Christoph Spahn

🦠🔬🤖🧑‍💻 #mAIcrobe is out! With @pinholab.bsky.social's lab, we launched an open-source framework for high-throughput bacterial image analysis. By rockstars A. Brito & B. Saraiva et al, making #DeepLearning for phenotyping accessible! Easy to use, plus model training

📜 www.biorxiv.org/content/10.1...

Congrats! Looking forward to see it growing :)

Check this out! A napari plugin for AI-based analysis of microbial bioimages! 🔬🦠💻

And we are done --- #SMLMS2025 is over, and it was great. Thank you Uli & Ulrike & all the helpers 👍, and thanks to everyone joining this event 🙏 ... safe travels home & see you soon!

Next on stage is Jonas Ries @jonasries.bsky.social from Max Perutz Labs in Vienna sharing great work on a MINFLUX simulator that helps in designing experiments 👉🏻 SimuFLUX #SMLMS2025

Great presentation of @gomez-mariscal.bsky.social. Covering PhotoFiTT, DL4MicEverywhere, resolution-matching and many other aspects of the FAIRy universe 💻🔬🧚‍♂️ #DeepLearning #Microscopy

Estibaliz Gomez de Marisca @gomez-mariscal.bsky.social from Lisbon going live and sharing great work on AI-empowered microscopy #SMLMS2025 and accessible AI

Johannes Hohlbein @hohlbeinlab.bsky.social from Wageningen presenting his great work on the dynamics of the E. coli replication initiator DnaA #SMLMS2025

Jarno Mäkelä @jmakela.bsky.social from Aalto University shares his great work on single-molecule dynamics of heat shock proteins in E. coli #SMLMS2025 (unpublished work, so no images here)

First on stage is Maja Klevanski @majaklevanski.bsky.social from Heidelberg University presenting her great work on multiplexed super-resolution imaging of proteins and glycans in tissue #SMLMS2025

We are so happy to have Zaida Luthey-Schulten here at #SMLMS2025 as a keynote speaker. Zaida is the Director of the NSF Science & Technology Center of Quantitative Cell Biology and Endowed Professor at UIUC. She pioneered 4D modelling of an entire cell integrating experimental data. So inspiring!

Yersinia actively downregulates type III secretion and adhesion at higher cell densities Author summary Bacteria can use the type III secretion system (T3SS), a molecular syringe-like device, to manipulate host cells by injecting effector proteins. Yersinia enterocolitica, a pathogenic ba...

Yersinia enterocolitica cells downregulate the T3 secretion machinery at high cell densities, likely to promote dissemination and infection spread. Nice work by the Diepold lab @diepold-lab.bsky.social, happy that I could contribute a little bit to it. #bacteria #infection
doi.org/10.1371/jour...

Thanks Till! 🙂

BPoD | Into the Nucleoid Into the Nucleoid - Biomedical pictures for April 2025.

Into the Nucleoid:

Single-molecule localisation 🔬 and live-cell imaging reveal fine details of chromosomal organisation in the bacterium E. coli 🦠

@michriscopy.bsky.social @uni-wuerzburg.de @heilemannlab.bsky.social @goetheuni.bsky.social
#microbiology

Freude über den Doppelerfolg: Zwei Würzburger Forschungsvorhaben haben sich im Exzellenzwettbewerb durchgesetzt und erhalten Mittel aus der begehrten Millionenförderung. Von links: Caroline Kisker (Würzburger Koordinatorin von NUCLEATE und Vizepräsidentin), Cynthia Sharma (Würzburger Speakerin von NUCLEATE), Ralph Claessen (Würzburger Speaker von ctd.qmat) und Universitätspräsident Paul Pauli (Bild: Jonas Blank / JMU)

Erfolg auf ganzer Linie: zwei Exzellenzcluster für Würzburg! 🥂🚀
Im Rahmen der #ExStra wird nicht nur der Quantenphysik-Cluster ctd.qmat weiterhin gefördert. Mit NUCLEATE, einem Forschungsprojekt zu Nukleinsäuren, kommt noch ein zweiter Cluster hinzu!
➡️ go.uniwue.de/xstra25

Thanks Séamus! It's always a joy to work with you 🙂

Deutschlandkarte der Verteilung der Exzellenzcluster auf Bundesländer und Universitäten.

Die #Exzellenzcluster stehen fest: Heute hat die Exzellenzkommission 70 Projekte zur Förderung ausgewählt. 45 Cluster werden fortgesetzt, 25 neu eingerichtet. Die Förderung beginnt ab 1. Jan. 2026 für 7 Jahre, die Fördersumme beträgt insg. 539 Mio. €/Jahr. Die Liste: www.dfg.de/resource/blo... 1/3

High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH Oligo-LiveFISH is an approach that can track diverse genomic loci at high spatial (20 nm) and temporal (50 ms) resolution and can work in diverse cell types, including primary cells. Combined with sup...

High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH
www.cell.com/cell/abstrac...
#spatialbiology

Call for applications 2025 - Creation of new research groups at the Institut Pasteur - Research The Institut Pasteur launches an international call to recruit new junior research group leaders in the application of cutting-edge transdisciplinary approaches to the exploration of host-microbe, tis...

Two more weeks to apply to join us in Paris !
research.pasteur.fr/en/call/call...

📣Fully funded PhD position available in our lab at @uniwuerzburg.bsky.social, in collaboration with Dr. Connolly at Newcastle University (@ruamicro.bsky.social). "Dissecting the RNA-centric landscape of microbiota-pathogen interactions in the gut”. 🦠

Apply here: www.uni-wuerzburg.de/karriere/sin...

New preprint from the Diepold lab describing major chromosome and plasmid rearrangements during secretion in Y. enterocolitica! 🦠🔬 Happy that I could contribute a bit 👇

Hi Henrik,
Thanks, this sounds to be exactly what we are looking for. Regarding periplasm, a colleague mentioned the pelB leader sequence to me. I can give you feedback once we tried it out!

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...

Hey bacteriologists!
I want to test fluorescent proteins on different locations within E. coli cells and search for good membrane anchoring and periplasmic leading sequences. What are good candidates?
#bacteria #fluorescentproteins #microscopy #fluorescence

Delighted to share our latest review: "Live-cell imaging in the deep learning era"
Written with @jwpylvanainen.bsky.social Estibaliz Gómez-de-Mariscal and @henriqueslab.bsky.social

www.sciencedirect.com/science/arti...