Fiji practical

Fiji is ImageJ bundled with plugins for bioimage analysis. In this practical you will inspect image intensities, apply a threshold, clean up a mask and measure objects through the graphical interface. The Python notebooks introduce how to make these steps reproducible and automate them for many images.

The Fiji manual explains every tool the exercises use; keep it open alongside them. Also, the Fiji cheatsheets can be useful (linked in the menu on the left).

The exercises

E1	Fiji basics	pixel size, intensities, histogram, scale bar, measuring a filament
E2	Segmentation	filter, threshold, clean up, measure
E3	Macros	recording and batch processing
E4	Machine learning	Trainable Weka Segmentation

The data

Everything is in the repository you cloned, under data/fiji/. Each exercise names the file it uses; E1 and E2 work on the same image.