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title: UCL Festival of Code Hackday - Group 2 (Python)

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# UCL Festival of Code Hackday - Group 2 (Python)


## Make-Over of the Python BioImage Analysis Tutorial


### Participants

- Jonas Hartmann (Mayor lab, UCL CDB)
- Alessandro Felder (Research Software Development, UCL)
- Ian Tan (UCL Medical School)



### Background

- The [Python BioImage Analysis Tutorial](https://github.com/WhoIsJack/hackday-pybioimage)...
    - ...is a self-explanatory introduction to biological image analysis with python 
    - ...is aimed at biologists with basic knowledge of scientific python
    - ...has been developed in 2016 and since updated several times
    - ...has been used in several successful courses and as an online learning resource
- **The goal of this Hackday session is to updated, improve and extend the tutorial!**



### Tutorial Philosophy

- The focus is on learning programmatic image analysis, not on the newest and fanciest tools!
- The materials must be self-explanatory!
- The learners write (most of) the code themselves!
- The main tutorial follows a pipeline start to finish!
- (Where possible limit dependencies to packages in the Anaconda distro)



### Hackday Ideas

- [Beginners+] **Testing & Feedback**
    - Test the tutorial on your computer/setup
    - Work through the materials, report issues and provide feedback

- [Intermediate+] **Adding a "Bonus Vignette"**
    - These are separate, short tutorial notebooks introducing additional concepts that build on the basic tutorial
    - Possible ideas could be:
        - Various downstream analyses of extracted measurements
            - Plots, stats, PCA, regression, classification, ...
        - Cell segmentation with machine learning (e.g. StarDist)
        - Cell tracking 
        - Colocalization
        - ...

- [Intermediate+] **Better example data?!**
    - Replace the example data with a new and more interesting dataset
    - *Ideally has 1 or more additional channels with interesting stuff to measure!*
    - Should still be a 2D slice of confluent epithelial cells
    - Must be freely and openly available
    - More than a single image must be available (for batch processing)
    - Analysis parameters must be adjusted so everything works
    - Where to look: [IDR](https://idr.openmicroscopy.org/)? [Allen Cell](https://www.allencell.org/)? Your data? ...?

- [Intermediate+] **Intro to Scientific Python**
    - Put together (fork & adapt?) a short intro/refresher to numpy & matplotlib for those taking on the tutorial following e.g. a basic python course
    - When the tutorial is run as a course, this material can be run as an optional pre-course the day before

- [Intermediate+] **Add a small test suite**

- [Intermediate+] **Make a website to host the tutorial?**

- [Anyone] **Add your own idea here!**



### Hackday Technicalities

- We work with [**this copy of the original repo**](https://github.com/WhoIsJack/hackday-pybioimage)
    - I will later consolidate the contributions to update the original
- Submit your changes via pull requests ([how to](https://opensource.com/article/19/7/create-pull-request-github)):
    1. Fork the repo
    2. Clone it to your local system
    3. Make a new branch
    4. Make your changes
    5. Push it back to your repo
    6. Click the `Compare & pull request` button
    7. Click `Create pull request` to open a new pull request
- If you're stuck or unsure about anything, don't hesitate to ask!
    - This event is as much (or more!) about learning as it is about improving the tutorial
- By participating in this Hackday group you agree to have fun