title: Detection of neuron membranes in electron microscopy images using a serial neural network architecture.
abstract: Study of nervous systems via the connectome, the map of connectivities of all neurons in that system, is a challenging problem in neuroscience. Towards this goal, neurobiologists are acquiring large electron microscopy datasets. However, the shear volume of these datasets renders manual analysis infeasible. Hence, automated image analysis methods are required for reconstructing the connectome from these very large image collections. Segmentation of neurons in these images, an essential step of the reconstruction pipeline, is challenging because of noise, anisotropic shapes and brightness, and the presence of confounding structures. The method described in this paper uses a series of artificial neural networks (ANNs) in a framework combined with a feature vector that is composed of image intensities sampled over a stencil neighborhood. Several ANNs are applied in series allowing each ANN to use the classification context provided by the previous network to improve detection accuracy. We develop the method of serial ANNs and show that the learned context does improve detection over traditional ANNs. We also demonstrate advantages over previous membrane detection methods. The results are a significant step towards an automated system for the reconstruction of the connectome.
authors.affiliation: Scientific Computing and Imaging Institute, Salt Lake City, UT 84112, United States. liz@sci.utah.edu
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Jurrus
authors.forename: Antonio R C
authors.initials: AR
authors.lastname: Paiva
authors.forename: Shigeki
authors.initials: S
authors.lastname: Watanabe
authors.forename: James R
authors.initials: JR
authors.lastname: Anderson
authors.forename: Bryan W
authors.initials: BW
authors.lastname: Jones
authors.forename: Ross T
authors.initials: RT
authors.lastname: Whitaker
authors.forename: Erik M
authors.initials: EM
authors.lastname: Jorgensen
authors.forename: Robert E
authors.initials: RE
authors.lastname: Marc
authors.forename: Tolga
authors.initials: T
authors.lastname: Tasdizen
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans; D002462:Cell Membrane / Q000648:ultrastructure*; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008854:Microscopy, Electron / Q000379:methods*; D016571:Neural Networks, Computer; D009474:Neurons / Q000648:ultrastructure*; D010363:Pattern Recognition, Automated / Q000379:methods*; D011817:Rabbits; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013382:Subtraction Technique