Advanced Image Segmentation Techniques for Neural Activity Detection via C-fos Immediate Early Gene Expression

Abstract

This paper investigates the application of advanced image segmentation techniques to analyze C-fos immediate early gene expression, a crucial marker for neural activity. Due to the complexity and high variability of neural circuits, accurate segmentation of C-fos images is paramount for the development of new insights into neural function. Amidst this backdrop, this research aims to improve accuracy and minimize manual intervention in C-fos image segmentation by leveraging the capabilities of CNNs and the Unet model. We describe the development of a novel workflow for the segmentation process involving Convolutional Neural Networks (CNNs) and the Unet model, demonstrating their efficiency in various image segmentation tasks. Our workflow incorporates pre-processing steps such as cropping, image feature extraction, and clustering for the training dataset selection. We used an AutoEncoder model to extract features and implement constrained clustering to identify similarities and differences in image types. Additionally, we utilized manual and automatic labeling approaches to enhance the performance of our model. We demonstrated the effectiveness of our method in distinguishing areas with significant C-fos expression from normal tissue areas. Lastly, we implemented a modified Unet network for the detection of C-fos expressions. This research contributes to the development of more efficient and automated image segmentation methods, advancing the understanding of neural function in neuroscience research.