Quantitative characterization of root system architecture and its development is important for assessing a complete plant phenotype. To enable high-throughput phenotyping of plant roots efficient solutions for automated image analysis are required. Here, the saRIA tool was developed to enable quantitative analysis of plant roots growing in an opaque soil environment or artificial substrates (e.g., Agar gels). The saRIA tool is implemented to semi-automatically process a series of images (a set of images in a folder) or one image at a time per user click to estimate root traits (like area, length, volume and statistical features) for each image. The project folder contains Linux and Windows compiled version tools for download and use by end users.