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The paper brings forward the parallel logarithmic subtraction template which is applicable to register microscopic images. The template is developed from the ratio template, and applying the template to image registration can reduce the computation by replacing the large number of division operations with subtraction operations. The method to automatically create and match the templates in the microscopic images is also proposed in the paper. At the end of the paper, an experiment is carried out comparing the speed of registering the images gathered by the auto-microscope with the parallel logarithmic subtraction template and with the ratio template. The result of the experiment demonstrates the efficiency improvement brought by the new template.