whoisjack / python_teaching

Various bits of code from python sessions I've taught.

Heya,

I'm Jonas, a systems biologist who combines experiments (mainly zebrafish fluorescence microscopy), computation (including image analysis, data science, and simulations), and theory (from modeling all the way to philosophy) to study how cells self-organize and coordinate to perform sophisticated biological functions, such as building organs during embryonic development. My computational work I do almost exclusively with python.

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

My scientific interests obviously start at cell and developmental biology, but range across evolution, complex systems, computer science, cognitive science, and philosophy - and most especially anything that builds bridges across these fields.

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Some ongoing projects and related links:

• Developing new conceptual perspectives to understand complex living systems
  • See e.g. the Core & Periphery hypothesis; preprint
• Studying the interplay of cell shape and cell fate in the vertebrate neural crest using systems microscopy
  • My earlier systems microscopy work (on a different tissue, the lateral line primordium) can be found here
  • Two blog posts on the topic written for non-experts can be read here and here
• Automating microscopes to track migratory cell populations (more on this soon!)

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Some repos worth highlighting (more to come!):

• My hands-on tutorial on bioimage analysis with python; a bit aged by now but still good; "vintage", one might say :p
• The repo accompanying my lateral line systems microscopy paper; it's cool but in good ol' python 2 and very much "research code"; my current work builds on this, so newer code is forthcoming!
• tissue_exploder: it's basic but it looks fancy, especially in 3D (see banner below)! :D
• TrackTree; another fancy visualization; the day will come when I will actually need it for a paper, I'm sure, at which point I'll be modernizing this code, pinky promise...

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My thoughts on...

• Complex systems and optogenetics (review)
• Synthetic developmental biology (review)

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