A software system for assisting a physician's diagnosis and reporting based on medical imaging includes software tools for pre-processing medical images, collecting findings, and automatically generating medical reports. A pre-processing software component generates an anatomical segmentation and/or computer-aided diagnosis based on an analysis of a medical image. A finding collecting software component displays the image, and facilitates rapid and efficient entry of associated findings by displaying a filtered list of templates associated with a selected region of the image and/or a computer-aided diagnosis. When the physician selects a template from the filtered list, the template may be displayed with entry options pre-filled based, e.g., on any computer-aided diagnosis. After the physician edits and/or confirms the entries, a report generation component uses the entries to generate a medical report.