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As a dense instance segmentation problem, rebar counting in a complex environment such as rebar yard and rebar transpotation has received significant attention in both academic and industrial contexts. Traditional counting approaches, such as manual counting and machine vision-based algorithms, are often inefficient or inaccurate since rebars with varied sizes and shapes are stacked overlapping, rebar image is not clear for complex light condition such as dawn, night and strong light, and other environmental noises exist in rebar image; thus, they no longer fulfil the requirements of modern automation. This paper proposes MaskID, an innovative counting method based on deep learning and heuristic strategies. First, an improved version of the Mask region-based convolutional neural network (Mask R-CNN) was designed to obtain the segmentation results through splitting and rescaling so as to capture more detail in a large-scale rebar image. Then, a series of intelligent denoising strategies corresponding to aspect ratio of recognized box, overlapping recognized objects, object distribution and environmental noise, were applied to improve the segmentation results. The performance of the proposed method was evaluated on open-competition and test-platform datasets. The F1-score was found to be over 0.99 on all datasets. The experimental results demonstrate that the proposed method is effective for dense rebar counting and significantly outperforms existing state-of-the-art methods. [ABSTRACT FROM AUTHOR]