Two-Stage Cascaded CNN Model for 3D Mitochondria EM Segmentation

Abstract

Mitochondria are the organelles that generate energy for the cells. Many studies have suggested that mitochondrial dysfunction or impairment may be related to cancer and other neurodegenerative disorders such as Alzheimer’s and Parkinson’s diseases. Therefore, morphologically detailed alterations in mitochondria and 3D reconstruction of mitochondria are highly demanded research problems in the performance of clinical diagnosis. Nevertheless, manual mitochondria segmentation over 3D electron microscopy volumes is not a trivial task. This study proposes a two-stage cascaded CNN architecture to achieve automated 3D mitochondria segmentation, combining the merits of top-down and bottom-up approaches. For top-down approaches, the segmentation is conducted on objects’ localization so that the delineations of objects’ contours can be more precise. However, the combinations of 2D segmentation from the top-down approaches are inadequate to perform proper 3D segmentation without the information on connectivity among frames. On the other hand, the bottom-up approach finds coherent groups of pixels and takes the information of 3D connectivity into account in segmentation to avoid the drawbacks of the 2D top-down approach. However, many small areas that share similar pixel properties with mitochondria become false positives due to insufficient information on objects’ localization. In the proposed method, the detection of mitochondria is carried out with multi-slice fusion in the first stage, forming the segmentation cues. Subsequently, the second stage is to perform 3D CNN segmentation that learns the pixel properties and the information of 3D connectivity under the supervision of cues from the detection stage. Experimental results show that the proposed structure alleviates the problems in both the top-down and bottom-up approaches, which significantly accomplishes better performance in segmentation and expedites clinical analysis.