BIIF Newsletter – June 2026

Hello,

I am sure I speak for many when I say that I am greatly looking forward to Midsommer and the summer season ahead. I hope you are all sharing in that anticipation.

Project Highlight

Maximilian Senftleben from the BIIF team developed Pyflux, a desktop Graphical User Interface for loading, filtering, visualizing, aligning, clustering, and exporting MINFLUX (Minimal fluorescence photon flux microscopy) localization data. Max built the tool with PySide6, Plotly, Pandas, SciPy, and Zarr.

The tool allows you to:

View data in interactive 2D/3D scatter plots
Compare datasets in a multicolor viewer
Generate heatmaps, Gaussian renderings, and TIFF exports
Align datasets using MBM bead-based registration
Run DBSCAN clustering on track-averaged localizations
Export filtered data and summary statistics to CSV
Filter localizations by trace length, EFO, and CFR

If you are curious about how it works, check it out 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.

MINFLUX – nanoscale fluorescence microscopy and novel applications symposium

Pyflux, a tool developed by Maximilian Senftleben from the BIIF team, was presented at the "3rd SciLifeLab MINFLUX symposium – nanoscale light microscopy". Feel free to check the details of the tool here.

CBA Day

BIIF had a very good presence at the CBA day, with team members presenting BIIF activities, TissUUmaps, and the image analysis pipeline developed for an isPLA (in situ Proximity Ligation Assay) project. BIIF also learned about the different image analysis projects being carried out in the image analysis division at Dept of IT, UU.

Cell Biology at Scale 2026

Cell Biology at Scale (CB@S) 2026 included both workshops and a one-day symposium co-hosted by SciLifeLab and Biohub that brought together researchers working at the intersection of cell biology, imaging, functional genomics, computational biology, and AI. Discussions focused on integrating multimodal cellular data, developing predictive models of cell function, and identifying key experimental and computational challenges. Carolina Wählby (pictured) participated in the technical workshop focused on multi-modal imaging technology with a talk on how to squeeze the most out of spatial omics data. Jonas Windhager also contributed to the multi-modal Imaging technical workshop. Both workshops and the general conference were hosted in Stockholm, and CB@S 2026 marked the first time the annual meeting was held in Europe.

NASSA (Nordic Alliance for Single-Cell and Spatial Analysis) Kick-Off Meeting

The kick-off meeting brought together experts in single-cell and spatial analysis from all four partner countries (Sweden, Denmark, Norway, and Finland) to discuss the rapidly evolving single-cell and spatial landscape!

Christophe Avenel from BIIF presented a poster on "TissUUmaps", a free and open-source browser-based tool for fast visualization and exploration of spatial data.

Publication Highlight

Image from Agnihotri, S.N. et al, 2026 CC BY

Antibiotic resistance is a threat to global health, and traditional antimicrobial susceptibility testing (AST) is essential to choosing the right treatment. Heteroresistance (HR) is a special form of resistance that is difficult to detect using standard AST methods. In their paper, Agnihotri et al. present a droplet microfluidics-based approach for detecting HR using digital image texture quantification, and Agustin Corbat and Jonas Windhager from BIIF helped devise the image analysis pipeline. We are looking forward to seeing the impact of this technology translated into clinics!

Read the full publication here: Sagar N. Agnihotri, Nikos Fatsis-Kavalopoulos, Emma Vikdahl, Jonas Windhager, Agustin A. Corbat, Dan I. Andersson & Maria Tenje. Droplet microfluidics with image texture quantification for detection of rare antibiotic-resistant subpopulations from bloodstream infections. npj Digit. Med. 9, 410 (2026). https://doi.org/10.1038/s41746-026-02808-x

Explore the code: https://zenodo.org/records/18717330

Upcoming Events

European Light Microscopy Initiative (ELMI) 2026

The 26th edition of the ELMI 2026 meeting takes place from 16th–19th June 2026 in Coimbra, Portugal. This year ELMI focuses on:

AI & Bioimaging Analysis
Spatial Biology & Multiplexing Imaging
Nanoscopy
Volumetric and Deep-Tissue Imaging
Novel sample processing techniques, probes, and biosensors
Label-free Imaging

For more details, check out the ELMI 2026 website.

If you plan to attend the meeting, don't miss the poster on BIIF activities by Maximilian Senftleben.

Premier European Meeting of the Society of Biomolecular Imaging and Informatics (SBI²)

This is the first European meeting of the Society of Biomolecular Imaging and Informatics (SBI²), to be held in Cambridge, UK on July 7th–8th, 2026.

The meeting focuses on the following themes:

Simulating Life: The Virtual Cell Revolution
Silicon Meets Cell: AI Seeing What We Can't
The Future is Now: Next-Wave High-Content Technologies
Image to Impact: High-Content Screening Delivered
Dimension Matters: Revolutionizing Drug Discovery in 3D

For more details and registration, click here.

Suganya Sivagurunathan will share about BIIF projects that are in line with the conference theme through a poster.

NBIS Workshop

NBIS training is offering the following course:

Statistical Methods in Life Sciences, 7–11th September 2026 (Uppsala). Apply by 23rd June 2026.

For more details on training, please check the NBIS training page.

NBIS Drop-Ins

A weekly drop-in open to any researcher with questions not only on image analysis but also 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.

BIIF(fun)

With summer approaching, BIIF had a BBQ + Henna party! 🎉

Regards,

Suganya Sivagurunathan,
On behalf of the BIIF team

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