steinbock: a toolkit for processing multiplexed tissue images

June 16, 2023, 09:00 – 10:00


Bioimage Informatics Unit
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Online event via Zoom

steinbock: a toolkit for processing multiplexed tissue images

June 16 @ 09:00 10:00 CEST

Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological molecules in tissues at single-cell resolution. Extracting biologically relevant information from multi-channel images involves computational tasks such as image segmentation and feature extraction, which can pose technology-specific challenges to experimental biologists lacking adequate bioinformatics training.

In this hands-on webinar, we will showcase steinbock, a computational toolkit for batch-processing multiplexed tissue images using established tools and approaches, without the need for additional programming. The steinbock toolkit can be used to rapidly extract spatially resolved single-cell data for downstream statistical analysis, interfacing with popular analysis environments such as Python or R/Bioconductor. It is an essential part of the Analysis workflow for IMC data (Bodenmiller Lab, ETH Zurich/University of Zurich) and further information can be found in the steinbock online documentation.

The webinar will be given by Jonas Windhager, the creator and former maintainer of steinbock, who recently joined the SciLifeLab BioImage Informatics Facility. It is aimed at experimental biologists with an interest in image analysis and is scheduled to last one hour or longer, depending on interest.

Last updated: 2023-06-07

Content Responsible: David Gotthold(