Cell Counting and Segmentation of Immunohistochemical Images in the Spinal Cord: Comparing Deep Learning and Traditional Approaches

Estimation of cell nuclei in images stained for the c-fos protein using immunohistochemistry (IHC) is infeasible in large image sets. Use of multiple human raters to increase throughput often creates variance in the data analysis. Machine learning techniques for biomedical image analysis have been explored for cell-counting in pathology, but their performance on IHC staining, especially to label activated cells in the spinal cord is unknown. In this study, we evaluate different machine learning techniques to segment and count spinal cord neurons that have been active during stepping. We present a qualitative as well as quantitative comparison of algorithmic performance versus two human raters. Quantitative ratings are presented with cell-count statistics and Dice (DSI) scores. We also show the degree of variability between multiple human raters' segmentations and observe that there is a higher degree of variability in segmentations produced by classic machine learning techniques (SVM and Random forest) as compared to the newer deep learning techniques. The work presented here, represents the first steps towards addressing the analysis time bottleneck of large image data sets generated by c-fos IHC staining techniques, a task that would be impossible to do manually.