 23/02/2026
Last 3 days to register for 𝐈𝐌𝐒𝟐𝟎𝟐𝟔 symposium organized by @itqbnova.bsky.social. DON´T miss these amazing researchers on 19/03: @seamusholden.bsky.social, @guijacquemet.bsky.social, @silvapereiralab.bsky.social, @pinholab.bsky.social, @henriqueslab.bsky.social. 🔗: ims2026.itqbnovacommunity.org
012
Reposted by Antoine Le Gall
Jolyon Troscianko @jtroscianko.bsky.social · 21/02/2026
Our BehaveAI paper has just come out! Easy & effective tracking & behavioural classification, even with tiny (2px), fast moving, camouflaged objects. Paper: doi.org/10.1371/jour... Download: github.com/troscianko/B... @uniexecec.bsky.social @kevinjgaston.bsky.social @jimamclgalloway.bsky.social
48836
Reposted by Antoine Le Gall
STCmicrobeblog @stcmicrobeblog.bsky.social · 17/02/2026
T4P anybody? sure enough! enjoy a great 🧵👇 #MicroSky
0124
Reposted by Antoine Le Gall
Vicky Lioy @vslioy.bsky.social · 14/02/2026
📢 Save the date! #Biophychrom2027 will take place at Paris-Saclay in July 2027. More details coming soon!
065
Reposted by Antoine Le Gall
EMBL Events @events.embl.org · 06/02/2026
Do you want to be part of a diverse community building a comprehensive understanding of mechanobiology across kingdoms? 🔬🧬 Then join us in Heidelberg or virtually for the #EESMechanobiology symposium: s.embl.org/ees26-06-bl Date: 9 – 12 June Abstract submission deadline: 3 March
043
Reposted by Antoine Le Gall
epithelial mechanics fan club @epimechfc.bsky.social · 31/01/2026
How do cells orchestrate themselves to achieve a directional movement as a group? Hi, I’m @sayukihirano.bsky.social. In this thread, I’ll highlight key mechanisms of how cells communicate with each other to perform directional collective migration.
25718
Reposted by Antoine Le Gall
Javier Apfeld @javierapfeld.bsky.social · 28/01/2026
Friends! I am so happy to share our new preprint! Hydrogen peroxide has been the most common reactive chemical threat to life forms since the Great Oxygenation Event 2.5 billion years ago. How do animals like C. elegans sense it fast and escape? www.biorxiv.org/content/10.6... Thread 1/
78631
Reposted by Antoine Le Gall
bioRxiv Biophysics @biorxiv-biophys.bsky.social · 25/01/2026
Analyzing single-molecule dynamics with both complex types of motion and complex transition kinetics: Benchmarking of ExaTrack www.biorxiv.org/content/10.64898/20…
033
Reposted by Antoine Le Gall
STCmicrobeblog @stcmicrobeblog.bsky.social · 30/12/2025
an excellent resource for anyone who doesn't dare to draw themselves 👏👏👏
0142
Reposted by Antoine Le Gall
Horst Obenhaus @octoscience.bsky.social · 23/12/2025
Do you love quantifying animal behavior as much as we do? We have just the tool for you! Presenting #OCTRON - a pipeline that helps you create rich annotation data and enables training of custom segmentation models. Have a look, particularly if you work with non-model / invertebrate organisms!
710241
Reposted by Antoine Le Gall
Stig Ove Bøe @stigoveboe.bsky.social · 29/12/2025
Our review article is now available in Annual Review of Condensed Matter Physics: “Full-Integer Topological Defects in Polar Active Matter.” @luizaangheluta.bsky.social @emmalaang.bsky.social doi.org/10.1146/annu...
0189
Reposted by Antoine Le Gall
Liselotte Jauffred @jauffred.bsky.social · 22/12/2025
Aspect Ratio as Driver of Bacterial Competition! Our latest work uncovers this simple and powerful determinant of bacterial competition. We demonstrate that longer bacteria consistently dominate colony fronts—even when outnumbered. The mechanism? Collective alignment. www.nature.com/articles/s41...
13011
Reposted by Antoine Le Gall
Ricardo Henriques @henriqueslab.bsky.social · 19/12/2025
🚀📰 End-of-year news for #RxivMaker =). Now it generates both #pdf and #docx from #markdown. Docx makes it easier to collaborate on a document for non-markdown users, making it simple to loop between docx and #RxivMaker to a professional-looking #preprint Preprint updated: arxiv.org/abs/2508.00836
1228
Reposted by Antoine Le Gall
Fusion Conferences @fusionconf.bsky.social · 16/12/2025
We are looking forward to sunnier days and some fantastic presentations at our #ProkaryoticCellBio meeting in Portugal next July! Grants, Early Bird pricing and Talk slots close on 12 Jan, register & submit today to join us! 🌞 👉https://bit.ly/48G29dP
166
Reposted by Antoine Le Gall
George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 16/12/2025
New in JB: Yarrington & Limoli review recent exciting advances in understanding mechanisms of directional movement for type IV-mediated twitching motility in P. aeruginosa. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology
043
Reposted by Antoine Le Gall
Institut Jacques Monod @ijmonod.bsky.social · 27/11/2025
📣 2nd meeting of France-BioImaging Mechanobiology Working Group 📆 March 26-27th, 2026 📍Institut Jacques Monod, Buffon amphitheater Registration are open until December 31st 🔗 buff.ly/cVzaoId @upcite.bsky.social @sbcf.bsky.social @gdraqv.bsky.social @cnrsbiologie.bsky.social @psl-univ.bsky.social
france-bioimaging.org
2nd meeting of France-BioImaging Mechanobiology Working Group
The second meeting of the FBI Mechanobiology WG will take place on the 26 and 27 of March 2026 at the Institut de Biologie Paris Seine and the Institut Jacques Monod in Paris. The programme will in…
079
Reposted by Antoine Le Gall
Ben Gallusser @bengallusser.bsky.social · 11/12/2025
🚀⭐️ Trackastra update 🚀⭐️ We just released a new model that uses pre-trained image features from Meta’s SAM2 model. This improves performance on many datasets, most notably for bacteria tracking. To give it a try, simply install with the new optional dep `etultra` github.com/weigertlab/t...
2174