CellScope Explorer is the companion app for the CellScope iPad-based microscope from UC Berkeley. It enables photo and video capture, annotation, and cloud sharing through Flickr. This app has been specifically designed for K-12 schools and museums for educational use. The app provides a number of key features specific to microscopy which are not available in standard camera apps: it includes a scale bar for measuring microscopic features, it enables zooming and panning across the microscopes field of view, and it orients the screen so it aligns properly with stage translation.