A workflow for the automatic segmentation of organelles in electron microscopy image stacks

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Publication Type pre-print
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Creator Seyedhosseini Tarzjani, Seyed Mojtaba
Other Author Perez, Alex J.; Deerinck, Thomas J.; Bushong, Eric A.; Panda, Satchidananda; Tasdizen, Tolga; Ellisman, Mark H.
Title A workflow for the automatic segmentation of organelles in electron microscopy image stacks
Date 2014-01-01
Description Electron microscopy(EM) facilitates analysis of the form,distribution, and functional status of key organelle systems in various pathological processes,including those associated with neurodegenerative disease.Such EM data often provide important new in sights into the underlying disease mechanisms. The development of more accurate and efficient methods to quantify changes in subcellular microanatomy has already proven key to understanding the pathogenesis of Parkinson's and Alzheimer's diseases,as well as glaucoma. While our ability to acquire large volumes of 3D EM data is progressing rapidly, more advanced analysis tools are needed to assist in measuring precise three-dimensional morphologies of organelles within data sets that can include hundreds to thousands of whole cells. Although new imaging instrument throughputs can exceed teravoxels of data per day, image segmentation and analysis remain significant bottlenecks to achieving quantitative descriptions of whole cell structural organellomes. Here, we present a novel method for the automatic segmentation of organelles in 3D EM image stacks. Segmentations are generated using only 2D image information, making the method suitable for anisotropic imaging techniques such as serial block-face scanning electron microscopy (SBEM). Additionally, no assumptions about 3D organelle morphology are made, ensuring the method can be easily expanded to any number of structurally and functionally diverse organelles. Following the presentation of our algorithm, we validate its performance by assessing the segmentation accuracy of different organelle targets in an example SBEM dataset and demonstrate that it can be efficiently parallelized on supercomputing resources, resulting in a dramatic reduction in runtime.
Type Text
Publisher Frontiers Media
Volume 8
Issue 126
First Page 1
Last Page 13
Language eng
Bibliographic Citation Perez, A. J., Seyedhosseini, M., Deerinck, T. J., Bushong, E. A., Panda, S., Tasdizen, T., & Ellisman, M. H. (2014). A workflow for the automatic segmentation of organelles in electron microscopy image stacks. Frontiers in Neuroanatomy, 8(November), 126, 1-13.
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Identifier uspace,19409
ARK ark:/87278/s6dz3jgx
Setname ir_uspace
Date Created 2015-05-04
Date Modified 2015-05-04
ID 713033
Reference URL https://collections.lib.utah.edu/ark:/87278/s6dz3jgx