# 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