Christoph Spahn
@michriscopy.bsky.social
Leader of the Nanoscale Bacteriology research group at the Rudolf Virchow Center @ JMU Würzburg. Revealing the inner life of #bacteria using #SuperResolutionMicroscopy.
Reposted by 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...
📜 www.biorxiv.org/content/10.1...
October 22, 2025 at 11:10 AM
🦠🔬🤖🧑💻 #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...
📜 www.biorxiv.org/content/10.1...
Check this out! A napari plugin for AI-based analysis of microbial bioimages! 🔬🦠💻
🦠🔬🤖🧑💻 #mAIcrobe interface preview, a platform for #DeepLearning enabled bacterial image-based phenotyping. Check it out
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
💻: github.com/HenriquesLab...
📄: www.biorxiv.org/content/10.1...
November 12, 2025 at 7:15 AM
Check this out! A napari plugin for AI-based analysis of microbial bioimages! 🔬🦠💻
Reposted by Christoph Spahn
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!
August 29, 2025 at 11:17 AM
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!
Reposted by Christoph Spahn
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
August 28, 2025 at 3:02 PM
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
August 29, 2025 at 10:04 AM
Great presentation of @gomez-mariscal.bsky.social. Covering PhotoFiTT, DL4MicEverywhere, resolution-matching and many other aspects of the FAIRy universe 💻🔬🧚♂️ #DeepLearning #Microscopy
Reposted by Christoph Spahn
Estibaliz Gomez de Marisca @gomez-mariscal.bsky.social from Lisbon going live and sharing great work on AI-empowered microscopy #SMLMS2025 and accessible AI
August 29, 2025 at 7:51 AM
Estibaliz Gomez de Marisca @gomez-mariscal.bsky.social from Lisbon going live and sharing great work on AI-empowered microscopy #SMLMS2025 and accessible AI
Reposted by Christoph Spahn
Johannes Hohlbein @hohlbeinlab.bsky.social from Wageningen presenting his great work on the dynamics of the E. coli replication initiator DnaA #SMLMS2025
August 28, 2025 at 8:16 AM
Johannes Hohlbein @hohlbeinlab.bsky.social from Wageningen presenting his great work on the dynamics of the E. coli replication initiator DnaA #SMLMS2025
Reposted by Christoph Spahn
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)
August 28, 2025 at 7:56 AM
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)
Reposted by Christoph Spahn
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
August 28, 2025 at 7:23 AM
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
Reposted by Christoph Spahn
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!
August 28, 2025 at 10:43 AM
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 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...
doi.org/10.1371/jour...
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...
doi.org
August 12, 2025 at 8:57 PM
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...
doi.org/10.1371/jour...
Reposted by Christoph Spahn
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
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
BPoD | Into the Nucleoid
Into the Nucleoid - Biomedical pictures for April 2025.
bit.ly
May 28, 2025 at 2:25 PM
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
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
Reposted by Christoph Spahn
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
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
May 22, 2025 at 4:49 PM
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
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
Reposted by Christoph Spahn
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
May 22, 2025 at 3:05 PM
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
Reposted by Christoph Spahn
High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH
www.cell.com/cell/abstrac...
#spatialbiology
www.cell.com/cell/abstrac...
#spatialbiology
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...
www.cell.com
April 23, 2025 at 9:47 AM
High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH
www.cell.com/cell/abstrac...
#spatialbiology
www.cell.com/cell/abstrac...
#spatialbiology
Reposted by Christoph Spahn
Two more weeks to apply to join us in Paris !
research.pasteur.fr/en/call/call...
research.pasteur.fr/en/call/call...
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...
research.pasteur.fr
February 13, 2025 at 6:09 PM
Two more weeks to apply to join us in Paris !
research.pasteur.fr/en/call/call...
research.pasteur.fr/en/call/call...
Reposted by Christoph Spahn
📣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...
Apply here: www.uni-wuerzburg.de/karriere/sin...
PhD student position at the Chair for Microbiology
www.uni-wuerzburg.de
February 14, 2025 at 8:25 AM
📣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...
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 👇
New preprint:
Virulence does not come for free - activity of the T3SS stops bacterial growth.
We show that in Y. enterocolitica, activating secretion triggers major DNA rearrangements.
Could this be the key to secretion-associated growth inhibition?
Read more here: www.biorxiv.org/content/10.1...
Virulence does not come for free - activity of the T3SS stops bacterial growth.
We show that in Y. enterocolitica, activating secretion triggers major DNA rearrangements.
Could this be the key to secretion-associated growth inhibition?
Read more here: www.biorxiv.org/content/10.1...
Activation of the Yersinia type III secretion system induces large-scale chromosomal and virulence plasmid DNA rearrangements
The type III secretion system (T3SS) is used by Gram-negative bacteria, including important pathogens, to manipulate eukaryotic target cells by injecting effector proteins. Type III secretion and bact...
www.biorxiv.org
February 12, 2025 at 9:59 PM
New preprint from the Diepold lab describing major chromosome and plasmid rearrangements during secretion in Y. enterocolitica! 🦠🔬 Happy that I could contribute a bit 👇
Reposted by Christoph Spahn
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...
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...
January 15, 2025 at 1:39 PM
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...
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
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
January 15, 2025 at 10:17 AM
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
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
Reposted by Christoph Spahn
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...
Written with @jwpylvanainen.bsky.social Estibaliz Gómez-de-Mariscal and @henriqueslab.bsky.social
www.sciencedirect.com/science/arti...
October 27, 2023 at 5:43 PM
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...
Written with @jwpylvanainen.bsky.social Estibaliz Gómez-de-Mariscal and @henriqueslab.bsky.social
www.sciencedirect.com/science/arti...