A modular hierarchical approach to 3D electron microscopy image segmentation.
The study of neural circuit reconstruction, i.e., connectomics, is a challenging problem in neuroscience. Automated and semi-automated electron microscopy (EM) image analysis can be tremendously helpful for connectomics research. In this paper, we propose a fully automatic approach for intra-section segmentation and inter-section reconstruction of neurons using EM images. A hierarchical merge tree structure is built to represent multiple region hypotheses and supervised classification techniques are used to evaluate their potentials, based on which we resolve the merge tree with consistency constraints to acquire final intra-section segmentation. Then, we use a supervised learning based linking procedure for the inter-section neuron reconstruction. Also, we develop a semi-automatic method that utilizes the intermediate outputs of our automatic algorithm and achieves intra-segmentation with minimal user intervention. The experimental results show that our automatic method can achieve close-to-human intra-segmentation accuracy and state-of-the-art inter-section reconstruction accuracy. We also show that our semi-automatic method can further improve the intra-segmentation accuracy.
Scientific Computing and Imaging Institute, University of Utah, United States; School of Computing, University of Utah, United States.
Ting
T
Liu
Scientific Computing and Imaging Institute, University of Utah, United States; Department of Electrical and Computer Engineering, University of Utah, United States.
Cory
C
Jones
Scientific Computing and Imaging Institute, University of Utah, United States; Department of Electrical and Computer Engineering, University of Utah, United States.
Mojtaba
M
Seyedhosseini
Scientific Computing and Imaging Institute, University of Utah, United States; School of Computing, University of Utah, United States; Department of Electrical and Computer Engineering, University of Utah, United States. Electronic address: tolga@sci.utah.edu.
Tolga
T
Tasdizen
D000465:Algorithms; D000818:Animals; D001185:Artificial Intelligence; D002490:Central Nervous System / Q000648:ultrastructure; D002540:Cerebral Cortex / Q000648:ultrastructure; D004330:Drosophila; D001330:Electronic Data Processing; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D051379:Mice; D008854:Microscopy, Electron / Q000379:methods*; D009474:Neurons / Q000648:ultrastructure*; D019581:Neuropil / Q000648:ultrastructure
Electron microscopy; Hierarchical segmentation; Image segmentation; Neuron reconstruction; Semi-automatic segmentation