Heya, I'm Jonas,

a systems biologist who studies how cells self-organize and cooperate to perform sophisticated biological functions, such as building organs during embryonic development. To do this, I combine experiments (mainly zebrafish fluorescence microscopy), computation (including image analysis, data science, & simulations), and theory (from modeling all the way to philosophy). For my computational work I primarily use python.

Currently, I work as a postdoctoral researcher in the Mayor lab at University College London.

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🔧 I'm currently (mainly) working on...

• Studying the interplay of cell shape and cell fate using systems microscopy 🔬🐟
  • My main postdoc project uses the zebrafish neural crest as a model system; more on this soon!
  • In earlier related work I analyzed the cellular architecture of the zebrafish lateral line primordium; see my PhD paper!
  • Two blog posts on systems microscopy for non-experts can be found here and here

• Developing new conceptual perspectives to understand complex living systems, namely the Core & Periphery (C&P) hypothesis 💥
  • Read the C&P hypothesis paper here!
  • An accompanying blog post can be found here

• Automating microscopes to track migratory cell populations 🤖🔬
  • I'm the lead dev of DySTrack (Dynamic Sample Tracking), a recently released open-source python tool for automated tracking of moving samples on common commercial microscopes
  • Find it here: GitHub repo, Documentation, Paper in JCS

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💡 My thoughts on...

• The present and future of developmental biology (blog)
• Synthetic developmental biology (review)
• Complex biological systems and optogenetics (review)
• Systems microscopy and digital tissues (blog)

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📜 Repos associated with my contributions to research papers:

• Le et al. (2026): Tissue flow acts as a guidance cue for immune cell polarization and directional migration
  • Paper: https://doi.org/10.1038/s41556-026-02058-9
  • Repo: https://github.com/WhoIsJack/ectoderm-myeloid-tracking-analysis

• Wu, ..., and Hartmann (2025): DySTrack: a modular smart microscopy tool for live tracking of dynamic samples on modern commercial microscopes
  • Paper: https://doi.org/10.1242/jcs.264728
  • Repo: https://github.com/WhoIsJack/DySTrack

• Alasaadi et al. (2024): Competence for neural crest induction is controlled by hydrostatic pressure through Yap
  • Paper: https://doi.org/10.1038/s41556-024-01378-y
  • Repo: https://github.com/WhoIsJack/cavity_expansion

• Viswanathan, Hartmann, et al. (2021): Desensitisation of Notch signalling through dynamic adaptation in the nucleus
  • Paper: https://doi.org/10.15252/embj.2020107245
  • Repo: https://github.com/WhoIsJack/opto-notch-adaptation

• Hartmann et al. (2020): An image-based data-driven analysis of cellular architecture in a developing tissue
  • Paper: https://doi.org/10.7554/eLife.55913
  • Repo: https://github.com/WhoIsJack/data-driven-analysis-lateralline

• Wong et al. (2020): Dynamic buffering of extracellular chemokine by a dedicated scavenger pathway enables robust adaptation during directed tissue migration
  • Paper: https://doi.org/10.1016/j.devcel.2020.01.013
  • Repo: https://github.com/WhoIsJack/chemokine_buffering_paper

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👀 Some other repos worth checking out:

• Bioimage analysis with python; my hands-on, self-explanatory tutorial; a bit aged by now but still good; "vintage", one might say :p
• tissue_exploder; it's basic but it does look fancy, especially in 3D (see banner below)! :D
• TrackTree; another pretty visualization; maybe I'll actually need it for a paper one day, at which point I'll definitely update the code...

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Links to other profiles: ORCID, Google Scholar, LinkedIn, StackOverflow