whoisjack/hackday-pybioimage

Repo for UCL Festival of Code Hackday python group working on modernizing and extending the python bioimage analysis tutorial.

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

hackday-pybioimage's Issues

Input/output handling

We want to separate the input and output data from git and restructure it to make it a bit more clean / following best practices.

• Create an outputs dir and ignore everything in it (except the .gitignore). See PR #1.
• Put the input data on figshare.
• Write a code cell in the main tutorial that pulls the data into example_data.
• Delete the example data files from git.
• Change all cases where data is being saved to use the outputs dir.

example data improvements

see issue #3 on the non-hackday version 😄

Continuous integration

Might be nice to have a CI system that checks all the notebooks keep running successfully at least (and possible runs some additional tests?).

Make development easier

Some thoughts on what might make development easier (not sure how feasible they are!)

• make notebook metadata ignore conda version etc
• automatic install of all dependencies
• ...

Dependencies in Binder

Binder still doesn't seem to load dependencies. Will have to look into this eventually.