ABSTRACT
This chapter discusses the image analysis component of tissue phenomics studies, together with the pre-analytical variables that are critical for the successful execution of these studies. A thorough understanding of the journey from tissue to data is essential for the proper implementation of tissue phenomics, especially in the context of precision medicine. Quality control (QC) inspection of all images and tissue should be performed at this point, to ensure that the starting material for image analysis is suitable. Automated QC methods trained and tested against expertly annotated "ground truth" of cells and regions in tissues can provide a way around time and resources required for manual processes and are the key to larger image analysis studies and tissue phenomics. An adequate procedure should consider variability of input data as well as variability caused by the image analysis solution. Correct sample handling, processing, and scanning are as important as experimental design in determining the quality and reliability of image analysis data.
