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 you can find a video that shows how the Fiji toolbar is built and how it can be used to analyze images. It is recommended to watch this video if you are using Fiji for the first time.
Additional information can be found here:
- https://imagej.nih.gov/ij/docs/guide/146-1.html#toc-Section-1
- https://imagej.nih.gov/ij/docs/guide/146-Part-IV.html#sub:Toolbar
- 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
Overview of Fiji tutorials:
- How to install ImageJ / Fiji
- How to install Plugins
- Basics - What are (raw) images
- Adjust color and add scale bar
- Distance measurements
- Intensity profiles
- Background correction
- Count objects based on intensity
- Segmentation + particle analysis
- Count objects based on morphology
- Classify objects based on pixel-values
- Single-particle fluorescence quantification
- Co-localization of fluorescence channels
- How to create macros
- Macro: Cell segmentation and fluorescence quantification
- 3D reconstruction of z-stacks
