Hello everyone, We are back with our BIIF newsletter!

Project highlight

Daphnia magna image

High-Throughput Analysis for Toxicological Assessment in Daphnia magna

This project aims to develop an image-based analysis method for toxicological effects in Daphnia magna, an ecotoxicological standard test species, after exposure to industrial chemicals or environmental samples. Molecular staining combined with fluorescence microscopy measures adverse effects on the organism. Light intensity data is extracted from fluorescence images of daphnia exposed to a range of concentrations of a chemical/sample to quantify the effects. The main goal of this study is to generate toxicological data in a time-efficient manner. Therefore, image acquisition was done with an automated multipoint confocal high-content imaging system suitable for experiments in multi-well plates. To achieve a high-throughput method, this project also requires a time-efficient image analysis method with accurate segmentation of the daphnia based on the transmitted light image. It further requires an easy application of the segmentation mask to the corresponding fluorescence images to extract intensity data. Therefore, we built a small GUI that allows segmentation of the body and head of the daphnia. 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.

BIIF Webinar

The BIIF team is organizing a webinar on "Image Registration for Microscopy Images" presented by Suganya Sivagurunathan on 25th March at 10:00 AM CET. Do you have microscopy images with drift? Or would you like to learn the basics of image registration? Join us! Date: 2026-03-25, 10:00 AM CET Register here

OME-NGFF Community Call

OME-NGFF Community Call image

Jonas Windhager from the BIIF team gave an update on the community efforts to standardize single-file storage of OME-Zarr in the OME-NGFF Community Call on the 3rd of March, 2026. New to OME-Zarr? Check out more information from the OME-Zarr community.

Publication highlight

Publication image

Kristína Lidayová and Christophe Avenel from the BIIF team contributed to a machine learning framework, differentiating microrheological features of native and artificial colonic mucus, identifying hydroxyethyl cellulose–based artificial mucus as the best mimic of native mucus. We provided an advanced image analysis pipeline to isolate and track nano- and micro-scale particles in complex mucus backgrounds and generated quantitative particle trajectory data that powered the machine learning analysis. Interested in the image analysis pipeline? Check out the code Read the full publication: Machine learning framework for investigating nano- and micro-scale particle diffusion in colonic mucus. Marco Tjakra, Kristína Lidayová, Christophe Avenel, Christel A.S. Bergström, Shakhawath Hossain. J Nanobiotechnol 23, 583 (2025).

Upcoming events

Focus on Microscopy (FOM) 2026 in Stockholm!

Join FOM to get updated on the innovations and the latest developments in optical microscopy. The conference begins with tutorials followed by poster sessions and talks in Stockholm from 29th March to 1st April, 2026. Maximilian Senftleben from the BIIF team will be presenting a poster about BIIF at the conference. If you are attending, feel free to stop by! For more details please check the conference website. Date: 2026-03-29 to 2026-04-01

NBIS workshop

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

Introduction to Data Management Practices, 17-19th March, 2026 (Uppsala)
Introduction to Metabolomics Data Analysis, 23-25th March, 2026 (Umeå)

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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