Singhal, Tushar; Kolkur, Prashant; Ellisman, Mark H.; Altintas, Ilkay (2019). Electron Microscopic Data Analysis. In Data Science & Engineering Master of Advanced Study (DSE MAS) Capstone Projects. UC San Diego Library Digital Collections. https://doi.org/10.6075/J03N21QH

Capstone Project for Data Science & Engineering Master's Program at UC Sand Diego (UCSD) 2019.

The “Electron Microscopic Data Analysis” project aims to support the processing, analysis and dissemination of large-scale 3D electron microscopic (EM) data derived from a remarkable collection of legacy biopsy brain samples from patients suffering from Alzheimer’s disease (AD). Alzheimer’s disease is a progressive neurodegenerative disease, leading to dementia accompanied by several structural changes in the brain of patients.
The project intends to facilitate the processing and downstream analysis of complete whole cell reconstructions of neurons from unique biopsy image samples of cerebral cortex taken from AD cases by Robert Terry in the 1960’s, focusing on early onset cases, where cells effected to differing extents are neighbored by cells without AD-associated forming paired helical filaments, (PHF) now known to be largely made up of tau proteins. These samples were screened and preliminarily reported on by Ellisman, Masliah and Terry (Ellisman et al., 1987) and manifest near perfect preservation of ultrastructure PHF and amyloid accumulations as well as modifications to subcellular organelles and cytoskeletons of the cell bodies, axonal and dendritic processes.
Raw data (or data) is coming from Cell Image Library (CIL: http://cellimagelibrary.org/cdeep3m). Cell Image library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular activity, with the ultimate goal of improving human health. This data is accessed manually from the website and copied to the memory disk for processing. The data is a serial block face scanning electron microscopy (SBEM) 3D data volumes. Serial block-face scanning electron microscopy (SBEM) is a way to obtain high resolution 3D images from a sample. This method is particularly good at imaging large fields-of-view in X,Y,Z that is 3dimension at nanometer resolution. The data is brain image samples of patients suffering from Alzheimer’s disease. The Alzheimer's image data images are of very high definition. The size of a typical image in multiple datasets is in the range of 16000x10000x400 pixels images.

• 2019-01 to 2019-06

• 2019

• Kolkur, Prashant
• Singhal, Tushar

• Altintas De Callafon, Ilkay
• Ellisman, Mark H.

• DSE MAS - 2019 Cohort

• Alzheimer's disease Serial block-face scanning electron microscopy (SBEM)
• Big data
• Capstone projects
• CDeep3M
• Cell Image Library (CIL)
• Convolutional Neural Network (CNN)
• Data Science & Engineering Master of Advanced Study (DSE MAS)
• DeepEM3D
• Menbranes
• Mitochondria
• MultiResUnet
• Neural networks (Computer science)
• Nuclei
• P100 latency
• Vesicles

• data
• text

Doi: https://doi.org/10.6075/J03N21QH

Source data

• Cell Image Library CDeep3M: http://cellimagelibrary.org/cdeep3m

Other resource

• Subset of large dataset from CIL used in this project is kept in Dropbox here: https://www.dropbox.com/sh/jmkhekzo1p4owbp/AACzKqSC8stOsWowNahxI6Osa?dl=0

Creative Commons Attribution 4.0 International Public License

• Singhal, Tushar; Kolkur, Prashant

Under copyright (US)

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2023-06-30