How to run the tutorials and examples using Jupyter Notebook¶
The tutorials are written as Jupyter notebooks, interactive web-apps to run, document, and visualize code: https://jupyter.org/. If you installed Python using Anaconda, it is possible that jupyter
is already installed - check py typing jupyter --version
into the console. Otherwise you can install it with pip
pip install jupyter notebook
After installing phenopype, clone the phenopype repository from github. After downloading, unpack the zip file, cd to the tutorial folder, open a terminal and run the notebooks:
jupyter notebook
Alternatively, you can copy the code from the jupyter code cells over to Spyder and execute them there. In this case you need to adjust the file paths given in the code cells accordingly.
Tip
If you want to use the tutorials or examples as a blueprint for your own project, simply save them as python a script by clicking File > Download as > Python (.py).
Tutorials¶
- Tutorial 1: A (very) brief python introduction
- Tutorial 2: Working with phenopype (prototyping, low throughput, high throughput)
- Tutorial 3: Setting up and managing phenopype projects
- Tutorial 4: Project wide actions (e.g. size and colour reference)
- Tutorial 5: GUI interactions (masks, lines and drawing tools)
- Tutorial 6: Video analysis
Examples¶
- Example 1: Measuring shape, size and colour of isopods
- Example 2: Stickleback morphometrics - landmarks
- Example 3: Fluorescence intensity and shape of phytoplankton cells
- Example 4: Video analysis - predator prey interactions
- Example 5: Stickleback morphometrics - body and armor-plate shape
- Example 6: Counting and measuring freshwater snails
- Example 7: Measuring worm length
- Example 8: Extracting shape features from fossil teeth of cichlids
- Single tooth case
- Multiple teeth