Automated mark localization in scatter images, greatly helpful for discovering knowledge and understanding enormous document images and reasoning in visual question answering AI systems, is a highly challenging problem because of the ubiquity of overlapping marks. Locating overlapping marks faces many difficulties such as no texture, less contextual information, hallow shape and tiny size. Here, we formulate it as a combinatorial optimization problem on clustering-based re-visualization from a non-training generative perspective, to locate scatter marks by finding the status of multi-variables when an objective function reaches a minimum. The objective function is constructed on difference between binarized scatter images and corresponding generated re-visualization based on their clustering. Fundamentally, re-visualization tries to generate a new scatter graph only taking a rasterized scatter image as an input, and clustering is employed to provide the information for such re-visualization. This method could stably locate severely-overlapping, variable-size and variable-shape marks in scatter images without dependence of any training dataset or reference. Meanwhile, we propose an adaptive variant of simulated annealing which can works on various connected regions. In addition, we especially built a dataset named SML2023 containing hundreds of scatter images with different markers and various levels of overlapping severity, and tested the proposed method and compared it to existing methods. The results show that it can accurately locate most marks in scatter images with different overlapping severity and marker types, with about 0.3 absolute increase on an assignment-cost-based metric in comparison with state-of-the-art methods. This work is of value to data mining on massive web pages and literatures, and shedding new light on image measurement such as bubble counting.