Portfolio

I am a computational scientist and passionate developer of (open-source) research software.

Research software (selection)

• Multiplexed tissue imaging:
  • readimc, a Python package for reading imaging mass cytometry data
  • steinbock, a containerized command-line tool for processing multiplexed tissue images
  • spellmatch, a Python-based command-line tool for spatial cell matching (discontinued)
  • imdlib, a C++ library with Python bindings for reading CyTOF .imd files (archived)
• Spatial biology visualization:
  • TissUUmaps4, a static web application for visualizing spatial biology (new version)
  • biobrowse, an ImageJ plugin for image browsing written in Java (unpublished)
• Bioimage data management & validation:
  • birka, a desktop application for interactive bioimage data validation and archival

I actively contribute to several open-source community projects, such as the napari image viewer or the OME-Zarr file format. You can find my most recent activities on my GitHub profile.

Publications (selection)

• Windhager et al. An end-to-end workflow for multiplexed image processing and analysis. Nature Protocols, 2023. https://doi.org/10.1038/s41596-023-00881-0
• Tognetti et al. Deciphering the signaling network of breast cancer improves drug sensitivity prediction. Cell Systems, 2021. https://doi.org/10.1016/j.cels.2021.04.002
• Windhager et al. A stochastic hybrid model of DNA replication incorporating 3D protein mobility dynamics. bioRxiv, 2019. https://doi.org/10.1101/583187

You can find a complete list of my publications on Google Scholar.

Teaching (selection)

• AI tools in biology 2025: AI and bioimage analysis
  Lecture at the Swedish University of Agricultural Sciences (SLU), January 2025 [Slides]
• Next-generation bioimage file formats in spatial biology
  Seminar at the Center for Image Analysis, Uppsala University, January 2024 [Recording]
• Introduction to the steinbock toolkit for multiplexed tissue image processing
  SciLifeLab webinar, June 2023 [Material] [Recording]
• Multiplexed tissue imaging workshop 2023
  International workshop at the University of Zurich, January 2023 [Material]
• Introduction to biological data analysis in R and Python
  Online course, March 2020 – May 2020 [Material]

I also assisted in several courses on scientific Python programming (University of Zurich, SciLifeLab/NBIS) and bioimage analysis (Uppsala University, EMBL Heidelberg).