We will first look at the tools that are available in ImageJ to select Regions Of Interest (ROIs). These tools can be useful if you wish to only process a small portion of your image. ROIs are a very important element in ImageJ, and there is also a specific manager to handle the ROIs: ROI Manager. It can be opened by going to Analyze | Tools | ROI Manager…, which will open the following window:

On the left-hand side, there is a list that will contain the ROIs, while on the right-hand side, there are several buttons that will perform certain actions on the ROIs. The checkboxes in the bottom-right corner allow the user to see all the regions at once (Show All), while the Labels checkbox displays the region label in the image.

There are different types of region that are supported by ImageJ. They can be divided into two major types: area selections and line selections. A third singular type is the Point ROI, which only has one member. When used for...