Rapid and Semi-automated Extraction of Neuronal Cell Bodies and Nuclei from Electron Microscopy Image Stacks.
Connectomics-the study of how neurons wire together in the brain-is at the forefront of modern neuroscience research. However, many connectomics studies are limited by the time and precision needed to correctly segment large volumes of electron microscopy (EM) image data. We present here a semi-automated segmentation pipeline using freely available software that can significantly decrease segmentation time for extracting both nuclei and cell bodies from EM image volumes.
Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, 26506-9303, USA.
Paul S
PS
Holcomb
Lane Department of Computer Science and Electrical Engineering, Benjamin M. Statler College of Engineering and Mineral Resources, West Virginia University, Morgantown, WV, 26506-6070, USA.
Michael
M
Morehead
Lane Department of Computer Science and Electrical Engineering, Benjamin M. Statler College of Engineering and Mineral Resources, West Virginia University, Morgantown, WV, 26506-6070, USA.
Gianfranco
G
Doretto
Lane Department of Computer Science and Electrical Engineering, Benjamin M. Statler College of Engineering and Mineral Resources, West Virginia University, Morgantown, WV, 26506-6070, USA.
Peter
P
Chen
Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA.
Stuart
S
Berg
Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA.
Stephen
S
Plaza
Center for Neuroscience, West Virginia University School of Medicine, Morgantown, WV, 26506-9303, USA. gspirou@hsc.wvu.edu.|Department of Physiology and Pharmacology, West Virginia University School of Medicine, Morgantown, WV, 26506-9303, USA. gspirou@hsc.wvu.edu.|Department of Otolaryngology, West Virginia University School of Medicine, Morgantown, WV, 26506-9303, USA. gspirou@hsc.wvu.edu.|West Virginia University School of Medicine, 1 Medical Center Dr., P.O. Box 9304, Morgantown, WV, 26506-9304, USA. gspirou@hsc.wvu.edu.
George
G
Spirou
D057205:Automation, Laboratory; D066146:Cell Body / Q000648:ultrastructure; D063132:Connectome; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D008854:Microscopy, Electron; D008959:Models, Neurological; D009474:Neurons / Q000648:ultrastructure*; D010363:Pattern Recognition, Automated / Q000379:methods*; D012984:Software
3D reconstruction; Connectomics; Electron microscopy; Segmentation; ilastik