Understanding the structure and working principle of brain neural networks requires three-dimensional reconstruction of brain tissue samples using array tomography method. In order to improve the reconstruction performance, the sequence of brain sections should be collected with silicon wafers for subsequent electron microscopic imaging. However, the current collection of brain sections based on silicon substrate involve mainly manual collection, which requires the involvement of automation techniques to increase collection efficiency. This paper presents the design of an automatic collection device for brain sections. First, a novel mechanism based on circular silicon substrates is proposed for collection of brain sections; second, an automatic collection system based on microscopic object detection and feedback control strategy is proposed. Experimental results verify the function of the proposed collection device. Three objects (brain section, left baffle, right baffle) can be detected from microscopic images by the proposed detection method. Collection efficiency can be further improved with position feedback of brain sections well. It has been experimentally verified that the proposed device can well fulfill the task of automatic collection of brain sections. With the help of the proposed automatic collection device, human operators can be partially liberated from the tedious manual collection process and collection efficiency can be improved.