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Bio-Image Data Science Training Schools 2024
Course Preparation
Setting up your computer
Monday
Python basics
Python code and Jupyter notebooks
Basics terms and types for Python
Pitfalls when working with Jupyter notebooks
Basic math in Python
Sequences in Python
Indexing and slicing of sequences
Masking NumPy arrays
Dictionaries
Conditions
Loops
Custom Functions
File handling and working with images
How process files in a folder
Image visualization with stackview
Reading files with AICSImageIO
Optional: Accessing image files in the nextcloud
Optional: Coding assistance
Image processing basics
Images are arrays of numbers
Opening and visualizing images
Brightness and Contrast
Cropping images
Image Processing Filters
Image Binarization
Morphological Image Processing
Simulation of image formation + image restoration
Tuesday
Image segmentation
Interactive bioimage analysis workflow design
Generating Jupyter Notebooks
Voronoi-Otsu-labeling
The [seeded] watershed algorithm
Scripting Napari using Python
3D Image Segmentation
Feature extraction
Counting bright objects in images
Statistics using Scikit-image
Statistics using SimpleITK
Shape features
Machine Learning
Interactive pixel classification and object segmentation in Napari
Interactive object classification in Napari
Object segmentation and classifiation on OpenCL-compatible GPUs
Tabular data wrangling
Introduction to working with DataFrames
Selecting data from DataFrames
Appending and extending DataFrames
Handling missing data
Group by: split-apply-combine
Tidy-Data
Wednesday
Explorative data science
Create a multichannel timelapse (DNA [DAPI], F-actin, and Β-tubulin) for each of these compounds, where each timepoint is different concentration
Segment DAPI channel - batch process a folder of images
Segment Actin Channel - batch process a folder of images
Segment Tubulin Channel - batch process a folder of images
Extracting Quantitative Measurements from All Channels
Dimensionality Reduction
k-Means Clustering
Data Visualization
Plotting Basics
Introduction to Seaborn
Plotting Distributions with Seaborn
Advanced Plotting
Part 0: Get data set for plotting
Part 1: Time series and other simple plots
Part 2 Data exploration by unsupervised learning
Part 3: Machine Learning insights by Data Viz
Information
Code of Conduct
Contributing
Imprint
Repository
Open issue
Index
