Here is the material of the workshop Analysis of the 3D spatial organization of cells and molecules with FIJI and Napari, held at the Mifobio Microscopy school in 2023.
- Slides (pdf)
- Data to be used in the exercises
- Exercise 1 - Spot Detection in ImageJ and Visualization in Napari
- Exercise 2 - Spot Detection with napari-bigfish
- Exercise 3 - Measuring and Visualizing Nearest Neighbor Distances
- Exercise 4 - Finding and displaying density based clusters with DBScan
- Exercise 5 - Displaying the empirical Cumulative Distribution Function of the distances
- Exercise 6 - Nearest Neighbor Spatial Statistics – The G-Function
- Exercise 7 - Nearest Neighbor Spatial Statistics – The F-Function
- Exercise 8 - Ripley’s K-Function