BIIF Newsletter – October 2026

Hello,

I hope everyone is enjoying the Fall season!

Project Highlight

To study how wood anatomy changes with wind disturbances, Kristína Lidayová developed an image analysis workflow for confocal microscopy images of Safranin-stained wood samples. A FIJI macro preprocesses the images, finds the well-preserved wood regions, and segments the individual cells into lumen and cell wall. A Python Jupyter Notebook then detects the annual tree rings and for every cell it measures the lumen area and calculates the average wall thickness.

The data was provided by Jakub Kašpar from VUKOZ, Brno, Czech Republic.

Explore the code.

Image analysis queries

If you have 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.

Images to Knowledge (I2K) 2026

The BIIF team, together with Leslie Solorzano from NBIS, held a virtual workshop titled “Integration of multi-modal data and visualization using TissUUmaps 4”.
The workshop covered the basics of image registration, working with SpatialData, and aligning spatial transcriptomics data with light microscopy images. A final session showed how to visualize the registered multi-modal data in TissUUmaps.

The session recording will be available soon on the I2K Conference YouTube channel.

Elixir Spatial Omics course

Christophe Avenel from BIIF co-organised the ELIXIR Spatial Omics Data Analysis course, held at BMC in Uppsala on 6–9 th October 2026, hosted by NBIS together with the ELIXIR Single-Cell Omics community. The four-day course brought together trainers from across Europe to teach participants how to analyse spatially resolved transcriptomics data. Christophe Avenel also gave lectures on data formats, cell segmentation and imaging-based spatial analysis, while Jonas Windhager, Maximilian Senftleben and Suganya Sivagurunathan helped with the practicals on data formats and cell segmentation.

All the course materials are available on this page.

scverse conference

Jonas Windhager presented a poster titled “TissUUmaps 4: Facilitating community contributions to spatial biology visualization” in the scverse conference that was held in Copenhagen, Denmark from 12-14th of October, 2026.

Publication Highlight

Image from Eleanor M O´Roberts et al, 2026 (CC BY)

In this paper, O´Roberts et al. present a protocol that combines multiplexed detection of genes using DNA FISH with multiplexed immunofluorescence detection of proteins on the PhenoCycler Fusion platform in large tissue sections. Christophe Avenel from BIIF built the image analysis pipeline, which segments cells, measures protein marker intensities and counts DNA FISH spots in each cell. The data can be explored interactively in TissUUmaps!

Read the full publication here: Eleanor M O Roberts, Pranauti Panshikar, Xiaoze Li Wang, Christophe Avenel, Quentin Verron, Eléna Coulier, Magda Bienko, Charlotte Stadler (2026). An integrated protocol for multiplexed DNA FISH and protein detection in large tissue sections. Journal of Histotechnology, 49(3), 199–215. https://doi.org/10.1080/01478885.2026.2703359

Explore the code.

Upcoming Events

OME-Zarr Hackathon

The OME-Zarr community is organising a hackathon from 2nd-6th November, 2026 in Zurich, Switzerland. Major topics of the hackathon are OME-Zarr viewers, OME-Zarr tooling and OME-Zarr workflows. Among other authors, Jonas Windhager from BIIF will present the latest OME-Zarr specification updates on 2nd November, 2026 at 15:45 CET. You can join the talks online through this link.

More details of the hackathon can be found here.

GloBIAS 2026 workshop

The GloBIAS 2026 Bioimage Analysts’ Workshop takes place on 10–13th November 2026 at ISAS Campus in Dortmund, Germany. This year’s workshop focusses on how AI is transforming bioimage analysis with discussions on AI foundational models and AI agents.

More details are on the workshop page.

Crick BioImage Analysis Symposium 2026

The seventh Crick BioImage Analysis Symposium (CBIAS 2026) takes place on 23–24 th November 2026 at the Francis Crick Institute in London. The two days of talks, poster sessions and panel discussions focusses on current topics in image analysis and image processing for microscopy.

The symposium is followed by a 2-day napari workshop on 25–26 th November.
Registration and details are on the event page.

NBIS Workshops

NBIS training is offering the following courses in the month of November:

R Programming Foundations for Data Analysis, 9–13th November, 2026
Introduction To Bioinformatics Using NGS Data, 16–20th November, 2026
Using AI in life science - A primer on 25th November, 2026. Apply by 24th November, 2026

For more details on training, please check the NBIS training 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 CET

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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