Jonas Wagner

Quantitative Biology · Systems Biology

Measuring living systems.

I’m Jonas Wagner, a systems biologist. I use imaging, machine learning, and multimodal data analysis to study how complex biological systems are organized and how they change.

Explore projects About me
From Organoid Explorer FIG. 01
Cluster of reconstructed organoid cells, with each cell in a different color
Reconstructed cell surfaces
Organoid to shape atlas

01 Portfolio

Selected projects

Quantitative approaches to cell shape, gene expression, and microbial behavior, alongside tools for exploring the underlying data.

Scientific software · Immersive imaging

Fiji VR

A Fiji plugin for examining how structures are arranged in 3D and how they change over time, in the browser or in VR.

  • ImageJ
  • WebXR
  • Volume rendering

Scientific software · 3D morphology

Organoid Explorer

A macOS app for comparing cell shapes in 3D and checking those comparisons against the original microscopy.

  • Swift
  • Segmentation
  • Shape analysis

Master’s thesis · Quantitative microscopy

Predation at the microscale

A multimodal microscopy analysis of how barrier openings affect protist movement and bacterial prey in a soil-like chip.

  • Nextflow
  • Deep learning
  • Microfluidics

Dewpoint Therapeutics · Industry research

Condensate profiling

I combined RNA sequencing and high-content microscopy to look for condensate-related drug targets in a cell model of type 2 diabetes.

  • MOFA2
  • RNA sequencing
  • High-content imaging

02 About & résumé

Jonas Wagner

I trained in systems biology at Heidelberg University. I’m interested in questions that take more than one kind of measurement to answer, from how cell morphology relates to gene expression to how spatial constraints shape microbial behavior.

LinkedIn GitHub ORCID

Selected experience

  • 2025–2026
    Scientific trainee · EMBL Heidelberg

    Developed deep-learning workflows for segmenting soil protists in time-lapse microscopy.

  • 2023–2026
    M.Sc. Molecular Biosciences · Heidelberg University

    Systems Biology major. Master’s research in the Van Gestel group.

  • 2024
    Research internship · Saez-Rodriguez group

    Curated benchmark datasets for automated knowledge graph construction in BioCypher.

  • 2022–2023
    Dewpoint Therapeutics · Dresden

    Exploratory biology intern. Integrated RNA sequencing and high-content microscopy with MOFA2 for multimodal condensate profiling.

    Research associate. Prototyped knowledge graphs that combined multi-omics and high-throughput screening data to help prioritize drug discovery targets. Integrated deep-learning segmentation into condensate imaging workflows.