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Background  Field-based high throughput phenotyping is a bottleneck for crop breeding research. We present a novel method for repeated remote phenotyping of maize genotypes using the Zeppelin NT aircraft as an experimental sensor platform. The system has the advantage of a low altitude and cruising speed compared to many drones or airplanes, thus enhancing image resolution while reducing blurring effects. Additionally there was no restriction in sensor weight. Using the platform, red, green and blue colour space (RGB), normalized difference vegetation index (NDVI) and thermal images were acquired throughout the growing season and compared with traits measured on the ground. Ground control points were used to co-register the images and to overlay them with a plot map.    Results  NDVI images were better suited than RGB images to segment plants from soil background leading to two separate traits: the canopy cover (CC) and its NDVI value (NDVI Plant ). Remotely sensed CC correlated well with plant density, early vigour, leaf size, and radiation interception. NDVI Plant  was less well related to ground truth data. However, it related well to the vigour rating, leaf area index (LAI) and leaf biomass around flowering and to very late senescence rating. Unexpectedly, NDVI Plant  correlated negatively with chlorophyll meter measurements. This could be explained, at least partially, by methodical differences between the used devices and effects imposed by the population structure. Thermal images revealed information about the combination of radiation interception, early vigour, biomass, plant height and LAI. Based on repeatability values, we consider two row plots as best choice to balance between precision and available field space. However, for thermography, more than two rows improve the precision.    Conclusions  We made important steps towards automated processing of remotely sensed data, and demonstrated the value of several procedural steps, facilitating the application in plant genetics and breeding. Important developments are: the ability to monitor throughout the season, robust image segmentation and the identification of individual plots in images from different sensor types at different dates. Remaining bottlenecks are: sufficient ground resolution, particularly for thermal imaging, as well as a deeper understanding of the relatedness of remotely sensed data and basic crop characteristics.    Electronic supplementary material  The online version of this article (doi:10.1186/s13007-015-0048-8) contains supplementary material, which is available to authorized users.

Remote, aerial phenotyping of maize traits with a mobile multi-sensor approach