Project highlight

Project image

Kristína Lidayová from the BIIF team developed a pipeline to align correlative light and electron microscopy (CLEM) images for ultrastructural mapping of protein distributions in cells. It aligns high-resolution TEM images with fluorescence microscopy channels using fiducial markers. Light microscopy (LM) provides multi-channel protein labeling, while electron microscopy (EM) offers nanoscale morphological details. Aligning these images enables comprehensive insights into cellular structures.

Key aspects of the image analysis pipeline include:

Fiducial particles detection in EM images using the template matching algorithm
Fiducial particles detection in LM images using the Big-FISH Python package
Finding correlation between EM and LM images using the Coherent Point Drift (CPD) registration

Explore the code here

If you have similar microscopy images or any image analysis questions feel free to reach us at biif@scilifelab.se or submit your project requests at https://nbis.se/services/bioimage-informatics. See more of our work on the BIIF projects page.

Publication highlight

Publication image

Jonas Windhager from the BIIF team supported a study utilizing a novel droplet microfluidics method to detect rare resistant E. coli subpopulations in bloodstream infections, addressing the clinical challenge of antibiotic heteroresistance. He developed a custom computational pipeline in Python to automate the analysis of time-lapse microscopy. By leveraging tunable image segmentation algorithms to quantify droplet shrinkage, the method successfully identified resistant cells at frequencies as low as 10^-6, demonstrating a robust, high-throughput approach for improved diagnostic sensitivity.

Interested in the image analysis pipeline? Check out the code

Read the full publication: Droplet microfluidics–based detection of rare antibiotic-resistant subpopulations in Escherichia coli from bloodstream infections. Sagar N. Agnihotri, Nikos Fatsis-Kavalopoulos, Jonas Windhager, Maria Tenje, and Dan I. Andersson. Sci. Adv. 11, eadv4558 (2025). DOI:10.1126/sciadv.adv4558

More new findings from this project are coming soon — stay tuned for updates!

Pre-Focus on Microscopy (FOM) discussion

We were delighted to host Dr. Oliver Biehlmaier and Dr. Alexia Loynton-Ferrand from the University of Basel. The visit included fruitful discussions on image analysis infrastructure, smart microscopy, and the tools used at our respective facilities.

Upcoming events

GloBIAS seminar

As part of the Global BioImage Analysts' Society (GloBIAS) seminar series, Nicholas Condon from the Institute for Molecular Bioscience, UQ, Australia will be speaking about "Big data infrastructure strategies for image analysis in a core facility" on 1st April, 2026 at 13:00 CEST.

Image data community days 2026

Euro-Bioimaging is organizing Image Data Community Days from 13-17th April, 2026 with a list of lectures, hands-on workshops and networking sessions focussed on image data.

Don't miss Jonas Windhager giving an update on the next major release of TissUUmaps in his talk "TissUUmaps 4: Facilitating Community Contributions to Spatial Biology Visualization" on 15th April, 2026 at 09:40 - 10:05 CET.

MIMER AI factory plenary kickoff

Interested in using AI for research? Curious about how AI is being applied in life sciences and other domains? This event might be for you.

19th OME Community Meeting

Open Microscopy Environment (OME) Community Meeting will be held at Düsseldorf from 28-30th April, 2026. More information here.

NBIS workshop in Neural Nets and Deep Learning

Christophe Avenel from the BIIF team along with other NBIS members is organizing an in-person course on "Neural Nets and Deep Learning" at Linköping University from 4-8th May, 2026. Check out the link for more details.

Apply by 4th April, 2026

NBIS workshop

NBIS training is offering the following courses in April and May:

Single Cell RNAseq Data Analysis, 13-27th April, 2026 (Online)
Tools for Reproducible Research, 20-24th April, 2026 (Lund, Stockholm)
Open Science in the Swedish context, 4-7th May, 2026 (Göteborg)
Programming Formalisms, 4-8th May, 2026 (Online)
Neural Networks and Deep Learning, 4-8th May, 2026 (Linköping)
Advanced Data Visualization in R, 5-7th May, 2026 (Lund)
Snakemake BYOC (bring-your-own-code) workshop, 25-27th May, 2026 (Online)

For more details on training please check this page.

NBIS drop-ins

A weekly drop-in that is open to any researcher with questions not only on image analysis but on bioinformatics, data management or HPC.

When: Tuesdays at 14:00 CEST

Where: https://meet.nbis.se/dropin to join the drop-in online

There are also options to attend on-site in Stockholm, Lund, Chalmers and Gothenburg. For more details check out this page.

Regards,

Suganya Sivagurunathan

On behalf of the BIIF team

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