This repository is a living collection of my resources to introduce/teach python and image analysis.
The Python Cheat Sheet, especially the Jupyter variant, is meant to be extended by the learner. Interactive Breaks are thought to explain/deepen concepts via widgets, often with a fun twist (or cute animals). Exercises will require some kind of coding. WarmUps are exercises that try to reduce frustration, especially for coding beginners.
If these things are helpful for you, please use them! Contributions, comments, mails, dm's etc. are very welcome. Let me know if these things help you :-)
If you use the Binders a lot, please consider donating to them, they're amazing.
Cheers,
Joe
Notebook Previews/Binder Links 🏠
Whole Repo 🏠
Python Cheat Sheet 🏠
Interactive Breaks 🏠
Break – LUTs/Colormaps 🏠
Break – Mean/Median/Thresholding 🏠
Break – Dilation/Erosion/Opening/Closing 🏠
Break – Image Processing with Filter Kernels 🏠
Exercises 🏠
Exercise - A Lot of Dogs 🏠
Exercise - Time Series Analysis 🏠
Exercise - 3D LUT 🏠
Exercise - Arrays 🏠
Exercise - Install Modules & Matplotlib 🏠
WarmUps 🏠
WarmUp – Paths & Syntax 🏠
Especially Recommended Further Resources 🏠
- Of course, this list is highly subjective, and by no means complete or exhaustive.
General 🏠
- Pete Bankhead's "Introduction to Bioimage Analysis"
- Pete Bankhead's "Introduction to Bioimage Analysis" (I know it's duplicated, but it is that good!)
- A Hitchhiker`s Guide through the Bio-image Analysis Software Universe
- image.sc Forum
- biii.eu - List of Image Analysis Tools
- NEUBIAS Academy @ Home
- Robert Haase's Youtube
More Specific 🏠
- ImageJ/FiJi Wiki
- Ilastik
- Napari
- QuPath
- Icy
- scikit-image's Tutorial Gallery
- cellpose
- CellProfiler
- KNIME
- 3D Slicer
- VesselVio - Vasculature Toolkit
- ITK Snap
- CSBDeep (StarDist, CARE, DenoiSeg, Noise2Void)