Hello,

I hope everyone is enjoying the Spring season!

Project highlight

Christophe Avenel from the BIIF team developed a pipeline to quantify the infiltration, migration and proliferation of cancer cells within a glioblastoma organoid model. The organoids were cultivated from human induced pluripotent stem cells and were cocultured with fluorescent reporter transduced glioma stem cell spheroids. After a set period of time, the organoid models were fixed, stained and cleared for imaging via light sheet microscopy. Quantification of the organoids over time helps to relate patient-derived cancer cells back to progression of cancer in the patients.

The images were from the lab of Mats Nilsson, Professor, Stockholm University.

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.

Image data community days 2026

Jonas Windhager from the BIIF team gave an update on the next major release of TissUUmaps in his talk "TissUUmaps 4: Facilitating Community Contributions to Spatial Biology Visualization" on 15th April, as a part of Euro-Bioimaging Image Data Community Days.

19th OME Community meeting

Jonas Windhager from the BIIF team delivered a lightning talk on TissUUmaps 4, attracting significant interest from multiple research teams eager to explore the tool's capabilities.

Neural Networks & Deep Learning NBIS workshop

Christophe Avenel from the BIIF team co-organized a course on Neural networks and Deep Learning through NBIS which was held in Linköping from 4th - 8th May, 2026. The course attracted participants from across Sweden and internationally, with representation from both academia and industry.

More such NBIS courses could be found below and also here

foundingGIDE

foundingGIDE community event was held in Heidelberg, Germany this year from 4-6th May, 2026 to discuss the standards, tools and recommendations for interoperable imaging data ecosystem.

Anna Klemm, Head of BIIF shared about Image Data at the BIIF and SciLifeLab, Sweden on 6th May.

For more details, check here

Publication highlight

Image adapted from Enikő Lázár et al, 2025 (CC BY)

This study combined spatial transcriptomics, single-cell transcriptomics and imaging-based validation across early human heart development. The authors identified the spatial organization of coarse- and fine-grained cell states and described their arrangement into functional niches. Christophe Avenel from BIIF contributed by making the data available within the TissUUmaps viewer, integrating 38 Visium sections, 9 in situ sequencing sections, and single-cell data, allowing the interactive exploration of the study's spatiotemporal transcriptomic data.

Read the full publication here: Enikő Lázár, Raphaël Mauron, Žaneta Andrusivová, Julia Foyer, Mengxiao He, Ludvig Larsson, Nick Shakari, Sergio Marco Salas, Christophe Avenel, Sanem Sariyar, Jan Niklas Hansen, Marco Vicari, Paulo Czarnewski, Emelie Braun, Xiaofei Li, Olaf Bergmann, Christer Sylvén, Emma Lundberg, Sten Linnarsson, Mats Nilsson, Erik Sundström, Igor Adameyko & Joakim Lundeberg. Spatiotemporal gene expression and cellular dynamics of the developing human heart. Nat Genet 57, 2756–2771 (2025) https://doi.org/10.1038/s41588-025-02352-6

Explore the code

Upcoming events

MINFLUX – nanoscale fluorescence microscopy and novel applications symposium

On the 13th of May the Advanced Light Microscopy Unit (ALM) at SciLifeLab Solna will host a symposium about the latest nanoscale fluorescence microscopy technology MINFLUX and its novel applications.

There will also be an exciting demonstration of a tool developed by Maximilian Senftleben from the BIIF to analyze MINFLUX data.

Find more information about the event at the link here.

CBA Day

The Centre for Image Analysis in the Department of Information Technology, Uppsala University is organizing a CBA day on the 19th May, 2026. The goal is to bring together researchers across Uppsala University who work with images as research data and who therefore need, develop, or use image analysis methods.

• Anna Klemm & Christophe Avenel from the BIIF team will present on: "BioImage Informatics Unit (BIIF): providing support, training, and tools for image data analysis"
• Anna Klemm will also have a digital poster on BIIF, and Christophe Avenel will have one on the usage of TissUUmaps
• Suganya Sivagurunathan will present a poster on an image analysis pipeline developed for a user project, which identifies isPLA signals in keratinocytes

Check the link here for more details.

Cell Biology at Scale 2026

CB@S 2026 is a one-day symposium co-organized by SciLifeLab and Biohub to bring together researchers working at the interface of cell biology, imaging, functional genomics, computational biology, and artificial intelligence. It will be held at Stockholm on 3rd June, 2026.

For more details, check out the link.

Nordic Microscopy Society SCANDEM 2026

The Annual Meeting of Nordic Microscopy Society is taking place in Oulu, Finland from June 9th – 12th bringing together researchers, professionals, and students from across the Nordic countries to explore the latest developments in microscopy and imaging in the fields of life and materials sciences.

For more details, check out the link

European Light Microscopy Initiative (ELMI) 2026

26th edition of the ELMI2026 meeting is taking place from 16th - 19th June 2026 in the vibrant city of Coimbra, Portugal. This year ELMI focusses on the following,

• 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 link

Cell Modeling in Space and Time

Cold Spring Harbor Laboratory (CSHL) meeting on Cell Modeling in Space and Time will be held from June 22 to June 25, 2026 in CSHL, New York with an option of attending the meeting virtually as well. The meeting will emphasize the interplay between experiment, bioimage analysis, data-driven and mathematical models and computer simulations to quantitatively represent dynamic, multi-scale, multimodal, and/or high-content imaging data, develop testable hypotheses and to gain deeper insights into systems level design principles that govern cellular organization and dynamics in health and disease.

For more details, check out the link here

Spatial Omics (2nd Edition)

The second edition of Spatial Omics conference will be held in Bruges, Belgium from 22-24 June, 2026 focussing on i) The Unimodal Track spotlighting innovations in single-modality spatial technologies, such as spatial transcriptomics, proteomics and metabolomics and ii) The Multimodal Track exploring the integrative strategies that combine multiple spatial omics modalities.

Carolina Wählby, the BIIF Platform Scientific Director will be talking about "Functional pathology - exploring tissue with spatial omics and AI" in the afternoon session on 23rd of June.

For more details, check out the link here

Statistical and AI methods for multi-modal multi-scale modeling of biological systems

The conference will be from 28th Jun - 3rd Jul in Ascona, Switzerland and will address critical challenges in integrating and interpreting multi-modal datasets across biological scales.

For more details, check out the link here

NBIS workshop

NBIS training is offering the following courses in the month of May,

• 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