One of the great benefits of the micaToolbox and its components is that it runs on ImageJ which comes with an extensive suite of tools for image manipulation. Particularly useful is the ability to do very easy and efficient selecting of Regions of Interest (ROIs) which can be used to then run pattern analyses (e.g. QCPA components) on specific image regions. E.g. if you wanted to compare an animal to its background. The ImageJ manual provides detailed information on how to achieve the best selection possible. Valuable functions include the ability to select regions and then to either combine these or subrtract one from the other.
The toolbox has built upon the basic ImageJ functionality by providing the ability to create automatically labelled and numbered ROIs with a single button click, and then to perform basic image measurements of these ROIs immediately. This tool is started automatically whenever an mspec image is created or loaded, however it can also be started manually by going:
plugins > micaToolbox > Tools > Save ROIs
Additionally, images can be segmented using the Naive Bayes Clustering or RNL Clustering tools, and these clusters can be converted to ROIs by running the Particle Analysis tool. The easiest way to perform these functions together is by using the Run QCPA Framework tool.