On this page you will find an overview of basic image analysis methods using ImageJ or Fiji. The focus here is on the quantification of various microscopy images. This includes the detection and counting of cells with and without labeling, as well as other functions like the colocalization of different color channels. Below is a 30 min overview video where I show some analysis examples of sample images which are provided by Fiji.
The ImageJ / Fiji website can be found here: https://imagej.net/
The original publication of ImageJ can be found here: https://www.nature.com/articles/nmeth.2089
The original publication of Fiji can be found here: https://www.nature.com/articles/nmeth.2019
