Next generation phenotyping of auxin response mutants will be greatly facilitated by the ability to record rapid growth responses in roots and hypocotyls at high throughput and at high temporal resolution. As Arabidopsis seedlings are very tiny and fragile, imaging is the only adequate way for data acquisition. As camera-based systems described before have a limited throughput, we used commercial flatbed scanners to record a large number of simultaneous experiments. We developed Hansa Trace, software for automatically detecting and measuring hypocotyl segments and roots in the images. We validated this system by measuring some well-characterized growth responses to auxins, non-auxins, ATPase activators and apoplastic acidification. The method can be shared on a cooperation basis and is able to perform measurements with minimal user intervention.