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SimonBon/README.md

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Hey, I'm Simon!

I'm a Ph.D. student at TU Vienna, working at the intersection of AI and biology with a focus on computer vision for single-cell and multiplex tissue imaging. In the Taschner-Mandl Lab, I build methods that help turn complex microscopy data into reliable, interpretable, and actionable biological insights.

What I work on

My research centers on weakly- and self-/unsupervised learning for high-dimensional imaging data, with particular emphasis on:

  • Representation learning and robust feature extraction
  • Uncertainty estimation and failure-case awareness
  • Interpretability and biologically meaningful model behavior

I work across multiple imaging modalities, including Immunofluorescence, FISH, and multiplex platforms such as IMC, CODEX, and MIBI.

Scientific illustration and communication

Alongside research, I’m also a scientific illustrator. I care deeply about making complex ideas understandable—not just correct. I design figures, posters, and visual stories, and I regularly give lectures and hands-on workshops on scientific illustration: how to build clear visual narratives, craft publication-ready figures, and communicate results effectively to both expert and non-expert audiences.

Posters and conference material

A selection of posters and materials from international conferences:

Interactive demos

I also presented my work at TEDxAI Vienna 2025. If you want to try the interactive demo:

Get in touch

If you’d like to connect or collaborate, feel free to reach out on LinkedIn.

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  1. CellPatchExtraction CellPatchExtraction Public

    Code to extract single cell patches from microscopic images

    Jupyter Notebook

  2. cellplot cellplot Public

    Jupyter Notebook

  3. FISHPainter FISHPainter Public

    Repository to create Fluorescence in Situ Hybridization with RGB color scheme

    Jupyter Notebook 1

  4. AI-and-Biology AI-and-Biology Public