<p>Cloud detection and cloud properties have significant applications in weather forecast, signal attenuation analysis, and other cloud-related fields. Cloud image segmentation is the fundamental and important step to derive cloud cover. However, traditional segmentation methods rely on low-level visual features of clouds, and often fail to achieve satisfactory performance. Deep Convolutional Neural Networks (CNNs) are able to extract high-level feature information of object and have become the dominant methods in many image segmentation fields. Inspired by that, a novel deep CNN model named SegCloud is proposed and applied to accurate cloud segmentation based on ground-based observation. Architecturally, SegCloud possesses symmetric encoder-decoder structure. The encoder network combines low-level cloud features to form high-level cloud feature maps with low resolution, and the decoder network restores the obtained high-level cloud feature maps to the same resolution of input images. The softmax classifier finally achieves pixel-wise classification and outputs segmentation results. SegCloud has powerful cloud discrimination ability and can automatically segment the whole sky images obtained by a ground-based all-sky-view camera. Furthermore, a new database, which includes 400 whole sky images and manual-marked labels, is built to train and test the SegCloud model. The performance of SegCloud is validated by extensive experiments, which show that SegCloud is effective and accurate for ground-based cloud segmentation and achieves better results than traditional methods. Moreover, the accuracy and practicability of SegCloud is further proved by applying it to cloud cover estimation.</p>