In recent years, deep learning-based networks have been able to achieve state-of-the-art performance in medical image segmentation. U-Net, one of the currently available networks, has proven to be effective when applied to the segmentation of medical images. A Convolutional Neural Network’s (CNN) performance is heavily dependent on the network’s architecture and associated parameters. There are many layers and parameters that need to be set up in order to manually create a CNN, making it a complex procedure. Designing a network is made more difficult by using a variety of connections to increase the network’s complexity. Evolutionary computation can be used to set the parameters of CNN and/or organize the CNN layers as an optimization strategy. This paper proposes an automatic evolutionary method for detecting an optimal network topology and its parameters for the segmentation of clinical image using Grey Wolf Optimization algorithm. Also, Bi-Directional LSTM integrated in the skip connection to extract dense feature characteristics of image by combining feature maps extracted from encoded and previous decoded path in nonlinear way (MIS-GW-U-Net-BiDCLSTM) is proposed. The experimental results demonstrate that the proposed method attains 98.49% accuracy with minimal parameters, which is much better than that of the other methods.