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Dear All,

Welcome to the latest edition of the BioImage Informatics Facility (BIIF) newsletter!


The next Call4Help session is coming up next Wednesday, November 8, 9:00 – 11:00, information here. Note that you can always contact us under to set-up a meeting and receive support on image analysis.
The idea of the Call4Help session is to provide combined support on both the image analysis and the microscopy part of a project. For this we team-up with Sylvie Le Guyader, Head of the LCI Microscopy Facility, KI.


An end-to-end workflow for multiplexed image processing and analysis

An end-to-end workflow for multiplexed image processing and analysis has recently been published by Jonas Windhager et al in Nature Protocols. The protocol introduces computational tools that Jonas and his former colleagues from the Bodenmiller Lab (ETH Zurich & University of Zurich) developed to readily extract relevant biological information from protein-based multiplexed tissue imaging (e.g., imaging mass cytometry) data. Among others, these include the steinbock toolkit for batch-processing multi-channel images using community-established tools and approaches, and the imcRtools R/Bioconductor package for spatial single-cell analysis. The steinbock toolkit was also the topic of a recent BIIF webinar given by Jonas, who joined the BIIF as a bioimage analyst / research software engineer earlier this year. An extended version of the protocol is available at and a recording of the BIIF steinbock webinar is available on our YouTube channel.


DDLS Annual Conference 2023: The emerging role of AI in data-driven life science

This DDLS Annual Conference brings together the data-driven community in Life Science, introduces newly appointed DDLS fellows, and provides opportunities for networking across the research community and SciLifeLab infrastructures. The theme for 2023 is “the emerging role of AI in data-driven life science”. There will be presentations from DDLS fellows, and invited speakers on how they use AI in their research and their future visions. BIIF will contribute with a pre-conference introductory lecture on AI for imaging.

Dates: November 15 – November 16, 2023
Registration and more info here

BioVisionCenter Kick-Off Symposium, University of Zurich and online

The BioVisionCenter is a newly-created structure cofounded by the Friedrich Miescher Institute and the University of Zurich that aims at centralizing activities related to the processing of complex bioimage datasets. The BioVisionCenter has three missions consisting of 1) coordinating research in bioimage analysis, 2) fostering the development of standardized open-source resources, and 3) training the next generation of bioimage analysts. This kick-off Symposium aims at celebrating the launch of the BioVisionCenter by highlighting current initiatives for bioimage analysis and identifying opportunities to connect across the bioimage analysis community. The Symposium will feature invited talks from local stakeholders as well as national and international leaders in the field.

Dates: November 9 - November 10, 2023
Registration and more info here

DanioReadout - Zebrafish service platform

DanioReadout is a service facility at Uppsala University that provides customised, genome engineering and substance exposure service integrated with phenotypic quantification and evaluation in the intact zebrafish embryo. The three main service areas are modelling of human genetic diseases, with experience in generating nearly 200 novel gene knock-out models, substance exposure studies and human cancer modelling. The zebrafish husbandry is under the recently opened, state-of-the-art zebrafish facility Centre for In Vivo.
For this newsletter we would like to highlight that all service areas are integrated with a unique in-house developed automated image capture pipeline and data quantification and analysis. Image analysis expert is Amin Allalou, affiliated with BIIF.

DanioReadout and Uppsala University Zebrafish Core Facility Information Meeting: December 6, 2023, 14:00 Navet, BMC, Uppsala Registration and more info here

Best regards
Anna, in behalf of BIIF

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