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A three-dimensional spatial bubble counting method is proposed to solve the problem of the existing crucible bubble detection only being able to perform two-dimensional statistics. First, spatial video images of the transparent layer of the crucible are acquired by a digital microscope, and a quartz crucible bubble dataset is constructed independently. Secondly, to address the problems of poor real-time and the insufficient small-target detection capability of existing methods for quartz crucible bubble detection, rich detailed feature information is retained by reducing the depth of down-sampling in the YOLOv5 network structure. In the neck, the dilated convolution algorithm is used to increase the feature map perceptual field to achieve the extraction of global semantic features; in front of the detection layer, an effective channel attention network (ECA-Net) mechanism is added to improve the capability of expressing significant channel characteristics. Furthermore, a tracking algorithm based on Kalman filtering and Hungarian matching is presented for bubble counting in crucible space. The experimental results demonstrate that the detector algorithm presented in this paper can effectively reduce the missed detection rate of tiny bubbles and increase the average detection precision from 96.27% to 98.76% while reducing weight by half and reaching a speed of 82 FPS. The excellent detector performance improves the tracker’s accuracy significantly, allowing for real-time and high-precision counting of bubbles in quartz crucibles. It is an effective method for detecting crucible spatial bubbles. Full article